Running as unit: rb-build-arm64_7-57942.service ==================================================================================== Sat Feb 22 03:04:29 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_arm64_7) on jenkins, called using "codethink04-arm64 codethink03-arm64" as arguments. Sat Feb 22 03:04:29 UTC 2025 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-3eLg5FEk" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Sat Feb 22 03:04:29 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink04-arm64.debian.net is marked as down. Sat Feb 22 03:04:29 UTC 2025 - checking via ssh if codethink04-arm64.debian.net is up. removed '/tmp/read-only-fs-test-SPjPnZ' Sat Feb 22 03:04:30 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink03-arm64.debian.net is marked as down. Sat Feb 22 03:04:30 UTC 2025 - checking via ssh if codethink03-arm64.debian.net is up. removed '/tmp/read-only-fs-test-yEV8MS' ok, let's check if libncl is building anywhere yet… ok, libncl is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of libncl in trixie on arm64 on jenkins now. 1st build will be done on codethink04-arm64.debian.net. 2nd build will be done on codethink03-arm64.debian.net. ============================================================================= Sat Feb 22 03:04:53 UTC 2025 I: starting to build libncl/trixie/arm64 on jenkins on '2025-02-22 03:04' Sat Feb 22 03:04:53 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_7/57942/console.log 1740193493 arm64 trixie libncl Sat Feb 22 03:04:53 UTC 2025 I: Downloading source for trixie/libncl=2.1.21+git20210811.b1213a7-6 --2025-02-22 03:04:54-- http://deb.debian.org/debian/pool/main/libn/libncl/libncl_2.1.21%2bgit20210811.b1213a7-6.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2422 (2.4K) [text/prs.lines.tag] Saving to: ‘libncl_2.1.21+git20210811.b1213a7-6.dsc’ 0K .. 100% 396M=0s 2025-02-22 03:04:54 (396 MB/s) - ‘libncl_2.1.21+git20210811.b1213a7-6.dsc’ saved [2422/2422] --2025-02-22 03:04:54-- http://deb.debian.org/debian/pool/main/libn/libncl/libncl_2.1.21%2bgit20210811.b1213a7-6.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2422 (2.4K) [text/prs.lines.tag] Saving to: ‘libncl_2.1.21+git20210811.b1213a7-6.dsc’ 0K .. 100% 396M=0s 2025-02-22 03:04:54 (396 MB/s) - ‘libncl_2.1.21+git20210811.b1213a7-6.dsc’ saved [2422/2422] Sat Feb 22 03:04:54 UTC 2025 I: libncl_2.1.21+git20210811.b1213a7-6.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: libncl Binary: ncl-tools, libncl2, libncl-dev Architecture: any Version: 2.1.21+git20210811.b1213a7-6 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Étienne Mollier Homepage: https://github.com/mtholder/ncl Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/libncl Vcs-Git: https://salsa.debian.org/med-team/libncl.git Testsuite: autopkgtest Testsuite-Triggers: build-essential Build-Depends: debhelper-compat (= 13), d-shlibs, python3 Package-List: libncl-dev deb libdevel optional arch=any libncl2 deb libs optional arch=any ncl-tools deb science optional arch=any Checksums-Sha1: 2cf4fdf16c8ea4fd7f252aaf1c28d0b1458cb287 544032 libncl_2.1.21+git20210811.b1213a7.orig.tar.xz 2a3b3d70a9f3e915a800ec62f93c27861d882dc8 20292 libncl_2.1.21+git20210811.b1213a7-6.debian.tar.xz Checksums-Sha256: 921db455387828e1e135febd177f7f1c69f4c204d5cadc0d0f47502f6fa608ed 544032 libncl_2.1.21+git20210811.b1213a7.orig.tar.xz 7be3f38ea803136f6776b180235681864d28775710e19b2cec89860bdaea0595 20292 libncl_2.1.21+git20210811.b1213a7-6.debian.tar.xz Files: a3af41d99fe04586c1f61bc942c5614b 544032 libncl_2.1.21+git20210811.b1213a7.orig.tar.xz c17d9c09d67787b7821f7ae519aebab4 20292 libncl_2.1.21+git20210811.b1213a7-6.debian.tar.xz Dgit: 9623cd3f49fcc435d9b3803296d8fbc9fd7dff1c debian archive/debian/2.1.21+git20210811.b1213a7-6 https://git.dgit.debian.org/libncl -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmbLBQkUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdpZ3g//eZ0pQ15HbJqS1sYfN/B9Lq045i9e wWMVQBu13LWFO7S0znLq/9s4EAKXocIUWURBDiddvJ5RQ5Kbc8cE0krPjyPpXiX4 ysiG9TPTxc1ZWwBnk2hnrB+xjQ+5UjZhOuMEYlgVMNnF0hxATYzN1XYIchZmGCo1 8nabDimP+gQf/jUMOK8odBn8QRwyNAHg75Kl9lq3D2LiPzg9Gk6AbctCMTuzDfgX bNb1aYk0Sk35iAIv+mH79auk+Ph4E4lTfVQXTHVWpJeuWmRruAp2Fy+EZirU/bRj XGoq6PLwTQIWv3cwnxeczPTV1g0x5VkEWJivJy1rAEX5RNChhzw/nS8TtJpiSRrp jGRxrtVwfzuKkUQk/3FMu+rLTmr5fPT8eLByvMrsGpAP6RMsnDNTEnMKPejanQ/x s2+LS1FdQlhyZM9JafhkuFIPnlLx2hH6FS+8zDUbVazI30HCnR4PJaCzrZLriL8i pvKt28oFWpyHGnEgNcokLSSpoA3dY3ZAQBSa5Jxkh0ts/xWJlRfa8OcE8yfq26BV bL9Se4mo4AQYsRCjbXxKp5e8NoucZFDcSY52qpOwBYdbqiX0r9J5nKkSVw0FoT6z BDrftRzdhM+2emwRgGbFg1IYJ9GI0Eb+y5ahN0jevKJOs2iE8Kha9Zn3aR+naIJh YHnlrc2XcUr0MFg= =15HM -----END PGP SIGNATURE----- Sat Feb 22 03:04:54 UTC 2025 I: Checking whether the package is not for us Sat Feb 22 03:04:54 UTC 2025 I: Starting 1st build on remote node codethink04-arm64.debian.net. Sat Feb 22 03:04:54 UTC 2025 I: Preparing to do remote build '1' on codethink04-arm64.debian.net. Sat Feb 22 03:04:54 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink04-arm64.debian.net is marked as down. Sat Feb 22 03:04:54 UTC 2025 - checking via ssh if codethink04-arm64.debian.net is up. removed '/tmp/read-only-fs-test-V8r7up' ==================================================================================== Sat Feb 22 03:04:55 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on codethink04-arm64, called using "1 libncl trixie /srv/reproducible-results/rbuild-debian/r-b-build.fEgknmXy 2.1.21+git20210811.b1213a7-6" as arguments. Sat Feb 22 03:04:55 UTC 2025 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-nPZsbsz8" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Sat Feb 22 03:04:55 UTC 2025 I: Downloading source for trixie/libncl=2.1.21+git20210811.b1213a7-6 Reading package lists... NOTICE: 'libncl' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/libncl.git Please use: git clone https://salsa.debian.org/med-team/libncl.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 567 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main libncl 2.1.21+git20210811.b1213a7-6 (dsc) [2422 B] Get:2 http://deb.debian.org/debian trixie/main libncl 2.1.21+git20210811.b1213a7-6 (tar) [544 kB] Get:3 http://deb.debian.org/debian trixie/main libncl 2.1.21+git20210811.b1213a7-6 (diff) [20.3 kB] Fetched 567 kB in 1s (1058 kB/s) Download complete and in download only mode Reading package lists... NOTICE: 'libncl' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/libncl.git Please use: git clone https://salsa.debian.org/med-team/libncl.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 567 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main libncl 2.1.21+git20210811.b1213a7-6 (dsc) [2422 B] Get:2 http://deb.debian.org/debian trixie/main libncl 2.1.21+git20210811.b1213a7-6 (tar) [544 kB] Get:3 http://deb.debian.org/debian trixie/main libncl 2.1.21+git20210811.b1213a7-6 (diff) [20.3 kB] Fetched 567 kB in 1s (1058 kB/s) Download complete and in download only mode ============================================================================= Building libncl in trixie on arm64 on codethink04-arm64 now. Date: Sat Feb 22 03:04:56 GMT 2025 Date UTC: Sat Feb 22 03:04:56 UTC 2025 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Fri Feb 21 15:04:56 -12 2025 I: pbuilder-time-stamp: 1740193496 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.b1213a7-6.dsc] I: copying [./libncl_2.1.21+git20210811.b1213a7.orig.tar.xz] I: copying [./libncl_2.1.21+git20210811.b1213a7-6.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./libncl_2.1.21+git20210811.b1213a7-6.dsc: unsupported subcommand 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.b1213a7-6.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/1336987/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='a935237c9925438ba78d593da280a1c8' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='1336987' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.fEgknmXy/pbuilderrc_q5Ji --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.fEgknmXy/b1 --logfile b1/build.log libncl_2.1.21+git20210811.b1213a7-6.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink04-arm64 6.1.0-31-cloud-arm64 #1 SMP Debian 6.1.128-1 (2025-02-07) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1336987/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: arm64 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 ... 19923 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} libffi8{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} python3{a} python3-minimal{a} python3.13{a} python3.13-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, 45 newly installed, 0 to remove and 0 not upgraded. Need to get 26.3 MB of archives. After unpacking 107 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 libpython3.13-minimal arm64 3.13.2-1 [853 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 libexpat1 arm64 2.6.4-1 [90.7 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 python3.13-minimal arm64 3.13.2-1 [1997 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 python3-minimal arm64 3.13.1-2 [27.0 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 tzdata all 2025a-2 [259 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 libffi8 arm64 3.4.7-1 [21.2 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 readline-common all 8.2-6 [69.4 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 libreadline8t64 arm64 8.2-6 [159 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 libpython3.13-stdlib arm64 3.13.2-1 [1914 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 python3.13 arm64 3.13.2-1 [745 kB] Get: 13 http://deb.debian.org/debian trixie/main arm64 libpython3-stdlib arm64 3.13.1-2 [9952 B] Get: 14 http://deb.debian.org/debian trixie/main arm64 python3 arm64 3.13.1-2 [28.0 kB] Get: 15 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.23.1-1 [241 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-7 [1129 kB] Get: 22 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40.4-3 [92.0 kB] Get: 23 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-5 [284 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.72-3 [493 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.17-3 [862 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.23.1-1 [770 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 d-shlibs all 0.109 [11.1 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 32 http://deb.debian.org/debian trixie/main arm64 libtool all 2.5.4-3 [539 kB] Get: 33 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 34 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 35 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 36 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 37 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 38 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 39 http://deb.debian.org/debian trixie/main arm64 libunistring5 arm64 1.3-1 [449 kB] Get: 40 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-6 [9239 kB] Get: 41 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB] Get: 42 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.23.1-1 [1610 kB] Get: 43 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 44 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 45 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.24.1 [920 kB] Fetched 26.3 MB in 0s (151 MB/s) Preconfiguring packages ... Selecting previously unselected package libpython3.13-minimal:arm64. (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 ... 19923 files and directories currently installed.) Preparing to unpack .../libpython3.13-minimal_3.13.2-1_arm64.deb ... Unpacking libpython3.13-minimal:arm64 (3.13.2-1) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.6.4-1_arm64.deb ... Unpacking libexpat1:arm64 (2.6.4-1) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../python3.13-minimal_3.13.2-1_arm64.deb ... Unpacking python3.13-minimal (3.13.2-1) ... Setting up libpython3.13-minimal:arm64 (3.13.2-1) ... Setting up libexpat1:arm64 (2.6.4-1) ... Setting up python3.13-minimal (3.13.2-1) ... 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 ... 20257 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.13.1-2_arm64.deb ... Unpacking python3-minimal (3.13.1-2) ... 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_2025a-2_all.deb ... Unpacking tzdata (2025a-2) ... Selecting previously unselected package libffi8:arm64. Preparing to unpack .../4-libffi8_3.4.7-1_arm64.deb ... Unpacking libffi8:arm64 (3.4.7-1) ... Selecting previously unselected package readline-common. Preparing to unpack .../5-readline-common_8.2-6_all.deb ... Unpacking readline-common (8.2-6) ... Selecting previously unselected package libreadline8t64:arm64. Preparing to unpack .../6-libreadline8t64_8.2-6_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.2-6) ... Selecting previously unselected package libpython3.13-stdlib:arm64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.2-1_arm64.deb ... Unpacking libpython3.13-stdlib:arm64 (3.13.2-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.2-1_arm64.deb ... Unpacking python3.13 (3.13.2-1) ... 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Setting up libuchardet0:arm64 (0.0.8-1+b2) ... Setting up netbase (6.4) ... Setting up readline-common (8.2-6) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up automake (1:1.17-3) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up gettext (0.23.1-1) ... Setting up libtool (2.5.4-3) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libreadline8t64:arm64 (8.2-6) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up groff-base (1.23.0-7) ... Setting up libpython3.13-stdlib:arm64 (3.13.2-1) ... Setting up libpython3-stdlib:arm64 (3.13.1-2) ... Setting up python3.13 (3.13.2-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up python3 (3.13.1-2) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.24.1) ... Processing triggers for libc-bin (2.40-7) ... 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: Running cd /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../libncl_2.1.21+git20210811.b1213a7-6_source.changes dpkg-buildpackage: info: source package libncl dpkg-buildpackage: info: source version 2.1.21+git20210811.b1213a7-6 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 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 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.m4:663: 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=aarch64-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/aarch64-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 sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 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 xargs -n works... yes checking whether UID '1111' is supported by ustar format... yes checking whether GID '1111' 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... aarch64-unknown-linux-gnu checking host system type... aarch64-unknown-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... BSD nm checking the maximum length of command line arguments... 1572864 checking how to convert aarch64-unknown-linux-gnu file names to aarch64-unknown-linux-gnu format... func_convert_file_noop checking how to convert aarch64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for file... file checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ranlib... ranlib checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /usr/bin/dd checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld) 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 checking if the linker (/usr/bin/ld) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld) 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) 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 or later... 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 -j12 make[1]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7' make all-recursive make[2]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7' Making all in ncl make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/ncl' /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. 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-Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c -o nxscharactersblock.lo nxscharactersblock.cpp /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c -o nxscxxdiscretematrix.lo nxscxxdiscretematrix.cpp /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c -o nxsdatablock.lo nxsdatablock.cpp /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c -o nxsdistancesblock.lo nxsdistancesblock.cpp /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c -o nxsexception.lo nxsexception.cpp /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c -o nxsmultiformat.lo nxsmultiformat.cpp /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c -o nxspublicblocks.lo nxspublicblocks.cpp /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c -o nxsreader.lo nxsreader.cpp /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c -o nxssetreader.lo nxssetreader.cpp /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c -o nxsstring.lo nxsstring.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxsexception.cpp -fPIC -DPIC -o .libs/nxsexception.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxscharactersblock.cpp -fPIC -DPIC -o .libs/nxscharactersblock.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxsdatablock.cpp -fPIC -DPIC -o .libs/nxsdatablock.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxsblock.cpp -fPIC -DPIC -o .libs/nxsblock.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxsassumptionsblock.cpp -fPIC -DPIC -o .libs/nxsassumptionsblock.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxspublicblocks.cpp -fPIC -DPIC -o .libs/nxspublicblocks.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxscxxdiscretematrix.cpp -fPIC -DPIC -o .libs/nxscxxdiscretematrix.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxssetreader.cpp -fPIC -DPIC -o .libs/nxssetreader.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxsdistancesblock.cpp -fPIC -DPIC -o .libs/nxsdistancesblock.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxsmultiformat.cpp -fPIC -DPIC -o .libs/nxsmultiformat.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxsreader.cpp -fPIC -DPIC -o .libs/nxsreader.o 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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from nxspublicblocks.cpp:22: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../ncl/nxsexception.h:23, from ../ncl/nxsblock.h:24, from nxsblock.cpp:21: ../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from ../ncl/nxsdefs.h:22, from nxsblock.cpp:20: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../ncl/nxsexception.h:23, from ../ncl/nxsblock.h:24, from ../ncl/nxstaxablock.h:23, from ../ncl/nxscharactersblock.h:29, from ../ncl/nxscxxdiscretematrix.h:28, from nxscxxdiscretematrix.cpp:20: ../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/streambuf:43, from /usr/include/c++/14/bits/streambuf_iterator.h:35, from /usr/include/c++/14/iterator:66, from nxscxxdiscretematrix.cpp:19: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../ncl/nxsexception.h:23, from ../ncl/nxsblock.h:24, from ../ncl/nxsassumptionsblock.h:26, from nxsassumptionsblock.cpp:22: ../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/iomanip:42, from nxsassumptionsblock.cpp:19: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ 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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/iomanip:42, from nxsdistancesblock.cpp:19: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../ncl/nxsexception.h:23, from nxsexception.cpp:20: ../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/functional:49, from ../ncl/nxsstring.h:26: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../ncl/nxsexception.h:23, from ../ncl/nxsblock.h:24, from ../ncl/nxstaxablock.h:23, from ../ncl/nxscharactersblock.h:29, from nxscharactersblock.cpp:26: ../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/iomanip:42, from nxscharactersblock.cpp:23: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../ncl/nxsexception.h:23, from ../ncl/nxsblock.h:24, from ../ncl/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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, from ../ncl/nxscharactersblock.h:23: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../ncl/nxsexception.h:23, from ../ncl/nxsblock.h:24, from ../ncl/nxspublicblocks.h:24, from ../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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from nxsmultiformat.cpp:48: /usr/include/c++/14/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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from ../ncl/nxsdefs.h:22, from nxsstring.cpp:24: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../ncl/nxsexception.h:23, from ../ncl/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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, from ../ncl/nxssetreader.h:22: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxsexception.cpp -o nxsexception.o >/dev/null 2>&1 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++/14/bits/stl_tree.h:65, from /usr/include/c++/14/set:62, from nxsreader.cpp:21: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxsstring.cpp -o nxsstring.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c -o nxstaxablock.lo nxstaxablock.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxstaxablock.cpp -fPIC -DPIC -o .libs/nxstaxablock.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxssetreader.cpp -o nxssetreader.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxsdistancesblock.cpp -o nxsdistancesblock.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxsblock.cpp -o nxsblock.o >/dev/null 2>&1 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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from ../ncl/nxsdefs.h:22, from ../ncl/nxstaxablock.h:22: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c -o nxstaxaassociationblock.lo nxstaxaassociationblock.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxstaxaassociationblock.cpp -fPIC -DPIC -o .libs/nxstaxaassociationblock.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxsdatablock.cpp -o nxsdatablock.o >/dev/null 2>&1 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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/iomanip:42, from nxstaxaassociationblock.cpp:20: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c -o nxstoken.lo nxstoken.cpp /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c -o nxstreesblock.lo nxstreesblock.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxstreesblock.cpp -fPIC -DPIC -o .libs/nxstreesblock.o /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c -o nxsunalignedblock.lo nxsunalignedblock.cpp 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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, from nxstoken.cpp:21: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxsunalignedblock.cpp -fPIC -DPIC -o .libs/nxsunalignedblock.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxscxxdiscretematrix.cpp -o nxscxxdiscretematrix.o >/dev/null 2>&1 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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, from nxstreesblock.cpp:20: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../ncl/nxsexception.h:23, from ../ncl/nxsblock.h:24, from ../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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from ../ncl/nxsdefs.h:22, from ../ncl/nxsunalignedblock.h:23: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxsmultiformat.cpp -o nxsmultiformat.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxspublicblocks.cpp -o nxspublicblocks.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxsreader.cpp -o nxsreader.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxstoken.cpp -o nxstoken.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxsassumptionsblock.cpp -o nxsassumptionsblock.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxstreesblock.cpp -o nxstreesblock.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxscharactersblock.cpp -o nxscharactersblock.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -version-info 2:0:0 -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o libncl.la -rpath /usr/lib/aarch64-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/aarch64-linux-gnu/14/../../../aarch64-linux-gnu/crti.o /usr/lib/gcc/aarch64-linux-gnu/14/crtbeginS.o .libs/nxsassumptionsblock.o .libs/nxsblock.o .libs/nxscharactersblock.o .libs/nxscxxdiscretematrix.o .libs/nxsdatablock.o .libs/nxsdistancesblock.o .libs/nxsexception.o .libs/nxsmultiformat.o .libs/nxspublicblocks.o .libs/nxsreader.o .libs/nxssetreader.o .libs/nxsstring.o .libs/nxstaxablock.o .libs/nxstaxaassociationblock.o .libs/nxstoken.o .libs/nxstreesblock.o .libs/nxsunalignedblock.o -L/usr/lib/gcc/aarch64-linux-gnu/14 -L/usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/14/../../../../lib -L/lib/aarch64-linux-gnu -L/lib/../lib -L/usr/lib/aarch64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/aarch64-linux-gnu/14/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/aarch64-linux-gnu/14/crtendS.o /usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu/crtn.o -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -fstack-protector-strong -Werror=format-security -mbranch-protection=standard -O3 -flto=auto -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,libncl.so.2 -o .libs/libncl.so.2.0.0 libtool: link: (cd ".libs" && rm -f "libncl.so.2" && ln -s "libncl.so.2.0.0" "libncl.so.2") libtool: link: (cd ".libs" && rm -f "libncl.so" && ln -s "libncl.so.2.0.0" "libncl.so") 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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o basiccmdline basiccmdline.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/basiccmdline basiccmdline.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/basiccmdline' Making all in check-taxo-nodes 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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o checktaxonnodes checktaxonnodes-checktaxonnodes.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/checktaxonnodes checktaxonnodes-checktaxonnodes.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/check-taxo-nodes' Making all in compressor 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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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++/14/string:49, from compressor.cpp:1: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o NEXUSCharacterCompressor NEXUSCharacterCompressor-compressor.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEXUSCharacterCompressor NEXUSCharacterCompressor-compressor.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/compressor' Making all in find-unsupported-edges 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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o findunsupportededges findunsupportededges-findunsupportededges.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/findunsupportededges findunsupportededges-findunsupportededges.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/find-unsupported-edges' Making all in gapcode 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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o NEXUSgapcode NEXUSgapcode-gapcode.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEXUSgapcode NEXUSgapcode-gapcode.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/gapcode' Making all in nclsimplest 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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o nclsimplest nclsimplest.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/nclsimplest nclsimplest.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/nclsimplest' Making all in ncltest 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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o ncltest ncltest.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/ncltest ncltest.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/ncltest' Making all in normalizer 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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c -o NCLconverter-us2ml.o `test -f 'us2ml.cpp' || echo './'`us2ml.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONVERTER_APP -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c -o NCLconverter-converter.o `test -f 'converter.cpp' || echo './'`converter.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DJUST_REPORT_NEXUS -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c -o NEXUSinspector-normalizer.o `test -f 'normalizer.cpp' || echo './'`normalizer.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DTO_NEXML_CONVERTER -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c -o NEX_us2ml-normalizer.o `test -f 'normalizer.cpp' || echo './'`normalizer.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DTO_NEXML_CONVERTER -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c -o NEX_us2ml-us2ml.o `test -f 'us2ml.cpp' || echo './'`us2ml.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DMULTIFILE_NEXUS_READER -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c -o NEXUSunion-normalizer.o `test -f 'normalizer.cpp' || echo './'`normalizer.cpp In file included from ../../ncl/ncl.h:79, from normalizer.cpp:46: ../../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../ncl/ncl.h:79, from normalizer.cpp:46: ../../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../ncl/ncl.h:79, from converter.cpp:48: ../../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../ncl/ncl.h:79, from normalizer.cpp:46: ../../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../ncl/ncl.h:79, from 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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../ncl/ncl.h:79, from normalizer.cpp:46: ../../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../ncl/ncl.h:79, from normalizer.cpp:46: ../../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../ncl/ncl.h:79, from normalizer.cpp:46: ../../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../ncl/ncl.h:79, from 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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o NEXUSinspector NEXUSinspector-normalizer.o ../../ncl/libncl.la /bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o NEXUSunion NEXUSunion-normalizer.o ../../ncl/libncl.la /bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o NEXUSnormalizer normalizer.o ../../ncl/libncl.la /bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o NEXUSvalidator NEXUSvalidator-normalizer.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEXUSunion NEXUSunion-normalizer.o ../../ncl/.libs/libncl.so libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEXUSinspector NEXUSinspector-normalizer.o ../../ncl/.libs/libncl.so libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEXUSnormalizer normalizer.o ../../ncl/.libs/libncl.so libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEXUSvalidator NEXUSvalidator-normalizer.o ../../ncl/.libs/libncl.so /bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o NCLconverter NCLconverter-normalizer.o NCLconverter-us2ml.o NCLconverter-converter.o ../../ncl/libncl.la /bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o NEX_us2ml NEX_us2ml-normalizer.o NEX_us2ml-us2ml.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NCLconverter NCLconverter-normalizer.o NCLconverter-us2ml.o NCLconverter-converter.o ../../ncl/.libs/libncl.so normalizer.cpp:102:14: warning: 'substituteSafeTaxaLabels' violates the C++ One Definition Rule [-Wodr] 102 | void substituteSafeTaxaLabels(PublicNexusReader & reader, std::string filepath, bool evenTrivial); | ^ converter.cpp:140:6: note: return value type mismatch 140 | bool substituteSafeTaxaLabels(PublicNexusReader &nexusReader, std::string filepath, bool evenTrivial) | ^ converter.cpp:140:6: note: type 'bool' should match type 'void' converter.cpp:140:6: note: 'substituteSafeTaxaLabels' was previously declared here libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEX_us2ml NEX_us2ml-normalizer.o NEX_us2ml-us2ml.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer' Making all in ot-subtree 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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o otsubtree otsubtree-otsubtree.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/otsubtree otsubtree-otsubtree.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/ot-subtree' Making all in ot-tree-inspect 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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o otTreeInspect otTreeInspect-ot_tree_inspect.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/otTreeInspect otTreeInspect-ot_tree_inspect.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/ot-tree-inspect' Making all in outdeg1count 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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o outdeg1count outdeg1count-outdeg1count.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/outdeg1count outdeg1count-outdeg1count.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/outdeg1count' Making all in patristic 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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o patristicmat patristic.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/patristicmat patristic.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/patristic' Making all in phylobaseinterface 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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o PhylobaseNCLInterfaceExample NCLInterface.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/PhylobaseNCLInterfaceExample NCLInterface.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/phylobaseinterface' Making all in polytomy-count 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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o polytomycount polytomycount-polytomy_count.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/polytomycount polytomycount-polytomy_count.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/polytomy-count' Making all in splitsinfile 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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 ../../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++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from splitsstructs.h:3: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from splitsstructs.h:3: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../ncl/ncl.h:79, from 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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../ncl/ncl.h:79, from 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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o NEXUStosplits NEXUStosplits-splitsinfile.o NEXUStosplits-splitsstructs.o ../../ncl/libncl.la /bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o majrule splitsinfile.o splitsstructs.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEXUStosplits NEXUStosplits-splitsinfile.o NEXUStosplits-splitsstructs.o ../../ncl/.libs/libncl.so libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/majrule splitsinfile.o splitsstructs.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/splitsinfile' Making all in subsetter 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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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++/14/string:49, from subsetter.cpp:1: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o NEXUSsubsetter NEXUSsubsetter-subsetter.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEXUSsubsetter NEXUSsubsetter-subsetter.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/subsetter' Making all in translate 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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o NEXUStranslate NEXUStranslate-translateNuc.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEXUStranslate NEXUStranslate-translateNuc.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/translate' make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example' 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 -j12 check "TESTSUITEFLAGS=-j12 --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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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-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/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/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/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/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/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/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/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" "-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" "-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" "-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" "-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" "-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" "-faaphylipinterleaved" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aaphylipinterleaved_emboss.phy" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aaphylipinterleaved_emboss.phy ] Executing storing implied block: TAXA storing read block: DATA ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aaphylipinterleaved_emboss.phy "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/aaphylipinterleaved_emboss.phy" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/aaphylipinterleaved_emboss.phy ] Executing storing read block: TAXA storing read block: CHARACTERS ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/aaphylipinterleaved_emboss.phy "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "-faaphylip" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aaphylip_emboss.phy" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aaphylip_emboss.phy ] Executing 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" "-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/aarch64-linux-gnu' /bin/bash ../libtool --mode=install /usr/bin/install -c libncl.la '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/lib/aarch64-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/aarch64-linux-gnu/libncl.so.2.0.0 libtool: install: (cd /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/lib/aarch64-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/aarch64-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/aarch64-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/aarch64-linux-gnu/libncl.a libtool: install: chmod 644 /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/lib/aarch64-linux-gnu/libncl.a libtool: install: ranlib /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/lib/aarch64-linux-gnu/libncl.a libtool: warning: remember to run 'libtool --finish /usr/lib/aarch64-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/bash ../../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/aarch64-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/bash ../../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/aarch64-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/bash ../../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/aarch64-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/aarch64-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/aarch64-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/bash ../../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/aarch64-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/bash ../../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/aarch64-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/bash ../../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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-linux-gnu install -d -m 755 debian/libncl2/usr/lib/aarch64-linux-gnu mv debian/tmp/usr/lib/aarch64-linux-gnu/libncl.a debian/libncl-dev/usr/lib/aarch64-linux-gnu mv debian/tmp/usr/lib/aarch64-linux-gnu/libncl.la debian/libncl-dev/usr/lib/aarch64-linux-gnu || true mv debian/tmp/usr/lib/aarch64-linux-gnu/libncl.so debian/libncl-dev/usr/lib/aarch64-linux-gnu mv /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/lib/aarch64-linux-gnu/libncl.so.2 debian/libncl2/usr/lib/aarch64-linux-gnu mv /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/lib/aarch64-linux-gnu/libncl.so.2.0.0 debian/libncl2/usr/lib/aarch64-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/aarch64-linux-gnu/pkgconfig mv debian/tmp/usr/lib/*/pkgconfig/*.pc debian/libncl-dev/usr/lib/aarch64-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 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged 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.b1213a7-6_arm64.deb'. dpkg-deb: building package 'ncl-tools-dbgsym' in '../ncl-tools-dbgsym_2.1.21+git20210811.b1213a7-6_arm64.deb'. dpkg-deb: building package 'libncl2' in '../libncl2_2.1.21+git20210811.b1213a7-6_arm64.deb'. dpkg-deb: building package 'libncl2-dbgsym' in '../libncl2-dbgsym_2.1.21+git20210811.b1213a7-6_arm64.deb'. dpkg-deb: building package 'libncl-dev' in '../libncl-dev_2.1.21+git20210811.b1213a7-6_arm64.deb'. dpkg-genbuildinfo --build=binary -O../libncl_2.1.21+git20210811.b1213a7-6_arm64.buildinfo dpkg-genchanges --build=binary -O../libncl_2.1.21+git20210811.b1213a7-6_arm64.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: 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/1336987 and its subdirectories I: Current time: Fri Feb 21 15:09:44 -12 2025 I: pbuilder-time-stamp: 1740193784 Sat Feb 22 03:09:44 UTC 2025 I: Signing ./b1/libncl_2.1.21+git20210811.b1213a7-6_arm64.buildinfo as libncl_2.1.21+git20210811.b1213a7-6_arm64.buildinfo.asc Sat Feb 22 03:09:44 UTC 2025 I: Signed ./b1/libncl_2.1.21+git20210811.b1213a7-6_arm64.buildinfo as ./b1/libncl_2.1.21+git20210811.b1213a7-6_arm64.buildinfo.asc Sat Feb 22 03:09:44 UTC 2025 - build #1 for libncl/trixie/arm64 on codethink04-arm64 done. Starting cleanup. All cleanup done. Sat Feb 22 03:09:44 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-nPZsbsz8, removing. /srv/reproducible-results/rbuild-debian/r-b-build.fEgknmXy: total 16 drwxr-xr-x 2 jenkins jenkins 4096 Feb 22 03:09 b1 drwxr-xr-x 2 jenkins jenkins 4096 Feb 22 03:04 b2 -rw-r--r-- 1 jenkins jenkins 2422 Aug 25 10:30 libncl_2.1.21+git20210811.b1213a7-6.dsc -rw------- 1 jenkins jenkins 3630 Feb 22 03:04 rbuildlog.eWPVFjl /srv/reproducible-results/rbuild-debian/r-b-build.fEgknmXy/b1: total 11644 -rw-r--r-- 1 jenkins jenkins 229422 Feb 22 03:09 build.log -rw-r--r-- 1 jenkins jenkins 557308 Feb 22 03:09 libncl-dev_2.1.21+git20210811.b1213a7-6_arm64.deb -rw-r--r-- 1 jenkins jenkins 6043432 Feb 22 03:09 libncl2-dbgsym_2.1.21+git20210811.b1213a7-6_arm64.deb -rw-r--r-- 1 jenkins jenkins 319856 Feb 22 03:09 libncl2_2.1.21+git20210811.b1213a7-6_arm64.deb -rw-r--r-- 1 jenkins jenkins 20292 Feb 22 03:09 libncl_2.1.21+git20210811.b1213a7-6.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2422 Feb 22 03:09 libncl_2.1.21+git20210811.b1213a7-6.dsc -rw-r--r-- 1 jenkins jenkins 6868 Feb 22 03:09 libncl_2.1.21+git20210811.b1213a7-6_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 7750 Feb 22 03:09 libncl_2.1.21+git20210811.b1213a7-6_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 2917 Feb 22 03:09 libncl_2.1.21+git20210811.b1213a7-6_arm64.changes -rw-r--r-- 1 jenkins jenkins 1646 Feb 22 03:09 libncl_2.1.21+git20210811.b1213a7-6_source.changes -rw-r--r-- 1 jenkins jenkins 4541004 Feb 22 03:09 ncl-tools-dbgsym_2.1.21+git20210811.b1213a7-6_arm64.deb -rw-r--r-- 1 jenkins jenkins 165612 Feb 22 03:09 ncl-tools_2.1.21+git20210811.b1213a7-6_arm64.deb /srv/reproducible-results/rbuild-debian/r-b-build.fEgknmXy/b2: total 0 Sat Feb 22 03:09:45 UTC 2025 I: Deleting $TMPDIR on codethink04-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Fri Feb 21 15:04:56 -12 2025 I: pbuilder-time-stamp: 1740193496 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.b1213a7-6.dsc] I: copying [./libncl_2.1.21+git20210811.b1213a7.orig.tar.xz] I: copying [./libncl_2.1.21+git20210811.b1213a7-6.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./libncl_2.1.21+git20210811.b1213a7-6.dsc: unsupported subcommand 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.b1213a7-6.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/1336987/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='a935237c9925438ba78d593da280a1c8' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='1336987' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.fEgknmXy/pbuilderrc_q5Ji --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.fEgknmXy/b1 --logfile b1/build.log libncl_2.1.21+git20210811.b1213a7-6.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink04-arm64 6.1.0-31-cloud-arm64 #1 SMP Debian 6.1.128-1 (2025-02-07) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1336987/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: arm64 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 ... 19923 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} libffi8{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} python3{a} python3-minimal{a} python3.13{a} python3.13-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, 45 newly installed, 0 to remove and 0 not upgraded. Need to get 26.3 MB of archives. After unpacking 107 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 libpython3.13-minimal arm64 3.13.2-1 [853 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 libexpat1 arm64 2.6.4-1 [90.7 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 python3.13-minimal arm64 3.13.2-1 [1997 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 python3-minimal arm64 3.13.1-2 [27.0 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 tzdata all 2025a-2 [259 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 libffi8 arm64 3.4.7-1 [21.2 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 readline-common all 8.2-6 [69.4 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 libreadline8t64 arm64 8.2-6 [159 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 libpython3.13-stdlib arm64 3.13.2-1 [1914 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 python3.13 arm64 3.13.2-1 [745 kB] Get: 13 http://deb.debian.org/debian trixie/main arm64 libpython3-stdlib arm64 3.13.1-2 [9952 B] Get: 14 http://deb.debian.org/debian trixie/main arm64 python3 arm64 3.13.1-2 [28.0 kB] Get: 15 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.23.1-1 [241 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-7 [1129 kB] Get: 22 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40.4-3 [92.0 kB] Get: 23 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-5 [284 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.72-3 [493 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.17-3 [862 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.23.1-1 [770 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 d-shlibs all 0.109 [11.1 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 32 http://deb.debian.org/debian trixie/main arm64 libtool all 2.5.4-3 [539 kB] Get: 33 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 34 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 35 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 36 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 37 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 38 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 39 http://deb.debian.org/debian trixie/main arm64 libunistring5 arm64 1.3-1 [449 kB] Get: 40 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-6 [9239 kB] Get: 41 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB] Get: 42 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.23.1-1 [1610 kB] Get: 43 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 44 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 45 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.24.1 [920 kB] Fetched 26.3 MB in 0s (151 MB/s) Preconfiguring packages ... Selecting previously unselected package libpython3.13-minimal:arm64. (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 ... 19923 files and directories currently installed.) Preparing to unpack .../libpython3.13-minimal_3.13.2-1_arm64.deb ... Unpacking libpython3.13-minimal:arm64 (3.13.2-1) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.6.4-1_arm64.deb ... Unpacking libexpat1:arm64 (2.6.4-1) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../python3.13-minimal_3.13.2-1_arm64.deb ... Unpacking python3.13-minimal (3.13.2-1) ... Setting up libpython3.13-minimal:arm64 (3.13.2-1) ... Setting up libexpat1:arm64 (2.6.4-1) ... Setting up python3.13-minimal (3.13.2-1) ... 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 ... 20257 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.13.1-2_arm64.deb ... Unpacking python3-minimal (3.13.1-2) ... 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_2025a-2_all.deb ... Unpacking tzdata (2025a-2) ... Selecting previously unselected package libffi8:arm64. Preparing to unpack .../4-libffi8_3.4.7-1_arm64.deb ... Unpacking libffi8:arm64 (3.4.7-1) ... Selecting previously unselected package readline-common. Preparing to unpack .../5-readline-common_8.2-6_all.deb ... Unpacking readline-common (8.2-6) ... Selecting previously unselected package libreadline8t64:arm64. Preparing to unpack .../6-libreadline8t64_8.2-6_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.2-6) ... Selecting previously unselected package libpython3.13-stdlib:arm64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.2-1_arm64.deb ... Unpacking libpython3.13-stdlib:arm64 (3.13.2-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.2-1_arm64.deb ... Unpacking python3.13 (3.13.2-1) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../9-libpython3-stdlib_3.13.1-2_arm64.deb ... Unpacking libpython3-stdlib:arm64 (3.13.1-2) ... Setting up python3-minimal (3.13.1-2) ... 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 ... 21267 files and directories currently installed.) Preparing to unpack .../00-python3_3.13.1-2_arm64.deb ... Unpacking python3 (3.13.1-2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../03-libmagic1t64_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.45-3+b1_arm64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../05-gettext-base_0.23.1-1_arm64.deb ... Unpacking gettext-base (0.23.1-1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../06-libuchardet0_0.0.8-1+b2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../07-groff-base_1.23.0-7_arm64.deb ... Unpacking groff-base (1.23.0-7) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../08-bsdextrautils_2.40.4-3_arm64.deb ... Unpacking bsdextrautils (2.40.4-3) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../09-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../10-man-db_2.13.0-1_arm64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../11-m4_1.4.19-5_arm64.deb ... Unpacking m4 (1.4.19-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../12-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../13-autotools-dev_20220109.1_all.deb ... 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../libncl_2.1.21+git20210811.b1213a7-6_source.changes dpkg-buildpackage: info: source package libncl dpkg-buildpackage: info: source version 2.1.21+git20210811.b1213a7-6 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 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 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.m4:663: 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=aarch64-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/aarch64-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 sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 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 xargs -n works... yes checking whether UID '1111' is supported by ustar format... yes checking whether GID '1111' 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... aarch64-unknown-linux-gnu checking host system type... aarch64-unknown-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... BSD nm checking the maximum length of command line arguments... 1572864 checking how to convert aarch64-unknown-linux-gnu file names to aarch64-unknown-linux-gnu format... func_convert_file_noop checking how to convert aarch64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for file... file checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ranlib... ranlib checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /usr/bin/dd checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld) 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 checking if the linker (/usr/bin/ld) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld) 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) 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 or later... 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 -j12 make[1]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7' make all-recursive make[2]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7' Making all in ncl make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/ncl' /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c -o nxsstring.lo nxsstring.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxsexception.cpp -fPIC -DPIC -o .libs/nxsexception.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxscharactersblock.cpp -fPIC -DPIC -o .libs/nxscharactersblock.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxsdatablock.cpp -fPIC -DPIC -o .libs/nxsdatablock.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxsblock.cpp -fPIC -DPIC -o .libs/nxsblock.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxsassumptionsblock.cpp -fPIC -DPIC -o .libs/nxsassumptionsblock.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxspublicblocks.cpp -fPIC -DPIC -o .libs/nxspublicblocks.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxscxxdiscretematrix.cpp -fPIC -DPIC -o .libs/nxscxxdiscretematrix.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxssetreader.cpp -fPIC -DPIC -o .libs/nxssetreader.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxsdistancesblock.cpp -fPIC -DPIC -o .libs/nxsdistancesblock.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxsmultiformat.cpp -fPIC -DPIC -o .libs/nxsmultiformat.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxsreader.cpp -fPIC -DPIC -o .libs/nxsreader.o 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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from nxspublicblocks.cpp:22: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../ncl/nxsexception.h:23, from ../ncl/nxsblock.h:24, from nxsblock.cpp:21: ../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from ../ncl/nxsdefs.h:22, from nxsblock.cpp:20: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../ncl/nxsexception.h:23, from ../ncl/nxsblock.h:24, from ../ncl/nxstaxablock.h:23, from ../ncl/nxscharactersblock.h:29, from ../ncl/nxscxxdiscretematrix.h:28, from nxscxxdiscretematrix.cpp:20: ../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/streambuf:43, from /usr/include/c++/14/bits/streambuf_iterator.h:35, from /usr/include/c++/14/iterator:66, from nxscxxdiscretematrix.cpp:19: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../ncl/nxsexception.h:23, from ../ncl/nxsblock.h:24, from ../ncl/nxsassumptionsblock.h:26, from nxsassumptionsblock.cpp:22: ../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/iomanip:42, from nxsassumptionsblock.cpp:19: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ 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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/iomanip:42, from nxsdistancesblock.cpp:19: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../ncl/nxsexception.h:23, from nxsexception.cpp:20: ../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/functional:49, from ../ncl/nxsstring.h:26: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../ncl/nxsexception.h:23, from ../ncl/nxsblock.h:24, from ../ncl/nxstaxablock.h:23, from ../ncl/nxscharactersblock.h:29, from nxscharactersblock.cpp:26: ../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/iomanip:42, from nxscharactersblock.cpp:23: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../ncl/nxsexception.h:23, from ../ncl/nxsblock.h:24, from ../ncl/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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, from ../ncl/nxscharactersblock.h:23: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../ncl/nxsexception.h:23, from ../ncl/nxsblock.h:24, from ../ncl/nxspublicblocks.h:24, from ../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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from nxsmultiformat.cpp:48: /usr/include/c++/14/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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from ../ncl/nxsdefs.h:22, from nxsstring.cpp:24: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../ncl/nxsexception.h:23, from ../ncl/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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, from ../ncl/nxssetreader.h:22: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxsexception.cpp -o nxsexception.o >/dev/null 2>&1 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++/14/bits/stl_tree.h:65, from /usr/include/c++/14/set:62, from nxsreader.cpp:21: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxsstring.cpp -o nxsstring.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c -o nxstaxablock.lo nxstaxablock.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxstaxablock.cpp -fPIC -DPIC -o .libs/nxstaxablock.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxssetreader.cpp -o nxssetreader.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxsdistancesblock.cpp -o nxsdistancesblock.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxsblock.cpp -o nxsblock.o >/dev/null 2>&1 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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from ../ncl/nxsdefs.h:22, from ../ncl/nxstaxablock.h:22: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c -o nxstaxaassociationblock.lo nxstaxaassociationblock.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxstaxaassociationblock.cpp -fPIC -DPIC -o .libs/nxstaxaassociationblock.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxsdatablock.cpp -o nxsdatablock.o >/dev/null 2>&1 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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/iomanip:42, from nxstaxaassociationblock.cpp:20: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c -o nxstoken.lo nxstoken.cpp /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c -o nxstreesblock.lo nxstreesblock.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxstreesblock.cpp -fPIC -DPIC -o .libs/nxstreesblock.o /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c -o nxsunalignedblock.lo nxsunalignedblock.cpp 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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, from nxstoken.cpp:21: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxsunalignedblock.cpp -fPIC -DPIC -o .libs/nxsunalignedblock.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxscxxdiscretematrix.cpp -o nxscxxdiscretematrix.o >/dev/null 2>&1 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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, from nxstreesblock.cpp:20: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../ncl/nxsexception.h:23, from ../ncl/nxsblock.h:24, from ../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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from ../ncl/nxsdefs.h:22, from ../ncl/nxsunalignedblock.h:23: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxsmultiformat.cpp -o nxsmultiformat.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxspublicblocks.cpp -o nxspublicblocks.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxsreader.cpp -o nxsreader.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxstoken.cpp -o nxstoken.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxsassumptionsblock.cpp -o nxsassumptionsblock.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxstreesblock.cpp -o nxstreesblock.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxscharactersblock.cpp -o nxscharactersblock.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -version-info 2:0:0 -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o libncl.la -rpath /usr/lib/aarch64-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/aarch64-linux-gnu/14/../../../aarch64-linux-gnu/crti.o /usr/lib/gcc/aarch64-linux-gnu/14/crtbeginS.o .libs/nxsassumptionsblock.o .libs/nxsblock.o .libs/nxscharactersblock.o .libs/nxscxxdiscretematrix.o .libs/nxsdatablock.o .libs/nxsdistancesblock.o .libs/nxsexception.o .libs/nxsmultiformat.o .libs/nxspublicblocks.o .libs/nxsreader.o .libs/nxssetreader.o .libs/nxsstring.o .libs/nxstaxablock.o .libs/nxstaxaassociationblock.o .libs/nxstoken.o .libs/nxstreesblock.o .libs/nxsunalignedblock.o -L/usr/lib/gcc/aarch64-linux-gnu/14 -L/usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/14/../../../../lib -L/lib/aarch64-linux-gnu -L/lib/../lib -L/usr/lib/aarch64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/aarch64-linux-gnu/14/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/aarch64-linux-gnu/14/crtendS.o /usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu/crtn.o -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -fstack-protector-strong -Werror=format-security -mbranch-protection=standard -O3 -flto=auto -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,libncl.so.2 -o .libs/libncl.so.2.0.0 libtool: link: (cd ".libs" && rm -f "libncl.so.2" && ln -s "libncl.so.2.0.0" "libncl.so.2") libtool: link: (cd ".libs" && rm -f "libncl.so" && ln -s "libncl.so.2.0.0" "libncl.so") 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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o basiccmdline basiccmdline.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/basiccmdline basiccmdline.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/basiccmdline' Making all in check-taxo-nodes 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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o checktaxonnodes checktaxonnodes-checktaxonnodes.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/checktaxonnodes checktaxonnodes-checktaxonnodes.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/check-taxo-nodes' Making all in compressor 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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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++/14/string:49, from compressor.cpp:1: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o NEXUSCharacterCompressor NEXUSCharacterCompressor-compressor.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEXUSCharacterCompressor NEXUSCharacterCompressor-compressor.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/compressor' Making all in find-unsupported-edges 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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o findunsupportededges findunsupportededges-findunsupportededges.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/findunsupportededges findunsupportededges-findunsupportededges.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/find-unsupported-edges' Making all in gapcode 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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o NEXUSgapcode NEXUSgapcode-gapcode.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEXUSgapcode NEXUSgapcode-gapcode.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/gapcode' Making all in nclsimplest 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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o nclsimplest nclsimplest.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/nclsimplest nclsimplest.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/nclsimplest' Making all in ncltest 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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o ncltest ncltest.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/ncltest ncltest.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/ncltest' Making all in normalizer 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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c -o NCLconverter-us2ml.o `test -f 'us2ml.cpp' || echo './'`us2ml.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONVERTER_APP -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c -o NCLconverter-converter.o `test -f 'converter.cpp' || echo './'`converter.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DJUST_REPORT_NEXUS -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c -o NEXUSinspector-normalizer.o `test -f 'normalizer.cpp' || echo './'`normalizer.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DTO_NEXML_CONVERTER -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c -o NEX_us2ml-normalizer.o `test -f 'normalizer.cpp' || echo './'`normalizer.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DTO_NEXML_CONVERTER -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c -o NEX_us2ml-us2ml.o `test -f 'us2ml.cpp' || echo './'`us2ml.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DMULTIFILE_NEXUS_READER -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c -o NEXUSunion-normalizer.o `test -f 'normalizer.cpp' || echo './'`normalizer.cpp In file included from ../../ncl/ncl.h:79, from normalizer.cpp:46: ../../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../ncl/ncl.h:79, from normalizer.cpp:46: ../../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../ncl/ncl.h:79, from converter.cpp:48: ../../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../ncl/ncl.h:79, from normalizer.cpp:46: ../../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../ncl/ncl.h:79, from 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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../ncl/ncl.h:79, from normalizer.cpp:46: ../../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../ncl/ncl.h:79, from normalizer.cpp:46: ../../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../ncl/ncl.h:79, from normalizer.cpp:46: ../../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../ncl/ncl.h:79, from 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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o NEXUSinspector NEXUSinspector-normalizer.o ../../ncl/libncl.la /bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o NEXUSunion NEXUSunion-normalizer.o ../../ncl/libncl.la /bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o NEXUSnormalizer normalizer.o ../../ncl/libncl.la /bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o NEXUSvalidator NEXUSvalidator-normalizer.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEXUSunion NEXUSunion-normalizer.o ../../ncl/.libs/libncl.so libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEXUSinspector NEXUSinspector-normalizer.o ../../ncl/.libs/libncl.so libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEXUSnormalizer normalizer.o ../../ncl/.libs/libncl.so libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEXUSvalidator NEXUSvalidator-normalizer.o ../../ncl/.libs/libncl.so /bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o NCLconverter NCLconverter-normalizer.o NCLconverter-us2ml.o NCLconverter-converter.o ../../ncl/libncl.la /bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o NEX_us2ml NEX_us2ml-normalizer.o NEX_us2ml-us2ml.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NCLconverter NCLconverter-normalizer.o NCLconverter-us2ml.o NCLconverter-converter.o ../../ncl/.libs/libncl.so normalizer.cpp:102:14: warning: 'substituteSafeTaxaLabels' violates the C++ One Definition Rule [-Wodr] 102 | void substituteSafeTaxaLabels(PublicNexusReader & reader, std::string filepath, bool evenTrivial); | ^ converter.cpp:140:6: note: return value type mismatch 140 | bool substituteSafeTaxaLabels(PublicNexusReader &nexusReader, std::string filepath, bool evenTrivial) | ^ converter.cpp:140:6: note: type 'bool' should match type 'void' converter.cpp:140:6: note: 'substituteSafeTaxaLabels' was previously declared here libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEX_us2ml NEX_us2ml-normalizer.o NEX_us2ml-us2ml.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer' Making all in ot-subtree 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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o otsubtree otsubtree-otsubtree.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/otsubtree otsubtree-otsubtree.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/ot-subtree' Making all in ot-tree-inspect 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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o otTreeInspect otTreeInspect-ot_tree_inspect.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/otTreeInspect otTreeInspect-ot_tree_inspect.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/ot-tree-inspect' Making all in outdeg1count 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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o outdeg1count outdeg1count-outdeg1count.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/outdeg1count outdeg1count-outdeg1count.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/outdeg1count' Making all in patristic 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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o patristicmat patristic.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/patristicmat patristic.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/patristic' Making all in phylobaseinterface 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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o PhylobaseNCLInterfaceExample NCLInterface.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/PhylobaseNCLInterfaceExample NCLInterface.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/phylobaseinterface' Making all in polytomy-count 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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o polytomycount polytomycount-polytomy_count.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/polytomycount polytomycount-polytomy_count.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/polytomy-count' Making all in splitsinfile 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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 ../../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++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from splitsstructs.h:3: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from splitsstructs.h:3: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../ncl/ncl.h:79, from 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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../ncl/ncl.h:79, from 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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o NEXUStosplits NEXUStosplits-splitsinfile.o NEXUStosplits-splitsstructs.o ../../ncl/libncl.la /bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o majrule splitsinfile.o splitsstructs.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEXUStosplits NEXUStosplits-splitsinfile.o NEXUStosplits-splitsstructs.o ../../ncl/.libs/libncl.so libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/majrule splitsinfile.o splitsstructs.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/splitsinfile' Making all in subsetter 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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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++/14/string:49, from subsetter.cpp:1: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o NEXUSsubsetter NEXUSsubsetter-subsetter.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEXUSsubsetter NEXUSsubsetter-subsetter.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/subsetter' Making all in translate 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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o NEXUStranslate NEXUStranslate-translateNuc.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEXUStranslate NEXUStranslate-translateNuc.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/translate' make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example' 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 -j12 check "TESTSUITEFLAGS=-j12 --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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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-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/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/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/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/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/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/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/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" "-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" "-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" "-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" "-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" "-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" "-faaphylipinterleaved" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aaphylipinterleaved_emboss.phy" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aaphylipinterleaved_emboss.phy ] Executing storing implied block: TAXA storing read block: DATA ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aaphylipinterleaved_emboss.phy "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/aaphylipinterleaved_emboss.phy" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/aaphylipinterleaved_emboss.phy ] Executing storing read block: TAXA storing read block: CHARACTERS ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/aaphylipinterleaved_emboss.phy "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "-faaphylip" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aaphylip_emboss.phy" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aaphylip_emboss.phy ] Executing 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" "-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/aarch64-linux-gnu' /bin/bash ../libtool --mode=install /usr/bin/install -c libncl.la '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/lib/aarch64-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/aarch64-linux-gnu/libncl.so.2.0.0 libtool: install: (cd /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/lib/aarch64-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/aarch64-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/aarch64-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/aarch64-linux-gnu/libncl.a libtool: install: chmod 644 /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/lib/aarch64-linux-gnu/libncl.a libtool: install: ranlib /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/lib/aarch64-linux-gnu/libncl.a libtool: warning: remember to run 'libtool --finish /usr/lib/aarch64-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/bash ../../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/aarch64-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/bash ../../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/aarch64-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/bash ../../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/aarch64-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/aarch64-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/aarch64-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/bash ../../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/aarch64-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/bash ../../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/aarch64-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/bash ../../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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-linux-gnu install -d -m 755 debian/libncl2/usr/lib/aarch64-linux-gnu mv debian/tmp/usr/lib/aarch64-linux-gnu/libncl.a debian/libncl-dev/usr/lib/aarch64-linux-gnu mv debian/tmp/usr/lib/aarch64-linux-gnu/libncl.la debian/libncl-dev/usr/lib/aarch64-linux-gnu || true mv debian/tmp/usr/lib/aarch64-linux-gnu/libncl.so debian/libncl-dev/usr/lib/aarch64-linux-gnu mv /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/lib/aarch64-linux-gnu/libncl.so.2 debian/libncl2/usr/lib/aarch64-linux-gnu mv /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/lib/aarch64-linux-gnu/libncl.so.2.0.0 debian/libncl2/usr/lib/aarch64-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/aarch64-linux-gnu/pkgconfig mv debian/tmp/usr/lib/*/pkgconfig/*.pc debian/libncl-dev/usr/lib/aarch64-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 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged 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.b1213a7-6_arm64.deb'. dpkg-deb: building package 'ncl-tools-dbgsym' in '../ncl-tools-dbgsym_2.1.21+git20210811.b1213a7-6_arm64.deb'. dpkg-deb: building package 'libncl2' in '../libncl2_2.1.21+git20210811.b1213a7-6_arm64.deb'. dpkg-deb: building package 'libncl2-dbgsym' in '../libncl2-dbgsym_2.1.21+git20210811.b1213a7-6_arm64.deb'. dpkg-deb: building package 'libncl-dev' in '../libncl-dev_2.1.21+git20210811.b1213a7-6_arm64.deb'. dpkg-genbuildinfo --build=binary -O../libncl_2.1.21+git20210811.b1213a7-6_arm64.buildinfo dpkg-genchanges --build=binary -O../libncl_2.1.21+git20210811.b1213a7-6_arm64.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: 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/1336987 and its subdirectories I: Current time: Fri Feb 21 15:09:44 -12 2025 I: pbuilder-time-stamp: 1740193784 Sat Feb 22 03:09:46 UTC 2025 I: 1st build successful. Starting 2nd build on remote node codethink03-arm64.debian.net. Sat Feb 22 03:09:46 UTC 2025 I: Preparing to do remote build '2' on codethink03-arm64.debian.net. Sat Feb 22 03:09:46 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink03-arm64.debian.net is marked as down. Sat Feb 22 03:09:46 UTC 2025 - checking via ssh if codethink03-arm64.debian.net is up. removed '/tmp/read-only-fs-test-jcCLpZ' ==================================================================================== Fri Mar 27 09:32:48 UTC 2026 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on codethink03-arm64, called using "2 libncl trixie /srv/reproducible-results/rbuild-debian/r-b-build.fEgknmXy 2.1.21+git20210811.b1213a7-6" as arguments. Fri Mar 27 09:32:48 UTC 2026 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-z7Ai93jJ" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Fri Mar 27 09:32:48 UTC 2026 I: Downloading source for trixie/libncl=2.1.21+git20210811.b1213a7-6 Reading package lists... NOTICE: 'libncl' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/libncl.git Please use: git clone https://salsa.debian.org/med-team/libncl.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 567 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main libncl 2.1.21+git20210811.b1213a7-6 (dsc) [2422 B] Get:2 http://deb.debian.org/debian trixie/main libncl 2.1.21+git20210811.b1213a7-6 (tar) [544 kB] Get:3 http://deb.debian.org/debian trixie/main libncl 2.1.21+git20210811.b1213a7-6 (diff) [20.3 kB] Fetched 567 kB in 0s (30.3 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'libncl' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/libncl.git Please use: git clone https://salsa.debian.org/med-team/libncl.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 567 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main libncl 2.1.21+git20210811.b1213a7-6 (dsc) [2422 B] Get:2 http://deb.debian.org/debian trixie/main libncl 2.1.21+git20210811.b1213a7-6 (tar) [544 kB] Get:3 http://deb.debian.org/debian trixie/main libncl 2.1.21+git20210811.b1213a7-6 (diff) [20.3 kB] Fetched 567 kB in 0s (30.3 MB/s) Download complete and in download only mode ============================================================================= Re-Building libncl in trixie on arm64 on codethink03-arm64 now. Date: Fri Mar 27 09:32:49 GMT 2026 Date UTC: Fri Mar 27 09:32:49 UTC 2026 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.fEgknmXy + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.fEgknmXy/pbuilderrc_1OgA + case ${ARCH} in + case $ARCH in + locale=nl_BE + language=nl + case "${SUITE}" in + reproducible_buildflags=+all + extra_deb_build_options= + case "${SRCPACKAGE}" in + cat + echo BUILDDIR=/build/reproducible-path + '[' libncl = debian-installer -o libncl = debian-installer-netboot-images ']' + pbuilder_options=() + local pbuilder_options + DEBBUILDOPTS=-b + BINARYTARGET= + '[' libncl = u-boot ']' + case "${SRCPACKAGE}" in + PBUILDERTIMEOUT=24 + local PRESULT=0 + sudo 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.fEgknmXy/pbuilderrc_1OgA --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.fEgknmXy/b2 --logfile b2/build.log libncl_2.1.21+git20210811.b1213a7-6.dsc W: /root/.pbuilderrc does not exist I: Logging to b2/build.log I: pbuilder: network access will be disabled during build I: Current time: Fri Mar 27 23:32:50 +14 2026 I: pbuilder-time-stamp: 1774603970 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.b1213a7-6.dsc] I: copying [./libncl_2.1.21+git20210811.b1213a7.orig.tar.xz] I: copying [./libncl_2.1.21+git20210811.b1213a7-6.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./libncl_2.1.21+git20210811.b1213a7-6.dsc: unsupported subcommand 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.b1213a7-6.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/2122414/tmp/hooks/D01_modify_environment starting debug: Running on codethink03-arm64. 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 Mar 27 09:32 /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/2122414/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/2122414/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]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") BASH_VERSION='5.2.37(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' INVOCATION_ID=3db6a5ee649641bd9ed5b94098f23d5f LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-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=2122414 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.fEgknmXy/pbuilderrc_1OgA --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.fEgknmXy/b2 --logfile b2/build.log libncl_2.1.21+git20210811.b1213a7-6.dsc' SUDO_GID=109 SUDO_UID=104 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://192.168.101.4:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-31-cloud-arm64 #1 SMP Debian 6.1.128-1 (2025-02-07) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2122414/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: arm64 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 ... 19923 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} libffi8{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} python3{a} python3-minimal{a} python3.13{a} python3.13-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, 45 newly installed, 0 to remove and 0 not upgraded. Need to get 26.3 MB of archives. After unpacking 107 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 libpython3.13-minimal arm64 3.13.2-1 [853 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 libexpat1 arm64 2.6.4-1 [90.7 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 python3.13-minimal arm64 3.13.2-1 [1997 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 python3-minimal arm64 3.13.1-2 [27.0 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 tzdata all 2025a-2 [259 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 libffi8 arm64 3.4.7-1 [21.2 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 readline-common all 8.2-6 [69.4 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 libreadline8t64 arm64 8.2-6 [159 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 libpython3.13-stdlib arm64 3.13.2-1 [1914 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 python3.13 arm64 3.13.2-1 [745 kB] Get: 13 http://deb.debian.org/debian trixie/main arm64 libpython3-stdlib arm64 3.13.1-2 [9952 B] Get: 14 http://deb.debian.org/debian trixie/main arm64 python3 arm64 3.13.1-2 [28.0 kB] Get: 15 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.23.1-1 [241 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-7 [1129 kB] Get: 22 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40.4-3 [92.0 kB] Get: 23 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-5 [284 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.72-3 [493 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.17-3 [862 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.23.1-1 [770 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 d-shlibs all 0.109 [11.1 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 32 http://deb.debian.org/debian trixie/main arm64 libtool all 2.5.4-3 [539 kB] Get: 33 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 34 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 35 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 36 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 37 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 38 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 39 http://deb.debian.org/debian trixie/main arm64 libunistring5 arm64 1.3-1 [449 kB] Get: 40 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-6 [9239 kB] Get: 41 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB] Get: 42 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.23.1-1 [1610 kB] Get: 43 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 44 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 45 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.24.1 [920 kB] Fetched 26.3 MB in 1s (46.7 MB/s) Preconfiguring packages ... Selecting previously unselected package libpython3.13-minimal:arm64. (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 ... 19923 files and directories currently installed.) Preparing to unpack .../libpython3.13-minimal_3.13.2-1_arm64.deb ... Unpacking libpython3.13-minimal:arm64 (3.13.2-1) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.6.4-1_arm64.deb ... Unpacking libexpat1:arm64 (2.6.4-1) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../python3.13-minimal_3.13.2-1_arm64.deb ... Unpacking python3.13-minimal (3.13.2-1) ... Setting up libpython3.13-minimal:arm64 (3.13.2-1) ... Setting up libexpat1:arm64 (2.6.4-1) ... Setting up python3.13-minimal (3.13.2-1) ... 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 ... 20257 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.13.1-2_arm64.deb ... Unpacking python3-minimal (3.13.1-2) ... 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_2025a-2_all.deb ... Unpacking tzdata (2025a-2) ... Selecting previously unselected package libffi8:arm64. Preparing to unpack .../4-libffi8_3.4.7-1_arm64.deb ... Unpacking libffi8:arm64 (3.4.7-1) ... Selecting previously unselected package readline-common. Preparing to unpack .../5-readline-common_8.2-6_all.deb ... Unpacking readline-common (8.2-6) ... Selecting previously unselected package libreadline8t64:arm64. Preparing to unpack .../6-libreadline8t64_8.2-6_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.2-6) ... Selecting previously unselected package libpython3.13-stdlib:arm64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.2-1_arm64.deb ... Unpacking libpython3.13-stdlib:arm64 (3.13.2-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.2-1_arm64.deb ... Unpacking python3.13 (3.13.2-1) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../9-libpython3-stdlib_3.13.1-2_arm64.deb ... Unpacking libpython3-stdlib:arm64 (3.13.1-2) ... Setting up python3-minimal (3.13.1-2) ... 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 ... 21267 files and directories currently installed.) Preparing to unpack .../00-python3_3.13.1-2_arm64.deb ... Unpacking python3 (3.13.1-2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../03-libmagic1t64_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.45-3+b1_arm64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../05-gettext-base_0.23.1-1_arm64.deb ... Unpacking gettext-base (0.23.1-1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../06-libuchardet0_0.0.8-1+b2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../07-groff-base_1.23.0-7_arm64.deb ... Unpacking groff-base (1.23.0-7) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../08-bsdextrautils_2.40.4-3_arm64.deb ... Unpacking bsdextrautils (2.40.4-3) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../09-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../10-man-db_2.13.0-1_arm64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../11-m4_1.4.19-5_arm64.deb ... Unpacking m4 (1.4.19-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../12-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... 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%3a1.17-3_all.deb ... Unpacking automake (1:1.17-3) ... Selecting previously unselected package autopoint. Preparing to unpack .../15-autopoint_0.23.1-1_all.deb ... Unpacking autopoint (0.23.1-1) ... Selecting previously unselected package d-shlibs. Preparing to unpack .../16-d-shlibs_0.109_all.deb ... Unpacking d-shlibs (0.109) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../17-libdebhelper-perl_13.24.1_all.deb ... Unpacking libdebhelper-perl (13.24.1) ... Selecting previously unselected package libtool. Preparing to unpack .../18-libtool_2.5.4-3_all.deb ... Unpacking libtool (2.5.4-3) ... 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 libfile-stripnondeterminism-perl. Preparing to unpack .../21-libfile-stripnondeterminism-perl_1.14.1-2_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.1-2) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../22-dh-strip-nondeterminism_1.14.1-2_all.deb ... Unpacking dh-strip-nondeterminism (1.14.1-2) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../23-libelf1t64_0.192-4_arm64.deb ... Unpacking libelf1t64:arm64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../24-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libunistring5:arm64. Preparing to unpack .../25-libunistring5_1.3-1_arm64.deb ... Unpacking libunistring5:arm64 (1.3-1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../26-libicu72_72.1-6_arm64.deb ... Unpacking libicu72:arm64 (72.1-6) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../27-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_arm64.deb ... Unpacking libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../28-gettext_0.23.1-1_arm64.deb ... Unpacking gettext (0.23.1-1) ... 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_13.24.1_all.deb ... Unpacking debhelper (13.24.1) ... Setting up media-types (10.1.0) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up libicu72:arm64 (72.1-6) ... Setting up bsdextrautils (2.40.4-3) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.24.1) ... Setting up libmagic1t64:arm64 (1:5.45-3+b1) ... Setting up gettext-base (0.23.1-1) ... Setting up m4 (1.4.19-5) ... Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up tzdata (2025a-2) ... Current default time zone: 'Etc/UTC' Local time is now: Fri Mar 27 09:33:33 UTC 2026. Universal Time is now: Fri Mar 27 09:33:33 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up libunistring5:arm64 (1.3-1) ... Setting up autopoint (0.23.1-1) ... Setting up d-shlibs (0.109) ... Setting up autoconf (2.72-3) ... Setting up libffi8:arm64 (3.4.7-1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... 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Processing triggers for libc-bin (2.40-7) ... 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/2122414/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/2122414/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../libncl_2.1.21+git20210811.b1213a7-6_source.changes dpkg-buildpackage: info: source package libncl dpkg-buildpackage: info: source version 2.1.21+git20210811.b1213a7-6 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 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 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.m4:663: 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=aarch64-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/aarch64-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 sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 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 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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... BSD nm checking the maximum length of command line arguments... 1572864 checking how to convert aarch64-unknown-linux-gnu file names to aarch64-unknown-linux-gnu format... func_convert_file_noop checking how to convert aarch64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for file... file checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ranlib... ranlib checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /usr/bin/dd checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld) 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 checking if the linker (/usr/bin/ld) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld) 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) 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 or later... 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 -j12 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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-D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxscharactersblock.cpp -fPIC -DPIC -o .libs/nxscharactersblock.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxsassumptionsblock.cpp -fPIC -DPIC -o .libs/nxsassumptionsblock.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxsdatablock.cpp -fPIC -DPIC -o .libs/nxsdatablock.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxsexception.cpp -fPIC -DPIC -o .libs/nxsexception.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxsreader.cpp -fPIC -DPIC -o .libs/nxsreader.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxspublicblocks.cpp -fPIC -DPIC -o .libs/nxspublicblocks.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxssetreader.cpp -fPIC -DPIC -o .libs/nxssetreader.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxsstring.cpp -fPIC -DPIC -o .libs/nxsstring.o In file included from ../ncl/nxsexception.h:23, from ../ncl/nxsblock.h:24, from ../ncl/nxspublicblocks.h:24, from ../ncl/nxsmultiformat.h:25, from nxsmultiformat.cpp:50: ../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from nxsmultiformat.cpp:48: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../ncl/nxsexception.h:23, from ../ncl/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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, from ../ncl/nxssetreader.h:22: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../ncl/nxsexception.h:23, from ../ncl/nxsblock.h:24, from ../ncl/nxstaxablock.h:23, from ../ncl/nxsdistancesblock.h:24, from nxsdistancesblock.cpp:23: ../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/iomanip:42, from nxsdistancesblock.cpp:19: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../ncl/nxsexception.h:23, from ../ncl/nxsblock.h:24, from ../ncl/nxstaxablock.h:23, from ../ncl/nxscharactersblock.h:29, from nxscharactersblock.cpp:26: ../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/iomanip:42, from nxscharactersblock.cpp:23: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../ncl/nxsexception.h:23, from nxsexception.cpp:20: ../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/functional:49, from ../ncl/nxsstring.h:26: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../ncl/nxsexception.h:23, from ../ncl/nxsblock.h:24, from nxsblock.cpp:21: ../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from ../ncl/nxsdefs.h:22, from nxsblock.cpp:20: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../ncl/nxsexception.h:23, from ../ncl/nxsblock.h:24, from ../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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/streambuf:43, from /usr/include/c++/14/bits/streambuf_iterator.h:35, from /usr/include/c++/14/iterator:66, from nxscxxdiscretematrix.cpp:19: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../ncl/nxsexception.h:23, from ../ncl/nxsblock.h:24, from ../ncl/nxspublicblocks.h:24, from nxspublicblocks.cpp:24: ../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from nxspublicblocks.cpp:22: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../ncl/nxsexception.h:23, from ../ncl/nxsblock.h:24, from ../ncl/nxstaxablock.h:23, from ../ncl/nxscharactersblock.h:29, from ../ncl/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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, from ../ncl/nxscharactersblock.h:23: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../ncl/nxsexception.h:23, from ../ncl/nxsblock.h:24, from ../ncl/nxsassumptionsblock.h:26, from nxsassumptionsblock.cpp:22: ../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/iomanip:42, from nxsassumptionsblock.cpp:19: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ 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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from ../ncl/nxsdefs.h:22, from nxsstring.cpp:24: /usr/include/c++/14/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++/14/bits/stl_tree.h:65, from /usr/include/c++/14/set:62, from nxsreader.cpp:21: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxsexception.cpp -o nxsexception.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxsstring.cpp -o nxsstring.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c -o nxstaxablock.lo nxstaxablock.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxssetreader.cpp -o nxssetreader.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxstaxablock.cpp -fPIC -DPIC -o .libs/nxstaxablock.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxsblock.cpp -o nxsblock.o >/dev/null 2>&1 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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from ../ncl/nxsdefs.h:22, from ../ncl/nxstaxablock.h:22: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxsdistancesblock.cpp -o nxsdistancesblock.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c -o nxstaxaassociationblock.lo nxstaxaassociationblock.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxstaxaassociationblock.cpp -fPIC -DPIC -o .libs/nxstaxaassociationblock.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxsdatablock.cpp -o nxsdatablock.o >/dev/null 2>&1 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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/iomanip:42, from nxstaxaassociationblock.cpp:20: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c -o nxstoken.lo nxstoken.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxsmultiformat.cpp -o nxsmultiformat.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxsreader.cpp -o nxsreader.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxspublicblocks.cpp -o nxspublicblocks.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c -o nxstreesblock.lo nxstreesblock.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxstreesblock.cpp -fPIC -DPIC -o .libs/nxstreesblock.o In file included from ../ncl/nxsexception.h:23, from ../ncl/nxsblock.h:24, from ../ncl/nxstaxablock.h:23, 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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, from nxstreesblock.cpp:20: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxscxxdiscretematrix.cpp -o nxscxxdiscretematrix.o >/dev/null 2>&1 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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, from nxstoken.cpp:21: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxstaxablock.cpp -o nxstaxablock.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c -o nxsunalignedblock.lo nxsunalignedblock.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxsunalignedblock.cpp -fPIC -DPIC -o .libs/nxsunalignedblock.o In file included from ../ncl/nxsexception.h:23, from ../ncl/nxsblock.h:24, 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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from ../ncl/nxsdefs.h:22, from ../ncl/nxsunalignedblock.h:23: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxstoken.cpp -o nxstoken.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxstreesblock.cpp -o nxstreesblock.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxsassumptionsblock.cpp -o nxsassumptionsblock.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxscharactersblock.cpp -o nxscharactersblock.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -version-info 2:0:0 -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o libncl.la -rpath /usr/lib/aarch64-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/aarch64-linux-gnu/14/../../../aarch64-linux-gnu/crti.o /usr/lib/gcc/aarch64-linux-gnu/14/crtbeginS.o .libs/nxsassumptionsblock.o .libs/nxsblock.o .libs/nxscharactersblock.o .libs/nxscxxdiscretematrix.o .libs/nxsdatablock.o .libs/nxsdistancesblock.o .libs/nxsexception.o .libs/nxsmultiformat.o .libs/nxspublicblocks.o .libs/nxsreader.o .libs/nxssetreader.o .libs/nxsstring.o .libs/nxstaxablock.o .libs/nxstaxaassociationblock.o .libs/nxstoken.o .libs/nxstreesblock.o .libs/nxsunalignedblock.o -L/usr/lib/gcc/aarch64-linux-gnu/14 -L/usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/14/../../../../lib -L/lib/aarch64-linux-gnu -L/lib/../lib -L/usr/lib/aarch64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/aarch64-linux-gnu/14/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/aarch64-linux-gnu/14/crtendS.o /usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu/crtn.o -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -fstack-protector-strong -Werror=format-security -mbranch-protection=standard -O3 -flto=auto -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,libncl.so.2 -o .libs/libncl.so.2.0.0 libtool: link: (cd ".libs" && rm -f "libncl.so.2" && ln -s "libncl.so.2.0.0" "libncl.so.2") libtool: link: (cd ".libs" && rm -f "libncl.so" && ln -s "libncl.so.2.0.0" "libncl.so") 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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o basiccmdline basiccmdline.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/basiccmdline basiccmdline.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/basiccmdline' Making all in check-taxo-nodes 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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o checktaxonnodes checktaxonnodes-checktaxonnodes.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/checktaxonnodes checktaxonnodes-checktaxonnodes.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/check-taxo-nodes' Making all in compressor 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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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++/14/string:49, from compressor.cpp:1: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o NEXUSCharacterCompressor NEXUSCharacterCompressor-compressor.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEXUSCharacterCompressor NEXUSCharacterCompressor-compressor.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/compressor' Making all in find-unsupported-edges 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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o findunsupportededges findunsupportededges-findunsupportededges.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/findunsupportededges findunsupportededges-findunsupportededges.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/find-unsupported-edges' Making all in gapcode 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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o NEXUSgapcode NEXUSgapcode-gapcode.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEXUSgapcode NEXUSgapcode-gapcode.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/gapcode' Making all in nclsimplest 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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o nclsimplest nclsimplest.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/nclsimplest nclsimplest.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/nclsimplest' Making all in ncltest 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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o ncltest ncltest.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/ncltest ncltest.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/ncltest' Making all in normalizer 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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c -o NCLconverter-us2ml.o `test -f 'us2ml.cpp' || echo './'`us2ml.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DNCL_CONVERTER_APP -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c -o NCLconverter-converter.o `test -f 'converter.cpp' || echo './'`converter.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DJUST_REPORT_NEXUS -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c -o NEXUSinspector-normalizer.o `test -f 'normalizer.cpp' || echo './'`normalizer.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DTO_NEXML_CONVERTER -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c -o NEX_us2ml-normalizer.o `test -f 'normalizer.cpp' || echo './'`normalizer.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DTO_NEXML_CONVERTER -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c -o NEX_us2ml-us2ml.o `test -f 'us2ml.cpp' || echo './'`us2ml.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -I../../ncl -DMULTIFILE_NEXUS_READER -DNCL_CONST_FUNCS -I../.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c -o NEXUSunion-normalizer.o `test -f 'normalizer.cpp' || echo './'`normalizer.cpp In file included from ../../ncl/ncl.h:79, from normalizer.cpp:46: ../../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../ncl/ncl.h:79, from normalizer.cpp:46: ../../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../ncl/ncl.h:79, from normalizer.cpp:46: ../../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../ncl/ncl.h:79, from 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 ../../ncl/ncl.h:79, from converter.cpp:48: ../../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../ncl/ncl.h:79, from 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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../ncl/ncl.h:79, from normalizer.cpp:46: ../../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../ncl/ncl.h:79, from normalizer.cpp:46: ../../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../ncl/ncl.h:79, from normalizer.cpp:46: ../../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o NEXUSunion NEXUSunion-normalizer.o ../../ncl/libncl.la /bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o NEXUSvalidator NEXUSvalidator-normalizer.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEXUSunion NEXUSunion-normalizer.o ../../ncl/.libs/libncl.so /bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o NEXUSnormalizer normalizer.o ../../ncl/libncl.la /bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o NEXUSinspector NEXUSinspector-normalizer.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEXUSvalidator NEXUSvalidator-normalizer.o ../../ncl/.libs/libncl.so libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEXUSnormalizer normalizer.o ../../ncl/.libs/libncl.so libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEXUSinspector NEXUSinspector-normalizer.o ../../ncl/.libs/libncl.so /bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o NCLconverter NCLconverter-normalizer.o NCLconverter-us2ml.o NCLconverter-converter.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NCLconverter NCLconverter-normalizer.o NCLconverter-us2ml.o NCLconverter-converter.o ../../ncl/.libs/libncl.so /bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o NEX_us2ml NEX_us2ml-normalizer.o NEX_us2ml-us2ml.o ../../ncl/libncl.la normalizer.cpp:102:14: warning: 'substituteSafeTaxaLabels' violates the C++ One Definition Rule [-Wodr] 102 | void substituteSafeTaxaLabels(PublicNexusReader & reader, std::string filepath, bool evenTrivial); | ^ converter.cpp:140:6: note: return value type mismatch 140 | bool substituteSafeTaxaLabels(PublicNexusReader &nexusReader, std::string filepath, bool evenTrivial) | ^ converter.cpp:140:6: note: type 'bool' should match type 'void' converter.cpp:140:6: note: 'substituteSafeTaxaLabels' was previously declared here libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEX_us2ml NEX_us2ml-normalizer.o NEX_us2ml-us2ml.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer' Making all in ot-subtree 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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o otsubtree otsubtree-otsubtree.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/otsubtree otsubtree-otsubtree.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/ot-subtree' Making all in ot-tree-inspect 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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o otTreeInspect otTreeInspect-ot_tree_inspect.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/otTreeInspect otTreeInspect-ot_tree_inspect.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/ot-tree-inspect' Making all in outdeg1count 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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o outdeg1count outdeg1count-outdeg1count.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/outdeg1count outdeg1count-outdeg1count.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/outdeg1count' Making all in patristic 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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o patristicmat patristic.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/patristicmat patristic.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/patristic' Making all in phylobaseinterface 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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o PhylobaseNCLInterfaceExample NCLInterface.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/PhylobaseNCLInterfaceExample NCLInterface.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/phylobaseinterface' Making all in polytomy-count 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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o polytomycount polytomycount-polytomy_count.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/polytomycount polytomycount-polytomy_count.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/polytomy-count' Making all in splitsinfile 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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from splitsstructs.h:3: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../ncl/nxsexception.h:23, from ../../ncl/nxsblock.h:24, from ../../ncl/nxstaxablock.h:23, from ../../ncl/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++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from splitsstructs.h:3: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../ncl/ncl.h:79, from 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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../ncl/ncl.h:79, from 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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o NEXUStosplits NEXUStosplits-splitsinfile.o NEXUStosplits-splitsstructs.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEXUStosplits NEXUStosplits-splitsinfile.o NEXUStosplits-splitsstructs.o ../../ncl/.libs/libncl.so /bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o majrule splitsinfile.o splitsstructs.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/majrule splitsinfile.o splitsstructs.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/splitsinfile' Making all in subsetter 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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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++/14/string:49, from subsetter.cpp:1: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o NEXUSsubsetter NEXUSsubsetter-subsetter.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEXUSsubsetter NEXUSsubsetter-subsetter.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/subsetter' Making all in translate 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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from ../../ncl/ncl.h:45: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o NEXUStranslate NEXUStranslate-translateNuc.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEXUStranslate NEXUStranslate-translateNuc.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/translate' make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example' 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 -j12 check "TESTSUITEFLAGS=-j12 --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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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-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/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/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/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/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/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/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/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" "-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" "-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" "-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" "-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" "-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" "-faaphylipinterleaved" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aaphylipinterleaved_emboss.phy" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aaphylipinterleaved_emboss.phy ] Executing storing implied block: TAXA storing read block: DATA ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aaphylipinterleaved_emboss.phy "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/aaphylipinterleaved_emboss.phy" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/aaphylipinterleaved_emboss.phy ] Executing storing read block: TAXA storing read block: CHARACTERS ../../test/roundTripNCLTest.py : Call to /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer succeeded for /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidOut/aaphylipinterleaved_emboss.phy "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer/NEXUSnormalizer" "-s2" "-faaphylip" "/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aaphylip_emboss.phy" [Reading /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/test/ExternalValidIn/aaphylip_emboss.phy ] Executing 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" "-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/aarch64-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/aarch64-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/aarch64-linux-gnu/libncl.so.2.0.0 libtool: install: (cd /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/lib/aarch64-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/aarch64-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/aarch64-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/aarch64-linux-gnu/libncl.a libtool: install: chmod 644 /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/lib/aarch64-linux-gnu/libncl.a libtool: install: ranlib /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/lib/aarch64-linux-gnu/libncl.a libtool: warning: remember to run 'libtool --finish /usr/lib/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-linux-gnu install -d -m 755 debian/libncl2/usr/lib/aarch64-linux-gnu mv debian/tmp/usr/lib/aarch64-linux-gnu/libncl.a debian/libncl-dev/usr/lib/aarch64-linux-gnu mv debian/tmp/usr/lib/aarch64-linux-gnu/libncl.la debian/libncl-dev/usr/lib/aarch64-linux-gnu || true mv debian/tmp/usr/lib/aarch64-linux-gnu/libncl.so debian/libncl-dev/usr/lib/aarch64-linux-gnu mv /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/lib/aarch64-linux-gnu/libncl.so.2 debian/libncl2/usr/lib/aarch64-linux-gnu mv /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/lib/aarch64-linux-gnu/libncl.so.2.0.0 debian/libncl2/usr/lib/aarch64-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/aarch64-linux-gnu/pkgconfig mv debian/tmp/usr/lib/*/pkgconfig/*.pc debian/libncl-dev/usr/lib/aarch64-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 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged 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 'libncl-dev' in '../libncl-dev_2.1.21+git20210811.b1213a7-6_arm64.deb'. dpkg-deb: building package 'libncl2' in '../libncl2_2.1.21+git20210811.b1213a7-6_arm64.deb'. dpkg-deb: building package 'ncl-tools' in '../ncl-tools_2.1.21+git20210811.b1213a7-6_arm64.deb'. dpkg-deb: building package 'libncl2-dbgsym' in '../libncl2-dbgsym_2.1.21+git20210811.b1213a7-6_arm64.deb'. dpkg-deb: building package 'ncl-tools-dbgsym' in '../ncl-tools-dbgsym_2.1.21+git20210811.b1213a7-6_arm64.deb'. dpkg-genbuildinfo --build=binary -O../libncl_2.1.21+git20210811.b1213a7-6_arm64.buildinfo dpkg-genchanges --build=binary -O../libncl_2.1.21+git20210811.b1213a7-6_arm64.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/2122414/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/2122414/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/2122414 and its subdirectories I: Current time: Fri Mar 27 23:44:33 +14 2026 I: pbuilder-time-stamp: 1774604673 + false + set +x Fri Mar 27 09:44:33 UTC 2026 I: Signing ./b2/libncl_2.1.21+git20210811.b1213a7-6_arm64.buildinfo as libncl_2.1.21+git20210811.b1213a7-6_arm64.buildinfo.asc Fri Mar 27 09:44:33 UTC 2026 I: Signed ./b2/libncl_2.1.21+git20210811.b1213a7-6_arm64.buildinfo as ./b2/libncl_2.1.21+git20210811.b1213a7-6_arm64.buildinfo.asc Fri Mar 27 09:44:33 UTC 2026 - build #2 for libncl/trixie/arm64 on codethink03-arm64 done. Starting cleanup. All cleanup done. Fri Mar 27 09:44:33 UTC 2026 - reproducible_build.sh stopped running as /tmp/jenkins-script-z7Ai93jJ, removing. /srv/reproducible-results/rbuild-debian/r-b-build.fEgknmXy: total 244 drwxr-xr-x 2 jenkins jenkins 4096 Feb 22 03:09 b1 drwxr-xr-x 2 jenkins jenkins 4096 Feb 22 03:21 b2 -rw-r--r-- 1 jenkins jenkins 2422 Aug 25 10:30 libncl_2.1.21+git20210811.b1213a7-6.dsc -rw------- 1 jenkins jenkins 233353 Feb 22 03:09 rbuildlog.eWPVFjl /srv/reproducible-results/rbuild-debian/r-b-build.fEgknmXy/b1: total 11684 -rw-r--r-- 1 jenkins jenkins 229422 Feb 22 03:09 build.log -rw-r--r-- 1 jenkins jenkins 557308 Feb 22 03:09 libncl-dev_2.1.21+git20210811.b1213a7-6_arm64.deb -rw-r--r-- 1 jenkins jenkins 6043432 Feb 22 03:09 libncl2-dbgsym_2.1.21+git20210811.b1213a7-6_arm64.deb -rw-r--r-- 1 jenkins jenkins 319856 Feb 22 03:09 libncl2_2.1.21+git20210811.b1213a7-6_arm64.deb -rw-r--r-- 1 jenkins jenkins 20292 Feb 22 03:09 libncl_2.1.21+git20210811.b1213a7-6.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2422 Feb 22 03:09 libncl_2.1.21+git20210811.b1213a7-6.dsc -rw-r--r-- 1 jenkins jenkins 6868 Feb 22 03:09 libncl_2.1.21+git20210811.b1213a7-6_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 7750 Feb 22 03:09 libncl_2.1.21+git20210811.b1213a7-6_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 2917 Feb 22 03:09 libncl_2.1.21+git20210811.b1213a7-6_arm64.changes -rw-r--r-- 1 jenkins jenkins 1646 Feb 22 03:09 libncl_2.1.21+git20210811.b1213a7-6_source.changes -rw-r--r-- 1 jenkins jenkins 4541004 Feb 22 03:09 ncl-tools-dbgsym_2.1.21+git20210811.b1213a7-6_arm64.deb -rw-r--r-- 1 jenkins jenkins 165612 Feb 22 03:09 ncl-tools_2.1.21+git20210811.b1213a7-6_arm64.deb /srv/reproducible-results/rbuild-debian/r-b-build.fEgknmXy/b2: total 11644 -rw-r--r-- 1 jenkins jenkins 231270 Feb 22 03:21 build.log -rw-r--r-- 1 jenkins jenkins 557308 Feb 22 03:21 libncl-dev_2.1.21+git20210811.b1213a7-6_arm64.deb -rw-r--r-- 1 jenkins jenkins 6043432 Feb 22 03:21 libncl2-dbgsym_2.1.21+git20210811.b1213a7-6_arm64.deb -rw-r--r-- 1 jenkins jenkins 319856 Feb 22 03:21 libncl2_2.1.21+git20210811.b1213a7-6_arm64.deb -rw-r--r-- 1 jenkins jenkins 20292 Feb 22 03:21 libncl_2.1.21+git20210811.b1213a7-6.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2422 Feb 22 03:21 libncl_2.1.21+git20210811.b1213a7-6.dsc -rw-r--r-- 1 jenkins jenkins 6868 Feb 22 03:21 libncl_2.1.21+git20210811.b1213a7-6_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 7750 Feb 22 03:21 libncl_2.1.21+git20210811.b1213a7-6_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 2917 Feb 22 03:21 libncl_2.1.21+git20210811.b1213a7-6_arm64.changes -rw-r--r-- 1 jenkins jenkins 1646 Feb 22 03:21 libncl_2.1.21+git20210811.b1213a7-6_source.changes -rw-r--r-- 1 jenkins jenkins 4541004 Feb 22 03:21 ncl-tools-dbgsym_2.1.21+git20210811.b1213a7-6_arm64.deb -rw-r--r-- 1 jenkins jenkins 165612 Feb 22 03:21 ncl-tools_2.1.21+git20210811.b1213a7-6_arm64.deb Sat Feb 22 03:21:34 UTC 2025 I: Deleting $TMPDIR on codethink03-arm64.debian.net. Sat Feb 22 03:21:35 UTC 2025 I: libncl_2.1.21+git20210811.b1213a7-6_arm64.changes: Format: 1.8 Date: Sun, 25 Aug 2024 11:33:47 +0200 Source: libncl Binary: libncl-dev libncl2 libncl2-dbgsym ncl-tools ncl-tools-dbgsym Architecture: arm64 Version: 2.1.21+git20210811.b1213a7-6 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: libncl-dev - NEXUS Class Library (static lib and header files) libncl2 - NEXUS Class Library ncl-tools - tools to deal with NEXUS files Closes: 1015505 1075191 Changes: libncl (2.1.21+git20210811.b1213a7-6) unstable; urgency=medium . * d/rules: forcefully run LTO builds. * d/libncl2.symbols.amd64: mark symbols leaked by the compiler optional. (Closes: #1015505, #1075191) * d/control: add myself to uploaders. * d/control: declare compliance to standards version 4.7.0. Checksums-Sha1: a254bbbc9383f6385bd5af54d7bb4cf25bca637f 557308 libncl-dev_2.1.21+git20210811.b1213a7-6_arm64.deb b692b64656b8c65a069363f7cbcceeaef650b39a 6043432 libncl2-dbgsym_2.1.21+git20210811.b1213a7-6_arm64.deb c8e56f517696d1b3b8a92895939c74dd32d8681c 319856 libncl2_2.1.21+git20210811.b1213a7-6_arm64.deb 695fd13fb1a6d1f6ef93994f01f12cf91486fc33 6868 libncl_2.1.21+git20210811.b1213a7-6_arm64.buildinfo a3866d7c138a9b29ca103742e8b784d76ad00ab6 4541004 ncl-tools-dbgsym_2.1.21+git20210811.b1213a7-6_arm64.deb 39edc8b4a19aa0181c8a8d63504ede4f345a4f5b 165612 ncl-tools_2.1.21+git20210811.b1213a7-6_arm64.deb Checksums-Sha256: 50c3c25c208f3e19be76ead3b61980ed3d6225eaf0e23c19cc9de7984cab9137 557308 libncl-dev_2.1.21+git20210811.b1213a7-6_arm64.deb 298ce4f698191f2153c96ae40ea762d688d40211466ae156fb1c7b5c804fffd6 6043432 libncl2-dbgsym_2.1.21+git20210811.b1213a7-6_arm64.deb b3cb5a7701d237dd7cd0d57b4e359704a067e794818237572e41c67ed6deffec 319856 libncl2_2.1.21+git20210811.b1213a7-6_arm64.deb 1f26d1aec0b6647b12a79f2eedd288b6fbc2fe71f45760eb0e8b0b945502d8b4 6868 libncl_2.1.21+git20210811.b1213a7-6_arm64.buildinfo 1ef3b0318164987665615f9774a3590ce305a6a5829fff66cbf612cfd3f8715e 4541004 ncl-tools-dbgsym_2.1.21+git20210811.b1213a7-6_arm64.deb 8a528c553c98fb9b0b669aaaca22f66b2f24e14ec58e8d8bce0cd50b33036201 165612 ncl-tools_2.1.21+git20210811.b1213a7-6_arm64.deb Files: 9aab470c1ac53ad3fb51c773d7703053 557308 libdevel optional libncl-dev_2.1.21+git20210811.b1213a7-6_arm64.deb 954b6f8a0c8077b02742ccfcfab4683b 6043432 debug optional libncl2-dbgsym_2.1.21+git20210811.b1213a7-6_arm64.deb ff0730df0a67e03bc66bb18ef84a0662 319856 libs optional libncl2_2.1.21+git20210811.b1213a7-6_arm64.deb 7dcda7c07a41606530df323515809ed9 6868 science optional libncl_2.1.21+git20210811.b1213a7-6_arm64.buildinfo a90339f8faa823545c5f5e1902c8d2a2 4541004 debug optional ncl-tools-dbgsym_2.1.21+git20210811.b1213a7-6_arm64.deb cb3f6fc446c54aa8c28e091caaa71435 165612 science optional ncl-tools_2.1.21+git20210811.b1213a7-6_arm64.deb removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/arm64/libncl_2.1.21+git20210811.b1213a7-6.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/arm64/libncl_2.1.21+git20210811.b1213a7-6.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/trixie/arm64/libncl_2.1.21+git20210811.b1213a7-6.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/trixie/arm64/libncl_2.1.21+git20210811.b1213a7-6.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/trixie/arm64/libncl_2.1.21+git20210811.b1213a7-6_arm64.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/arm64/libncl_2.1.21+git20210811.b1213a7-6.diff.gz' Diff of the two buildlogs: -- --- b1/build.log 2025-02-22 03:09:45.254335228 +0000 +++ b2/build.log 2025-02-22 03:21:34.054270330 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Feb 21 15:04:56 -12 2025 -I: pbuilder-time-stamp: 1740193496 +I: Current time: Fri Mar 27 23:32:50 +14 2026 +I: pbuilder-time-stamp: 1774603970 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -28,52 +28,84 @@ 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/1336987/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2122414/tmp/hooks/D01_modify_environment starting +debug: Running on codethink03-arm64. +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 Mar 27 09:32 /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/2122414/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2122414/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='a935237c9925438ba78d593da280a1c8' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='1336987' - PS1='# ' - PS2='> ' + INVOCATION_ID=3db6a5ee649641bd9ed5b94098f23d5f + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-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=2122414 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.fEgknmXy/pbuilderrc_q5Ji --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.fEgknmXy/b1 --logfile b1/build.log libncl_2.1.21+git20210811.b1213a7-6.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + 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.fEgknmXy/pbuilderrc_1OgA --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.fEgknmXy/b2 --logfile b2/build.log libncl_2.1.21+git20210811.b1213a7-6.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink04-arm64 6.1.0-31-cloud-arm64 #1 SMP Debian 6.1.128-1 (2025-02-07) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-31-cloud-arm64 #1 SMP Debian 6.1.128-1 (2025-02-07) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1336987/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2122414/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -158,7 +190,7 @@ Get: 43 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 44 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 45 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.24.1 [920 kB] -Fetched 26.3 MB in 0s (151 MB/s) +Fetched 26.3 MB in 1s (46.7 MB/s) Preconfiguring packages ... Selecting previously unselected package libpython3.13-minimal:arm64. (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 ... 19923 files and directories currently installed.) @@ -321,8 +353,8 @@ Setting up tzdata (2025a-2) ... Current default time zone: 'Etc/UTC' -Local time is now: Sat Feb 22 03:05:12 UTC 2025. -Universal Time is now: Sat Feb 22 03:05:12 UTC 2025. +Local time is now: Fri Mar 27 09:33:33 UTC 2026. +Universal Time is now: Fri Mar 27 09:33:33 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... @@ -365,7 +397,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../libncl_2.1.21+git20210811.b1213a7-6_source.changes +I: user script /srv/workspace/pbuilder/2122414/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/2122414/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../libncl_2.1.21+git20210811.b1213a7-6_source.changes dpkg-buildpackage: info: source package libncl dpkg-buildpackage: info: source version 2.1.21+git20210811.b1213a7-6 dpkg-buildpackage: info: source distribution unstable @@ -429,8 +465,8 @@ checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking xargs -n works... yes -checking whether UID '1111' is supported by ustar format... yes -checking whether GID '1111' is supported by ustar format... yes +checking whether UID '2222' is supported by ustar format... yes +checking whether GID '2222' is supported by ustar format... yes checking how to create a ustar tar archive... gnutar checking whether ln -s works... yes checking build system type... aarch64-unknown-linux-gnu @@ -571,34 +607,35 @@ make[2]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7' Making all in ncl make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/ncl' -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c -o nxsassumptionsblock.lo nxsassumptionsblock.cpp -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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nxspublicblocks.cpp -fPIC -DPIC -o .libs/nxspublicblocks.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxssetreader.cpp -fPIC -DPIC -o .libs/nxssetreader.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxsstring.cpp -fPIC -DPIC -o .libs/nxsstring.o In file included from ../ncl/nxsexception.h:23, from ../ncl/nxsblock.h:24, from ../ncl/nxspublicblocks.h:24, - from nxspublicblocks.cpp:24: + from ../ncl/nxsmultiformat.h:25, + from nxsmultiformat.cpp:50: ../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ @@ -607,13 +644,15 @@ from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, - from nxspublicblocks.cpp:22: + from /usr/include/c++/14/fstream:40, + from nxsmultiformat.cpp:48: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../ncl/nxsexception.h:23, - from ../ncl/nxsblock.h:24, - from nxsblock.cpp:21: + 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 | ^~~~~~~~~~~~~~~ @@ -621,36 +660,33 @@ from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, - from /usr/include/c++/14/ostream:40, - from /usr/include/c++/14/iostream:41, - from ../ncl/nxsdefs.h:22, - from nxsblock.cpp:20: + from /usr/include/c++/14/istream:40, + from /usr/include/c++/14/sstream:40, + from ../ncl/nxssetreader.h:22: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../ncl/nxsexception.h:23, from ../ncl/nxsblock.h:24, from ../ncl/nxstaxablock.h:23, - from ../ncl/nxscharactersblock.h:29, - from ../ncl/nxscxxdiscretematrix.h:28, - from nxscxxdiscretematrix.cpp:20: + from ../ncl/nxsdistancesblock.h:24, + from nxsdistancesblock.cpp:23: ../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/streambuf:43, - from /usr/include/c++/14/bits/streambuf_iterator.h:35, - from /usr/include/c++/14/iterator:66, - from nxscxxdiscretematrix.cpp:19: + from /usr/include/c++/14/iomanip:42, + from nxsdistancesblock.cpp:19: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../ncl/nxsexception.h:23, from ../ncl/nxsblock.h:24, - from ../ncl/nxsassumptionsblock.h:26, - from nxsassumptionsblock.cpp:22: + 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 | ^~~~~~~~~~~~~~~ @@ -658,49 +694,69 @@ from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/iomanip:42, - from nxsassumptionsblock.cpp:19: + from nxscharactersblock.cpp:23: +/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +In file included from ../ncl/nxsexception.h:23, + from nxsexception.cpp:20: +../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 266 | : public std::binary_function + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/14/functional:49, + from ../ncl/nxsstring.h:26: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../ncl/nxsexception.h:23, from ../ncl/nxsblock.h:24, - from ../ncl/nxstaxablock.h:23, - from ../ncl/nxsdistancesblock.h:24, - from nxsdistancesblock.cpp:23: + from nxsblock.cpp:21: ../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/iomanip:42, - from nxsdistancesblock.cpp:19: + from /usr/include/c++/14/ios:44, + from /usr/include/c++/14/ostream:40, + from /usr/include/c++/14/iostream:41, + from ../ncl/nxsdefs.h:22, + from nxsblock.cpp:20: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../ncl/nxsexception.h:23, - from nxsexception.cpp:20: + 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++/14/functional:49, - from ../ncl/nxsstring.h:26: +In file included from /usr/include/c++/14/string:49, + from /usr/include/c++/14/bits/locale_classes.h:40, + from /usr/include/c++/14/bits/ios_base.h:41, + from /usr/include/c++/14/streambuf:43, + from /usr/include/c++/14/bits/streambuf_iterator.h:35, + from /usr/include/c++/14/iterator:66, + from nxscxxdiscretematrix.cpp:19: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../ncl/nxsexception.h:23, from ../ncl/nxsblock.h:24, - from ../ncl/nxstaxablock.h:23, - from ../ncl/nxscharactersblock.h:29, - from nxscharactersblock.cpp:26: + from ../ncl/nxspublicblocks.h:24, + from nxspublicblocks.cpp:24: ../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/iomanip:42, - from nxscharactersblock.cpp:23: + from /usr/include/c++/14/ios:44, + from /usr/include/c++/14/istream:40, + from nxspublicblocks.cpp:22: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -725,19 +781,16 @@ | ^~~~~~~~~~~~~~~ In file included from ../ncl/nxsexception.h:23, from ../ncl/nxsblock.h:24, - from ../ncl/nxspublicblocks.h:24, - from ../ncl/nxsmultiformat.h:25, - from nxsmultiformat.cpp:50: + from ../ncl/nxsassumptionsblock.h:26, + from nxsassumptionsblock.cpp:22: ../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/ios:44, - from /usr/include/c++/14/istream:40, - from /usr/include/c++/14/fstream:40, - from nxsmultiformat.cpp:48: + from /usr/include/c++/14/iomanip:42, + from nxsassumptionsblock.cpp:19: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -756,24 +809,6 @@ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from ../ncl/nxsexception.h:23, - from ../ncl/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++/14/string:49, - from /usr/include/c++/14/bits/locale_classes.h:40, - from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/ios:44, - from /usr/include/c++/14/istream:40, - from /usr/include/c++/14/sstream:40, - from ../ncl/nxssetreader.h:22: -/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxsexception.cpp -o nxsexception.o >/dev/null 2>&1 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] @@ -785,11 +820,11 @@ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxsexception.cpp -o nxsexception.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxsstring.cpp -o nxsstring.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c -o nxstaxablock.lo nxstaxablock.cpp -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxstaxablock.cpp -fPIC -DPIC -o .libs/nxstaxablock.o +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c -o nxstaxablock.lo nxstaxablock.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxssetreader.cpp -o nxssetreader.o >/dev/null 2>&1 -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxsdistancesblock.cpp -o nxsdistancesblock.o >/dev/null 2>&1 +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxstaxablock.cpp -fPIC -DPIC -o .libs/nxstaxablock.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxsblock.cpp -o nxsblock.o >/dev/null 2>&1 In file included from ../ncl/nxsexception.h:23, from ../ncl/nxsblock.h:24, @@ -809,7 +844,8 @@ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c -o nxstaxaassociationblock.lo nxstaxaassociationblock.cpp +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxsdistancesblock.cpp -o nxsdistancesblock.o >/dev/null 2>&1 +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c -o nxstaxaassociationblock.lo nxstaxaassociationblock.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxstaxaassociationblock.cpp -fPIC -DPIC -o .libs/nxstaxaassociationblock.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxsdatablock.cpp -o nxsdatablock.o >/dev/null 2>&1 In file included from ../ncl/nxsexception.h:23, @@ -828,14 +864,18 @@ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c -o nxstoken.lo nxstoken.cpp -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c -o nxstreesblock.lo nxstreesblock.cpp +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c -o nxstoken.lo nxstoken.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxsmultiformat.cpp -o nxsmultiformat.o >/dev/null 2>&1 +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxsreader.cpp -o nxsreader.o >/dev/null 2>&1 +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxspublicblocks.cpp -o nxspublicblocks.o >/dev/null 2>&1 +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c -o nxstreesblock.lo nxstreesblock.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxstreesblock.cpp -fPIC -DPIC -o .libs/nxstreesblock.o -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c -o nxsunalignedblock.lo nxsunalignedblock.cpp In file included from ../ncl/nxsexception.h:23, - from ../ncl/nxstoken.h:23, - from nxstoken.cpp:22: + 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 | ^~~~~~~~~~~~~~~ @@ -845,17 +885,14 @@ from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, - from nxstoken.cpp:21: + from nxstreesblock.cpp:20: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxsunalignedblock.cpp -fPIC -DPIC -o .libs/nxsunalignedblock.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxscxxdiscretematrix.cpp -o nxscxxdiscretematrix.o >/dev/null 2>&1 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: + 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 | ^~~~~~~~~~~~~~~ @@ -865,10 +902,14 @@ from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, - from nxstreesblock.cpp:20: + from nxstoken.cpp:21: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxstaxablock.cpp -o nxstaxablock.o >/dev/null 2>&1 +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c -o nxsunalignedblock.lo nxsunalignedblock.cpp +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxsunalignedblock.cpp -fPIC -DPIC -o .libs/nxsunalignedblock.o In file included from ../ncl/nxsexception.h:23, from ../ncl/nxsblock.h:24, from ../ncl/nxstaxablock.h:23, @@ -888,17 +929,12 @@ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxsmultiformat.cpp -o nxsmultiformat.o >/dev/null 2>&1 -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxspublicblocks.cpp -o nxspublicblocks.o >/dev/null 2>&1 -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxsreader.cpp -o nxsreader.o >/dev/null 2>&1 -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxstoken.cpp -o nxstoken.o >/dev/null 2>&1 -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxsassumptionsblock.cpp -o nxsassumptionsblock.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxstreesblock.cpp -o nxstreesblock.o >/dev/null 2>&1 +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxsassumptionsblock.cpp -o nxsassumptionsblock.o >/dev/null 2>&1 +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -DNCL_CONST_FUNCS -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -c nxscharactersblock.cpp -o nxscharactersblock.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -version-info 2:0:0 -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o libncl.la -rpath /usr/lib/aarch64-linux-gnu nxsassumptionsblock.lo nxsblock.lo nxscharactersblock.lo nxscxxdiscretematrix.lo nxsdatablock.lo nxsdistancesblock.lo nxsexception.lo nxsmultiformat.lo nxspublicblocks.lo nxsreader.lo nxssetreader.lo nxsstring.lo nxstaxablock.lo nxstaxaassociationblock.lo nxstoken.lo nxstreesblock.lo nxsunalignedblock.lo +/bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -version-info 2:0:0 -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o libncl.la -rpath /usr/lib/aarch64-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/aarch64-linux-gnu/14/../../../aarch64-linux-gnu/crti.o /usr/lib/gcc/aarch64-linux-gnu/14/crtbeginS.o .libs/nxsassumptionsblock.o .libs/nxsblock.o .libs/nxscharactersblock.o .libs/nxscxxdiscretematrix.o .libs/nxsdatablock.o .libs/nxsdistancesblock.o .libs/nxsexception.o .libs/nxsmultiformat.o .libs/nxspublicblocks.o .libs/nxsreader.o .libs/nxssetreader.o .libs/nxsstring.o .libs/nxstaxablock.o .libs/nxstaxaassociationblock.o .libs/nxstoken.o .libs/nxstreesblock.o .libs/nxsunalignedblock.o -L/usr/lib/gcc/aarch64-linux-gnu/14 -L/usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/14/../../../../lib -L/lib/aarch64-linux-gnu -L/lib/../lib -L/usr/lib/aarch64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/aarch64-linux-gnu/14/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/aarch64-linux-gnu/14/crtendS.o /usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu/crtn.o -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -fstack-protector-strong -Werror=format-security -mbranch-protection=standard -O3 -flto=auto -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,libncl.so.2 -o .libs/libncl.so.2.0.0 libtool: link: (cd ".libs" && rm -f "libncl.so.2" && ln -s "libncl.so.2.0.0" "libncl.so.2") libtool: link: (cd ".libs" && rm -f "libncl.so" && ln -s "libncl.so.2.0.0" "libncl.so") @@ -926,7 +962,7 @@ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o basiccmdline basiccmdline.o ../../ncl/libncl.la +/bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o basiccmdline basiccmdline.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/basiccmdline basiccmdline.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/basiccmdline' Making all in check-taxo-nodes @@ -947,7 +983,7 @@ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o checktaxonnodes checktaxonnodes-checktaxonnodes.o ../../ncl/libncl.la +/bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o checktaxonnodes checktaxonnodes-checktaxonnodes.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/checktaxonnodes checktaxonnodes-checktaxonnodes.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/check-taxo-nodes' Making all in compressor @@ -967,7 +1003,7 @@ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o NEXUSCharacterCompressor NEXUSCharacterCompressor-compressor.o ../../ncl/libncl.la +/bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o NEXUSCharacterCompressor NEXUSCharacterCompressor-compressor.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEXUSCharacterCompressor NEXUSCharacterCompressor-compressor.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/compressor' Making all in find-unsupported-edges @@ -988,7 +1024,7 @@ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o findunsupportededges findunsupportededges-findunsupportededges.o ../../ncl/libncl.la +/bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o findunsupportededges findunsupportededges-findunsupportededges.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/findunsupportededges findunsupportededges-findunsupportededges.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/find-unsupported-edges' Making all in gapcode @@ -1009,7 +1045,7 @@ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o NEXUSgapcode NEXUSgapcode-gapcode.o ../../ncl/libncl.la +/bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o NEXUSgapcode NEXUSgapcode-gapcode.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEXUSgapcode NEXUSgapcode-gapcode.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/gapcode' Making all in nclsimplest @@ -1030,7 +1066,7 @@ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o nclsimplest nclsimplest.o ../../ncl/libncl.la +/bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o nclsimplest nclsimplest.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/nclsimplest nclsimplest.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/nclsimplest' Making all in ncltest @@ -1051,7 +1087,7 @@ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o ncltest ncltest.o ../../ncl/libncl.la +/bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o ncltest ncltest.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/ncltest ncltest.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/ncltest' Making all in normalizer @@ -1096,7 +1132,7 @@ 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../ncl/ncl.h:79, - from converter.cpp:48: + from normalizer.cpp:46: ../../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ @@ -1111,7 +1147,12 @@ 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../ncl/ncl.h:79, - from normalizer.cpp:46: + from us2ml.cpp:22: +../../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 266 | : public std::binary_function + | ^~~~~~~~~~~~~~~ +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 | ^~~~~~~~~~~~~~~ @@ -1125,11 +1166,6 @@ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from ../../ncl/ncl.h:79, - from 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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, @@ -1141,7 +1177,7 @@ 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../ncl/ncl.h:79, - from normalizer.cpp:46: + from us2ml.cpp:22: ../../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ @@ -1186,7 +1222,7 @@ 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../ncl/ncl.h:79, - from us2ml.cpp:22: + from normalizer.cpp:46: ../../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ @@ -1200,17 +1236,17 @@ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o NEXUSinspector NEXUSinspector-normalizer.o ../../ncl/libncl.la -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o NEXUSunion NEXUSunion-normalizer.o ../../ncl/libncl.la -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o NEXUSnormalizer normalizer.o ../../ncl/libncl.la -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o NEXUSvalidator NEXUSvalidator-normalizer.o ../../ncl/libncl.la +/bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o NEXUSunion NEXUSunion-normalizer.o ../../ncl/libncl.la +/bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o NEXUSvalidator NEXUSvalidator-normalizer.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEXUSunion NEXUSunion-normalizer.o ../../ncl/.libs/libncl.so -libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEXUSinspector NEXUSinspector-normalizer.o ../../ncl/.libs/libncl.so -libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEXUSnormalizer normalizer.o ../../ncl/.libs/libncl.so +/bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o NEXUSnormalizer normalizer.o ../../ncl/libncl.la +/bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o NEXUSinspector NEXUSinspector-normalizer.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEXUSvalidator NEXUSvalidator-normalizer.o ../../ncl/.libs/libncl.so -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o NCLconverter NCLconverter-normalizer.o NCLconverter-us2ml.o NCLconverter-converter.o ../../ncl/libncl.la -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o NEX_us2ml NEX_us2ml-normalizer.o NEX_us2ml-us2ml.o ../../ncl/libncl.la +libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEXUSnormalizer normalizer.o ../../ncl/.libs/libncl.so +libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEXUSinspector NEXUSinspector-normalizer.o ../../ncl/.libs/libncl.so +/bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o NCLconverter NCLconverter-normalizer.o NCLconverter-us2ml.o NCLconverter-converter.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NCLconverter NCLconverter-normalizer.o NCLconverter-us2ml.o NCLconverter-converter.o ../../ncl/.libs/libncl.so +/bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o NEX_us2ml NEX_us2ml-normalizer.o NEX_us2ml-us2ml.o ../../ncl/libncl.la normalizer.cpp:102:14: warning: 'substituteSafeTaxaLabels' violates the C++ One Definition Rule [-Wodr] 102 | void substituteSafeTaxaLabels(PublicNexusReader & reader, std::string filepath, bool evenTrivial); | ^ @@ -1239,7 +1275,7 @@ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o otsubtree otsubtree-otsubtree.o ../../ncl/libncl.la +/bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o otsubtree otsubtree-otsubtree.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/otsubtree otsubtree-otsubtree.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/ot-subtree' Making all in ot-tree-inspect @@ -1260,7 +1296,7 @@ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o otTreeInspect otTreeInspect-ot_tree_inspect.o ../../ncl/libncl.la +/bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o otTreeInspect otTreeInspect-ot_tree_inspect.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/otTreeInspect otTreeInspect-ot_tree_inspect.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/ot-tree-inspect' Making all in outdeg1count @@ -1281,7 +1317,7 @@ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o outdeg1count outdeg1count-outdeg1count.o ../../ncl/libncl.la +/bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o outdeg1count outdeg1count-outdeg1count.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/outdeg1count outdeg1count-outdeg1count.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/outdeg1count' Making all in patristic @@ -1302,7 +1338,7 @@ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o patristicmat patristic.o ../../ncl/libncl.la +/bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o patristicmat patristic.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/patristicmat patristic.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/patristic' Making all in phylobaseinterface @@ -1323,7 +1359,7 @@ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o PhylobaseNCLInterfaceExample NCLInterface.o ../../ncl/libncl.la +/bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o PhylobaseNCLInterfaceExample NCLInterface.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/PhylobaseNCLInterfaceExample NCLInterface.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/phylobaseinterface' Making all in polytomy-count @@ -1344,7 +1380,7 @@ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o polytomycount polytomycount-polytomy_count.o ../../ncl/libncl.la +/bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o polytomycount polytomycount-polytomy_count.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/polytomycount polytomycount-polytomy_count.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/polytomy-count' Making all in splitsinfile @@ -1362,6 +1398,12 @@ ../../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 266 | : public std::binary_function | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/14/bits/refwrap.h:39, + from /usr/include/c++/14/vector:68, + from splitsstructs.h:3: +/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ In file included from ../../ncl/nxsexception.h:23, from ../../ncl/nxsblock.h:24, from ../../ncl/nxstaxablock.h:23, @@ -1377,12 +1419,6 @@ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/bits/refwrap.h:39, - from /usr/include/c++/14/vector:68, - from splitsstructs.h:3: -/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ In file included from ../../ncl/ncl.h:79, from splitsinfile.cpp:46: ../../ncl/nxsstring.h:266:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] @@ -1413,9 +1449,9 @@ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o NEXUStosplits NEXUStosplits-splitsinfile.o NEXUStosplits-splitsstructs.o ../../ncl/libncl.la -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o majrule splitsinfile.o splitsstructs.o ../../ncl/libncl.la +/bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o NEXUStosplits NEXUStosplits-splitsinfile.o NEXUStosplits-splitsstructs.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEXUStosplits NEXUStosplits-splitsinfile.o NEXUStosplits-splitsstructs.o ../../ncl/.libs/libncl.so +/bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o majrule splitsinfile.o splitsstructs.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/majrule splitsinfile.o splitsstructs.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/splitsinfile' Making all in subsetter @@ -1434,7 +1470,7 @@ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o NEXUSsubsetter NEXUSsubsetter-subsetter.o ../../ncl/libncl.la +/bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o NEXUSsubsetter NEXUSsubsetter-subsetter.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEXUSsubsetter NEXUSsubsetter-subsetter.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/subsetter' Making all in translate @@ -1455,7 +1491,7 @@ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o NEXUStranslate NEXUStranslate-translateNuc.o ../../ncl/libncl.la +/bin/sh ../../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o NEXUStranslate NEXUStranslate-translateNuc.o ../../ncl/libncl.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -ffast-math -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/NEXUStranslate NEXUStranslate-translateNuc.o ../../ncl/.libs/libncl.so make[4]: Leaving directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/translate' make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example' @@ -2355,7 +2391,7 @@ make[2]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/ncl' make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/ncl' /usr/bin/mkdir -p '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/lib/aarch64-linux-gnu' - /bin/bash ../libtool --mode=install /usr/bin/install -c libncl.la '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/lib/aarch64-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/aarch64-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/aarch64-linux-gnu/libncl.so.2.0.0 libtool: install: (cd /build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/lib/aarch64-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/aarch64-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; }; }) @@ -2381,7 +2417,7 @@ make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/check-taxo-nodes' make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/check-taxo-nodes' /usr/bin/mkdir -p '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin' - /bin/bash ../../libtool --mode=install /usr/bin/install -c checktaxonnodes '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin' + /bin/sh ../../libtool --mode=install /usr/bin/install -c checktaxonnodes '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin' libtool: warning: '../../ncl/libncl.la' has not been installed in '/usr/lib/aarch64-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'. @@ -2398,7 +2434,7 @@ make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/find-unsupported-edges' make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/find-unsupported-edges' /usr/bin/mkdir -p '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin' - /bin/bash ../../libtool --mode=install /usr/bin/install -c findunsupportededges '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin' + /bin/sh ../../libtool --mode=install /usr/bin/install -c findunsupportededges '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin' libtool: warning: '../../ncl/libncl.la' has not been installed in '/usr/lib/aarch64-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'. @@ -2429,7 +2465,7 @@ make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer' make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/normalizer' /usr/bin/mkdir -p '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin' - /bin/bash ../../libtool --mode=install /usr/bin/install -c NEXUSnormalizer NEXUSvalidator NCLconverter '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin' + /bin/sh ../../libtool --mode=install /usr/bin/install -c NEXUSnormalizer NEXUSvalidator NCLconverter '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin' libtool: warning: '../../ncl/libncl.la' has not been installed in '/usr/lib/aarch64-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/aarch64-linux-gnu' @@ -2443,7 +2479,7 @@ make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/ot-subtree' make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/ot-subtree' /usr/bin/mkdir -p '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin' - /bin/bash ../../libtool --mode=install /usr/bin/install -c otsubtree '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin' + /bin/sh ../../libtool --mode=install /usr/bin/install -c otsubtree '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin' libtool: warning: '../../ncl/libncl.la' has not been installed in '/usr/lib/aarch64-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'. @@ -2453,7 +2489,7 @@ make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/ot-tree-inspect' make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/ot-tree-inspect' /usr/bin/mkdir -p '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin' - /bin/bash ../../libtool --mode=install /usr/bin/install -c otTreeInspect '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin' + /bin/sh ../../libtool --mode=install /usr/bin/install -c otTreeInspect '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin' libtool: warning: '../../ncl/libncl.la' has not been installed in '/usr/lib/aarch64-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'. @@ -2463,7 +2499,7 @@ make[3]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/outdeg1count' make[4]: Entering directory '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/example/outdeg1count' /usr/bin/mkdir -p '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin' - /bin/bash ../../libtool --mode=install /usr/bin/install -c outdeg1count '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin' + /bin/sh ../../libtool --mode=install /usr/bin/install -c outdeg1count '/build/reproducible-path/libncl-2.1.21+git20210811.b1213a7/debian/tmp/usr/bin' libtool: warning: '../../ncl/libncl.la' has not been installed in '/usr/lib/aarch64-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'. @@ -2585,11 +2621,11 @@ dpkg-gencontrol: warning: Depends field of package libncl-dev: substitution variable ${shlibs:Depends} used, but is not defined dh_md5sums dh_builddeb -dpkg-deb: building package 'ncl-tools' in '../ncl-tools_2.1.21+git20210811.b1213a7-6_arm64.deb'. -dpkg-deb: building package 'ncl-tools-dbgsym' in '../ncl-tools-dbgsym_2.1.21+git20210811.b1213a7-6_arm64.deb'. +dpkg-deb: building package 'libncl-dev' in '../libncl-dev_2.1.21+git20210811.b1213a7-6_arm64.deb'. dpkg-deb: building package 'libncl2' in '../libncl2_2.1.21+git20210811.b1213a7-6_arm64.deb'. +dpkg-deb: building package 'ncl-tools' in '../ncl-tools_2.1.21+git20210811.b1213a7-6_arm64.deb'. dpkg-deb: building package 'libncl2-dbgsym' in '../libncl2-dbgsym_2.1.21+git20210811.b1213a7-6_arm64.deb'. -dpkg-deb: building package 'libncl-dev' in '../libncl-dev_2.1.21+git20210811.b1213a7-6_arm64.deb'. +dpkg-deb: building package 'ncl-tools-dbgsym' in '../ncl-tools-dbgsym_2.1.21+git20210811.b1213a7-6_arm64.deb'. dpkg-genbuildinfo --build=binary -O../libncl_2.1.21+git20210811.b1213a7-6_arm64.buildinfo dpkg-genchanges --build=binary -O../libncl_2.1.21+git20210811.b1213a7-6_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -2597,12 +2633,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/2122414/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2122414/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/1336987 and its subdirectories -I: Current time: Fri Feb 21 15:09:44 -12 2025 -I: pbuilder-time-stamp: 1740193784 +I: removing directory /srv/workspace/pbuilder/2122414 and its subdirectories +I: Current time: Fri Mar 27 23:44:33 +14 2026 +I: pbuilder-time-stamp: 1774604673 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/arm64/libncl_2.1.21+git20210811.b1213a7-6.diff: 92.4% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/arm64/libncl_2.1.21+git20210811.b1213a7-6.diff.gz b2/build.log: 92.3% -- replaced with stdout Compressing the 1st log... b1/build.log: 92.5% -- replaced with stdout Sat Feb 22 03:21:36 UTC 2025 I: diffoscope 289 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_libncl_trixie_arm64_1740194496 + touch /var/log/reproducible-builds/diffoscope_stamp_libncl_trixie_arm64_1740194496 + RESULT=0 + systemd-run '--description=diffoscope on libncl/2.1.21+git20210811.b1213a7-6 in trixie/arm64' --slice=rb-build-diffoscope.slice -u rb-diffoscope-arm64_7-57942 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.fEgknmXy --run-session -c jenkins-reproducible-trixie-diffoscope-9323370b-0461-4329-b075-b87f8f0b51bb -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.fEgknmXy/dbd-tmp-5v7DZhF ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.fEgknmXy/libncl_2.1.21+git20210811.b1213a7-6.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.fEgknmXy/libncl_2.1.21+git20210811.b1213a7-6.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.fEgknmXy/libncl_2.1.21+git20210811.b1213a7-6.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.fEgknmXy/b1/libncl_2.1.21+git20210811.b1213a7-6_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.fEgknmXy/b2/libncl_2.1.21+git20210811.b1213a7-6_arm64.changes' + false + set +x Running as unit: rb-diffoscope-arm64_7-57942.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.fEgknmXy/libncl_2.1.21+git20210811.b1213a7-6.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.fEgknmXy/libncl_2.1.21+git20210811.b1213a7-6.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.fEgknmXy/libncl_2.1.21+git20210811.b1213a7-6.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.fEgknmXy/b1/libncl_2.1.21+git20210811.b1213a7-6_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.fEgknmXy/b2/libncl_2.1.21+git20210811.b1213a7-6_arm64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call diffoscope.comparators.binary.FilesystemFile ## main (total time: 0.004s) 0.004s 2 calls outputs 0.000s 1 call cleanup Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 251ms CPU time consumed: 250ms _ _ _ _ | (_) |__ _ __ ___| | | | | '_ \| '_ \ / __| | | | | |_) | | | | (__| | |_|_|_.__/|_| |_|\___|_| Sat Feb 22 03:21:36 UTC 2025 I: diffoscope 289 found no differences in the changes files, and a .buildinfo file also exists. Sat Feb 22 03:21:36 UTC 2025 I: libncl from trixie built successfully and reproducibly on arm64. INSERT 0 1 INSERT 0 1 DELETE 1 [2025-02-22 03:21:37] INFO: Starting at 2025-02-22 03:21:37.423930 [2025-02-22 03:21:37] INFO: Generating the pages of 1 package(s) [2025-02-22 03:21:37] CRITICAL: https://tests.reproducible-builds.org/debian/trixie/arm64/libncl didn't produce a buildlog, even though it has been built. [2025-02-22 03:21:37] INFO: Finished at 2025-02-22 03:21:37.863119, took: 0:00:00.439197 Sat Feb 22 03:21:37 UTC 2025 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/trixie/arm64/libncl.html Sat Feb 22 03:21:37 UTC 2025 I: Submitting .buildinfo files to external archives: Sat Feb 22 03:21:37 UTC 2025 I: Submitting 8.0K b1/libncl_2.1.21+git20210811.b1213a7-6_arm64.buildinfo.asc https://buildinfo.debian.net/695fd13fb1a6d1f6ef93994f01f12cf91486fc33/libncl_2.1.21+git20210811.b1213a7-6_arm64 Sat Feb 22 03:21:39 UTC 2025 I: Submitting 8.0K b2/libncl_2.1.21+git20210811.b1213a7-6_arm64.buildinfo.asc https://buildinfo.debian.net/a6871ec34e8c5ade726272439a7a0ea6474912b6/libncl_2.1.21+git20210811.b1213a7-6_arm64 Sat Feb 22 03:21:41 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sat Feb 22 03:21:41 UTC 2025 I: Done submitting .buildinfo files. Sat Feb 22 03:21:41 UTC 2025 I: Removing signed libncl_2.1.21+git20210811.b1213a7-6_arm64.buildinfo.asc files: removed './b1/libncl_2.1.21+git20210811.b1213a7-6_arm64.buildinfo.asc' removed './b2/libncl_2.1.21+git20210811.b1213a7-6_arm64.buildinfo.asc' 1740194501 arm64 trixie libncl Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/arm64/libncl_2.1.21+git20210811.b1213a7-6.rbuild.log: 91.2% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/arm64/libncl_2.1.21+git20210811.b1213a7-6.rbuild.log.gz [2025-02-22 03:21:42] INFO: Starting at 2025-02-22 03:21:42.022369 [2025-02-22 03:21:42] INFO: Generating the pages of 1 package(s) [2025-02-22 03:21:42] INFO: Finished at 2025-02-22 03:21:42.434389, took: 0:00:00.412028 All cleanup done. Sat Feb 22 03:21:42 UTC 2025 - total duration: 0h 17m 7s. Sat Feb 22 03:21:42 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-3eLg5FEk, removing. Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 17min 13.394s CPU time consumed: 7.236s