I: pbuilder: network access will be disabled during build I: Current time: Mon Jan 5 23:59:47 +14 2026 I: pbuilder-time-stamp: 1767607187 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-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 [murasaki_1.68.6-14.dsc] I: copying [./murasaki_1.68.6.orig-debian-tests-data.tar.gz] I: copying [./murasaki_1.68.6.orig.tar.gz] I: copying [./murasaki_1.68.6-14.debian.tar.xz] I: Extracting source gpgv: Signature made Sat Nov 9 11:46:58 2024 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./murasaki_1.68.6-14.dsc: no acceptable signature found dpkg-source: info: extracting murasaki in murasaki-1.68.6 dpkg-source: info: unpacking murasaki_1.68.6.orig.tar.gz dpkg-source: info: unpacking murasaki_1.68.6.orig-debian-tests-data.tar.gz dpkg-source: info: unpacking murasaki_1.68.6-14.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying gcc11.patch dpkg-source: info: applying use_proper_libboost_names.patch dpkg-source: info: applying include_libpstream.patch dpkg-source: info: applying hardening.patch dpkg-source: info: applying spelling.patch dpkg-source: info: applying man_syntax.patch dpkg-source: info: applying freebsd.patch dpkg-source: info: applying gcc-6.patch dpkg-source: info: applying fix_mpi.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2081948/tmp/hooks/D01_modify_environment starting debug: Running on codethink01-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 Jan 5 09:59 /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/2081948/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/2081948/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]="32" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") BASH_VERSION='5.2.32(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=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' INVOCATION_ID=9cec585f10424eeab95cdf424c8fb6bd 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=2081948 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.AsnGYOUs/pbuilderrc_Ud08 --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.AsnGYOUs/b2 --logfile b2/build.log murasaki_1.68.6-14.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 6.1.0-28-cloud-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2081948/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), libboost-regex-dev, libboost-iostreams-dev, libboost-filesystem-dev, libterm-readkey-perl, libtext-wrapper-perl, libcrypto++-dev, libpstreams-dev, mpi-default-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 20087 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 libboost-regex-dev; however: Package libboost-regex-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-iostreams-dev; however: Package libboost-iostreams-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-filesystem-dev; however: Package libboost-filesystem-dev is not installed. pbuilder-satisfydepends-dummy depends on libterm-readkey-perl; however: Package libterm-readkey-perl is not installed. pbuilder-satisfydepends-dummy depends on libtext-wrapper-perl; however: Package libtext-wrapper-perl is not installed. pbuilder-satisfydepends-dummy depends on libcrypto++-dev; however: Package libcrypto++-dev is not installed. pbuilder-satisfydepends-dummy depends on libpstreams-dev; however: Package libpstreams-dev is not installed. pbuilder-satisfydepends-dummy depends on mpi-default-dev; however: Package mpi-default-dev 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} ca-certificates{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} docutils-common{a} dwz{a} file{a} gettext{a} gettext-base{a} gfortran-14{a} gfortran-14-aarch64-linux-gnu{a} groff-base{a} ibverbs-providers{a} icu-devtools{a} intltool-debian{a} libamd-comgr2{a} libamdhip64-5{a} libarchive-zip-perl{a} libboost-atomic1.83-dev{a} libboost-atomic1.83.0{a} libboost-filesystem-dev{a} libboost-filesystem1.83-dev{a} libboost-filesystem1.83.0{a} libboost-iostreams-dev{a} libboost-iostreams1.83-dev{a} libboost-regex-dev{a} libboost-regex1.83-dev{a} libboost-regex1.83.0{a} libboost-system1.83-dev{a} libboost-system1.83.0{a} libboost1.83-dev{a} libcbor0.10{a} libcom-err2{a} libcrypto++-dev{a} libcrypto++8t64{a} libdebhelper-perl{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm2{a} libedit2{a} libelf1t64{a} libevent-2.1-7t64{a} libevent-core-2.1-7t64{a} libevent-dev{a} libevent-extra-2.1-7t64{a} libevent-openssl-2.1-7t64{a} libevent-pthreads-2.1-7t64{a} libexpat1{a} libfabric1{a} libfido2-1{a} libfile-stripnondeterminism-perl{a} libgfortran-14-dev{a} libgfortran5{a} libgssapi-krb5-2{a} libhsa-runtime64-1{a} libhsakmt1{a} libhwloc-dev{a} libhwloc-plugins{a} libhwloc15{a} libibmad5{a} libibumad3{a} libibverbs-dev{a} libibverbs1{a} libicu-dev{a} libicu72{a} libjs-jquery{a} libjs-jquery-ui{a} libjs-sphinxdoc{a} libjs-underscore{a} libjson-perl{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libllvm17t64{a} libltdl-dev{a} libltdl7{a} libmagic-mgc{a} libmagic1t64{a} libmunge2{a} libnl-3-200{a} libnl-3-dev{a} libnl-route-3-200{a} libnl-route-3-dev{a} libnsl2{a} libnuma-dev{a} libnuma1{a} libopenmpi-dev{a} libopenmpi40{a} libpciaccess0{a} libpipeline1{a} libpmix-dev{a} libpmix2t64{a} libpstreams-dev{a} libpython3-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} librdmacm1t64{a} libreadline8t64{a} libterm-readkey-perl{a} libtext-wrapper-perl{a} libtirpc-common{a} libtirpc3t64{a} libtool{a} libuchardet0{a} libucx0{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml2{a} libxnvctrl0{a} libz3-4{a} m4{a} man-db{a} media-types{a} mpi-default-dev{a} netbase{a} ocl-icd-libopencl1{a} openmpi-bin{a} openmpi-common{a} openssh-client{a} openssl{a} po-debconf{a} python-babel-localedata{a} python3{a} python3-alabaster{a} python3-autocommand{a} python3-babel{a} python3-certifi{a} python3-chardet{a} python3-charset-normalizer{a} python3-defusedxml{a} python3-docutils{a} python3-idna{a} python3-imagesize{a} python3-inflect{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jinja2{a} python3-markupsafe{a} python3-minimal{a} python3-more-itertools{a} python3-packaging{a} python3-pkg-resources{a} python3-pygments{a} python3-requests{a} python3-roman{a} python3-snowballstemmer{a} python3-sphinx{a} python3-typeguard{a} python3-typing-extensions{a} python3-urllib3{a} python3.12{a} python3.12-minimal{a} readline-common{a} sensible-utils{a} sgml-base{a} sphinx-common{a} tzdata{a} xml-core{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl javascript-common krb5-locales libarchive-cpio-perl libcoarrays-openmpi-dev libjson-xs-perl libmail-sendmail-perl libpaper-utils lynx python3-pil wget xauth 0 packages upgraded, 169 newly installed, 0 to remove and 0 not upgraded. Need to get 142 MB of archives. After unpacking 762 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 libpython3.12-minimal arm64 3.12.7-3 [808 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libexpat1 arm64 2.6.4-1 [90.7 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 python3.12-minimal arm64 3.12.7-3 [1940 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 python3-minimal arm64 3.12.7-1 [26.8 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 tzdata all 2024b-3 [255 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 libkrb5support0 arm64 1.21.3-3 [32.1 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 libcom-err2 arm64 1.47.2~rc1-1 [23.5 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 libk5crypto3 arm64 1.21.3-3 [80.8 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 libkeyutils1 arm64 1.6.3-4 [9352 B] Get: 12 http://deb.debian.org/debian unstable/main arm64 libkrb5-3 arm64 1.21.3-3 [310 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.21.3-3 [126 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 libtirpc3t64 arm64 1.3.4+ds-1.3+b1 [78.7 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 libnsl2 arm64 1.3.0-3+b3 [37.9 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 readline-common all 8.2-5 [69.3 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 libreadline8t64 arm64 8.2-5 [159 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 libpython3.12-stdlib arm64 3.12.7-3 [1902 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 python3.12 arm64 3.12.7-3 [671 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 libpython3-stdlib arm64 3.12.7-1 [9708 B] Get: 22 http://deb.debian.org/debian unstable/main arm64 python3 arm64 3.12.7-1 [27.8 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 sgml-base all 1.31 [15.4 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 openssl arm64 3.3.2-2 [1347 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 ca-certificates all 20240203 [158 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.22.5-2 [198 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-5 [1129 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.2-11 [91.2 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 libedit2 arm64 3.1-20240808-1 [89.2 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 libcbor0.10 arm64 0.10.2-2 [27.4 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 libfido2-1 arm64 1.15.0-1+b1 [74.3 kB] Get: 39 http://deb.debian.org/debian unstable/main arm64 openssh-client arm64 1:9.9p1-3 [928 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3 [493 kB] Get: 42 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.22.5-2 [723 kB] Get: 45 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.20 [89.7 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 libtool all 2.4.7-8 [517 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 48 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 49 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 51 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 52 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 53 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-5+b1 [9239 kB] Get: 54 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB] Get: 55 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.22.5-2 [1532 kB] Get: 56 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 57 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.20 [915 kB] Get: 59 http://deb.debian.org/debian unstable/main arm64 xml-core all 0.19 [20.1 kB] Get: 60 http://deb.debian.org/debian unstable/main arm64 docutils-common all 0.21.2+dfsg-2 [128 kB] Get: 61 http://deb.debian.org/debian unstable/main arm64 libgfortran5 arm64 14.2.0-9 [361 kB] Get: 62 http://deb.debian.org/debian unstable/main arm64 libgfortran-14-dev arm64 14.2.0-9 [427 kB] Get: 63 http://deb.debian.org/debian unstable/main arm64 gfortran-14-aarch64-linux-gnu arm64 14.2.0-9 [9793 kB] Get: 64 http://deb.debian.org/debian unstable/main arm64 gfortran-14 arm64 14.2.0-9 [12.8 kB] Get: 65 http://deb.debian.org/debian unstable/main arm64 libnl-3-200 arm64 3.7.0-0.3+b1 [57.0 kB] Get: 66 http://deb.debian.org/debian unstable/main arm64 libnl-route-3-200 arm64 3.7.0-0.3+b1 [167 kB] Get: 67 http://deb.debian.org/debian unstable/main arm64 libibverbs1 arm64 52.0-2+b1 [58.8 kB] Get: 68 http://deb.debian.org/debian unstable/main arm64 ibverbs-providers arm64 52.0-2+b1 [321 kB] Get: 69 http://deb.debian.org/debian unstable/main arm64 icu-devtools arm64 72.1-5+b1 [195 kB] Get: 70 http://deb.debian.org/debian unstable/main arm64 libz3-4 arm64 4.13.3-1 [7507 kB] Get: 71 http://deb.debian.org/debian unstable/main arm64 libllvm17t64 arm64 1:17.0.6-18 [21.3 MB] Get: 72 http://deb.debian.org/debian unstable/main arm64 libamd-comgr2 arm64 6.0+git20231212.4510c28+dfsg-3+b2 [12.1 MB] Get: 73 http://deb.debian.org/debian unstable/main arm64 libdrm-common all 2.4.123-1 [8084 B] Get: 74 http://deb.debian.org/debian unstable/main arm64 libdrm2 arm64 2.4.123-1 [38.0 kB] Get: 75 http://deb.debian.org/debian unstable/main arm64 libdrm-amdgpu1 arm64 2.4.123-1 [21.6 kB] Get: 76 http://deb.debian.org/debian unstable/main arm64 libnuma1 arm64 2.0.18-1+b1 [21.8 kB] Get: 77 http://deb.debian.org/debian unstable/main arm64 libhsakmt1 arm64 6.1.2+ds-1 [56.9 kB] Get: 78 http://deb.debian.org/debian unstable/main arm64 libhsa-runtime64-1 arm64 6.1.2-2 [300 kB] Get: 79 http://deb.debian.org/debian unstable/main arm64 libamdhip64-5 arm64 5.7.1-5 [8823 kB] Get: 80 http://deb.debian.org/debian unstable/main arm64 libboost1.83-dev arm64 1.83.0-3.2+b2 [10.6 MB] Get: 81 http://deb.debian.org/debian unstable/main arm64 libboost-atomic1.83.0 arm64 1.83.0-3.2+b2 [234 kB] Get: 82 http://deb.debian.org/debian unstable/main arm64 libboost-atomic1.83-dev arm64 1.83.0-3.2+b2 [234 kB] Get: 83 http://deb.debian.org/debian unstable/main arm64 libboost-filesystem1.83.0 arm64 1.83.0-3.2+b2 [273 kB] Get: 84 http://deb.debian.org/debian unstable/main arm64 libboost-system1.83.0 arm64 1.83.0-3.2+b2 [231 kB] Get: 85 http://deb.debian.org/debian unstable/main arm64 libboost-system1.83-dev arm64 1.83.0-3.2+b2 [232 kB] Get: 86 http://deb.debian.org/debian unstable/main arm64 libboost-filesystem1.83-dev arm64 1.83.0-3.2+b2 [293 kB] Get: 87 http://deb.debian.org/debian unstable/main arm64 libboost-filesystem-dev arm64 1.83.0.2+b2 [3616 B] Get: 88 http://deb.debian.org/debian unstable/main arm64 libboost-regex1.83.0 arm64 1.83.0-3.2+b2 [314 kB] Get: 89 http://deb.debian.org/debian unstable/main arm64 libicu-dev arm64 72.1-5+b1 [10.3 MB] Get: 90 http://deb.debian.org/debian unstable/main arm64 libboost-regex1.83-dev arm64 1.83.0-3.2+b2 [338 kB] Get: 91 http://deb.debian.org/debian unstable/main arm64 libboost-iostreams1.83-dev arm64 1.83.0-3.2+b2 [261 kB] Get: 92 http://deb.debian.org/debian unstable/main arm64 libboost-iostreams-dev arm64 1.83.0.2+b2 [3568 B] Get: 93 http://deb.debian.org/debian unstable/main arm64 libboost-regex-dev arm64 1.83.0.2+b2 [3852 B] Get: 94 http://deb.debian.org/debian unstable/main arm64 libcrypto++8t64 arm64 8.9.0-1.1+b1 [1068 kB] Get: 95 http://deb.debian.org/debian unstable/main arm64 libcrypto++-dev arm64 8.9.0-1.1+b1 [1814 kB] Get: 96 http://deb.debian.org/debian unstable/main arm64 libevent-2.1-7t64 arm64 2.1.12-stable-10+b1 [170 kB] Get: 97 http://deb.debian.org/debian unstable/main arm64 libevent-core-2.1-7t64 arm64 2.1.12-stable-10+b1 [126 kB] Get: 98 http://deb.debian.org/debian unstable/main arm64 libevent-extra-2.1-7t64 arm64 2.1.12-stable-10+b1 [102 kB] Get: 99 http://deb.debian.org/debian unstable/main arm64 libevent-pthreads-2.1-7t64 arm64 2.1.12-stable-10+b1 [54.4 kB] Get: 100 http://deb.debian.org/debian unstable/main arm64 libevent-openssl-2.1-7t64 arm64 2.1.12-stable-10+b1 [60.4 kB] Get: 101 http://deb.debian.org/debian unstable/main arm64 libevent-dev arm64 2.1.12-stable-10+b1 [304 kB] Get: 102 http://deb.debian.org/debian unstable/main arm64 librdmacm1t64 arm64 52.0-2+b1 [67.4 kB] Get: 103 http://deb.debian.org/debian unstable/main arm64 libfabric1 arm64 1.17.0-3.1 [480 kB] Get: 104 http://deb.debian.org/debian unstable/main arm64 libhwloc15 arm64 2.11.2-1 [141 kB] Get: 105 http://deb.debian.org/debian unstable/main arm64 libnuma-dev arm64 2.0.18-1+b1 [37.8 kB] Get: 106 http://deb.debian.org/debian unstable/main arm64 libltdl7 arm64 2.4.7-8 [392 kB] Get: 107 http://deb.debian.org/debian unstable/main arm64 libltdl-dev arm64 2.4.7-8 [165 kB] Get: 108 http://deb.debian.org/debian unstable/main arm64 libhwloc-dev arm64 2.11.2-1 [237 kB] Get: 109 http://deb.debian.org/debian unstable/main arm64 libpciaccess0 arm64 0.17-3+b2 [51.2 kB] Get: 110 http://deb.debian.org/debian unstable/main arm64 libxau6 arm64 1:1.0.11-1 [20.6 kB] Get: 111 http://deb.debian.org/debian unstable/main arm64 libxdmcp6 arm64 1:1.1.5-1 [27.8 kB] Get: 112 http://deb.debian.org/debian unstable/main arm64 libxcb1 arm64 1.17.0-2+b1 [143 kB] Get: 113 http://deb.debian.org/debian unstable/main arm64 libx11-data all 2:1.8.10-2 [337 kB] Get: 114 http://deb.debian.org/debian unstable/main arm64 libx11-6 arm64 2:1.8.10-2 [789 kB] Get: 115 http://deb.debian.org/debian unstable/main arm64 libxext6 arm64 2:1.3.4-1+b2 [49.3 kB] Get: 116 http://deb.debian.org/debian unstable/main arm64 libxnvctrl0 arm64 535.171.04-1+b1 [14.1 kB] Get: 117 http://deb.debian.org/debian unstable/main arm64 ocl-icd-libopencl1 arm64 2.3.2-1+b2 [39.3 kB] Get: 118 http://deb.debian.org/debian unstable/main arm64 libhwloc-plugins arm64 2.11.2-1 [17.9 kB] Get: 119 http://deb.debian.org/debian unstable/main arm64 libibumad3 arm64 52.0-2+b1 [27.1 kB] Get: 120 http://deb.debian.org/debian unstable/main arm64 libibmad5 arm64 52.0-2+b1 [41.5 kB] Get: 121 http://deb.debian.org/debian unstable/main arm64 libnl-3-dev arm64 3.7.0-0.3+b1 [101 kB] Get: 122 http://deb.debian.org/debian unstable/main arm64 libnl-route-3-dev arm64 3.7.0-0.3+b1 [198 kB] Get: 123 http://deb.debian.org/debian unstable/main arm64 libibverbs-dev arm64 52.0-2+b1 [625 kB] Get: 124 http://deb.debian.org/debian unstable/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 125 http://deb.debian.org/debian unstable/main arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 126 http://deb.debian.org/debian unstable/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 127 http://deb.debian.org/debian unstable/main arm64 libjs-sphinxdoc all 7.4.7-4 [158 kB] Get: 128 http://deb.debian.org/debian unstable/main arm64 libjson-perl all 4.10000-1 [87.5 kB] Get: 129 http://deb.debian.org/debian unstable/main arm64 libmunge2 arm64 0.5.15-4+b1 [19.4 kB] Get: 130 http://deb.debian.org/debian unstable/main arm64 libpmix2t64 arm64 5.0.4-1 [586 kB] Get: 131 http://deb.debian.org/debian unstable/main arm64 libucx0 arm64 1.17.0+ds-3 [959 kB] Get: 132 http://deb.debian.org/debian unstable/main arm64 libopenmpi40 arm64 5.0.6-3 [2087 kB] Get: 133 http://deb.debian.org/debian unstable/main arm64 openmpi-common all 5.0.6-3 [97.0 kB] Get: 134 http://deb.debian.org/debian unstable/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] Get: 135 http://deb.debian.org/debian unstable/main arm64 python3-defusedxml all 0.7.1-2 [43.3 kB] Get: 136 http://deb.debian.org/debian unstable/main arm64 sphinx-common all 7.4.7-4 [731 kB] Get: 137 http://deb.debian.org/debian unstable/main arm64 python3-alabaster all 0.7.16-0.1 [27.9 kB] Get: 138 http://deb.debian.org/debian unstable/main arm64 python-babel-localedata all 2.16.0-1 [5696 kB] Get: 139 http://deb.debian.org/debian unstable/main arm64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 140 http://deb.debian.org/debian unstable/main arm64 python3-more-itertools all 10.5.0-1 [63.8 kB] Get: 141 http://deb.debian.org/debian unstable/main arm64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 142 http://deb.debian.org/debian unstable/main arm64 python3-typeguard all 4.4.1-1 [37.0 kB] Get: 143 http://deb.debian.org/debian unstable/main arm64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 144 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 145 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 146 http://deb.debian.org/debian unstable/main arm64 python3-pkg-resources all 75.2.0-1 [213 kB] Get: 147 http://deb.debian.org/debian unstable/main arm64 python3-babel all 2.16.0-1 [114 kB] Get: 148 http://deb.debian.org/debian unstable/main arm64 python3-roman all 4.2-1 [10.4 kB] Get: 149 http://deb.debian.org/debian unstable/main arm64 python3-docutils all 0.21.2+dfsg-2 [403 kB] Get: 150 http://deb.debian.org/debian unstable/main arm64 python3-imagesize all 1.4.1-1 [6688 B] Get: 151 http://deb.debian.org/debian unstable/main arm64 python3-markupsafe arm64 2.1.5-1+b3 [14.0 kB] Get: 152 http://deb.debian.org/debian unstable/main arm64 python3-jinja2 all 3.1.3-1 [119 kB] Get: 153 http://deb.debian.org/debian unstable/main arm64 python3-packaging all 24.2-1 [55.3 kB] Get: 154 http://deb.debian.org/debian unstable/main arm64 python3-pygments all 2.18.0+dfsg-1 [836 kB] Get: 155 http://deb.debian.org/debian unstable/main arm64 python3-certifi all 2024.8.30+dfsg-1 [9576 B] Get: 156 http://deb.debian.org/debian unstable/main arm64 python3-charset-normalizer arm64 3.4.0-1+b1 [129 kB] Get: 157 http://deb.debian.org/debian unstable/main arm64 python3-idna all 3.8-2 [41.6 kB] Get: 158 http://deb.debian.org/debian unstable/main arm64 python3-urllib3 all 2.2.3-3 [112 kB] Get: 159 http://deb.debian.org/debian unstable/main arm64 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get: 160 http://deb.debian.org/debian unstable/main arm64 python3-requests all 2.32.3+dfsg-1 [71.9 kB] Get: 161 http://deb.debian.org/debian unstable/main arm64 python3-snowballstemmer all 2.2.0-4 [58.0 kB] Get: 162 http://deb.debian.org/debian unstable/main arm64 python3-sphinx all 7.4.7-4 [588 kB] Get: 163 http://deb.debian.org/debian unstable/main arm64 libpmix-dev arm64 5.0.4-1 [3942 kB] Get: 164 http://deb.debian.org/debian unstable/main arm64 openmpi-bin arm64 5.0.6-3 [180 kB] Get: 165 http://deb.debian.org/debian unstable/main arm64 libopenmpi-dev arm64 5.0.6-3 [1088 kB] Get: 166 http://deb.debian.org/debian unstable/main arm64 libpstreams-dev all 1.0.3-1 [134 kB] Get: 167 http://deb.debian.org/debian unstable/main arm64 libterm-readkey-perl arm64 2.38-2+b4 [24.5 kB] Get: 168 http://deb.debian.org/debian unstable/main arm64 libtext-wrapper-perl all 1.05-4 [10.3 kB] Get: 169 http://deb.debian.org/debian unstable/main arm64 mpi-default-dev arm64 1.17 [3148 B] Fetched 142 MB in 1s (201 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-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 ... 20087 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.7-3_arm64.deb ... Unpacking libpython3.12-minimal:arm64 (3.12.7-3) ... 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 python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.7-3_arm64.deb ... Unpacking python3.12-minimal (3.12.7-3) ... Setting up libpython3.12-minimal:arm64 (3.12.7-3) ... Setting up libexpat1:arm64 (2.6.4-1) ... Setting up python3.12-minimal (3.12.7-3) ... 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 ... 20407 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.7-1_arm64.deb ... Unpacking python3-minimal (3.12.7-1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../03-tzdata_2024b-3_all.deb ... Unpacking tzdata (2024b-3) ... Selecting previously unselected package libkrb5support0:arm64. Preparing to unpack .../04-libkrb5support0_1.21.3-3_arm64.deb ... Unpacking libkrb5support0:arm64 (1.21.3-3) ... Selecting previously unselected package libcom-err2:arm64. Preparing to unpack .../05-libcom-err2_1.47.2~rc1-1_arm64.deb ... Unpacking libcom-err2:arm64 (1.47.2~rc1-1) ... Selecting previously unselected package libk5crypto3:arm64. Preparing to unpack .../06-libk5crypto3_1.21.3-3_arm64.deb ... Unpacking libk5crypto3:arm64 (1.21.3-3) ... Selecting previously unselected package libkeyutils1:arm64. Preparing to unpack .../07-libkeyutils1_1.6.3-4_arm64.deb ... Unpacking libkeyutils1:arm64 (1.6.3-4) ... Selecting previously unselected package libkrb5-3:arm64. Preparing to unpack .../08-libkrb5-3_1.21.3-3_arm64.deb ... Unpacking libkrb5-3:arm64 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:arm64. Preparing to unpack .../09-libgssapi-krb5-2_1.21.3-3_arm64.deb ... Unpacking libgssapi-krb5-2:arm64 (1.21.3-3) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../10-libtirpc-common_1.3.4+ds-1.3_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.3) ... Selecting previously unselected package libtirpc3t64:arm64. Preparing to unpack .../11-libtirpc3t64_1.3.4+ds-1.3+b1_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3 to /lib/aarch64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3.0.0 to /lib/aarch64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:arm64 (1.3.4+ds-1.3+b1) ... Selecting previously unselected package libnsl2:arm64. Preparing to unpack .../12-libnsl2_1.3.0-3+b3_arm64.deb ... Unpacking libnsl2:arm64 (1.3.0-3+b3) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package libreadline8t64:arm64. Preparing to unpack .../14-libreadline8t64_8.2-5_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 (8.2-5) ... Selecting previously unselected package libpython3.12-stdlib:arm64. Preparing to unpack .../15-libpython3.12-stdlib_3.12.7-3_arm64.deb ... Unpacking libpython3.12-stdlib:arm64 (3.12.7-3) ... Selecting previously unselected package python3.12. Preparing to unpack .../16-python3.12_3.12.7-3_arm64.deb ... Unpacking python3.12 (3.12.7-3) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../17-libpython3-stdlib_3.12.7-1_arm64.deb ... Unpacking libpython3-stdlib:arm64 (3.12.7-1) ... Setting up python3-minimal (3.12.7-1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21468 files and directories currently installed.) Preparing to unpack .../000-python3_3.12.7-1_arm64.deb ... Unpacking python3 (3.12.7-1) ... Selecting previously unselected package sgml-base. Preparing to unpack .../001-sgml-base_1.31_all.deb ... Unpacking sgml-base (1.31) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../002-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package openssl. Preparing to unpack .../003-openssl_3.3.2-2_arm64.deb ... Unpacking openssl (3.3.2-2) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../004-ca-certificates_20240203_all.deb ... Unpacking ca-certificates (20240203) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../005-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 .../006-libmagic1t64_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../007-file_1%3a5.45-3+b1_arm64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../008-gettext-base_0.22.5-2_arm64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../009-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 .../010-groff-base_1.23.0-5_arm64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../011-bsdextrautils_2.40.2-11_arm64.deb ... Unpacking bsdextrautils (2.40.2-11) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../012-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../013-man-db_2.13.0-1_arm64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package libedit2:arm64. Preparing to unpack .../014-libedit2_3.1-20240808-1_arm64.deb ... Unpacking libedit2:arm64 (3.1-20240808-1) ... Selecting previously unselected package libcbor0.10:arm64. Preparing to unpack .../015-libcbor0.10_0.10.2-2_arm64.deb ... Unpacking libcbor0.10:arm64 (0.10.2-2) ... Selecting previously unselected package libfido2-1:arm64. Preparing to unpack .../016-libfido2-1_1.15.0-1+b1_arm64.deb ... Unpacking libfido2-1:arm64 (1.15.0-1+b1) ... Selecting previously unselected package openssh-client. Preparing to unpack .../017-openssh-client_1%3a9.9p1-3_arm64.deb ... Unpacking openssh-client (1:9.9p1-3) ... Selecting previously unselected package m4. Preparing to unpack .../018-m4_1.4.19-4_arm64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../019-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../020-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../021-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../022-autopoint_0.22.5-2_all.deb ... Unpacking autopoint (0.22.5-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../023-libdebhelper-perl_13.20_all.deb ... Unpacking libdebhelper-perl (13.20) ... Selecting previously unselected package libtool. Preparing to unpack .../024-libtool_2.4.7-8_all.deb ... Unpacking libtool (2.4.7-8) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../025-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../026-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 .../027-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../028-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../029-libelf1t64_0.192-4_arm64.deb ... Unpacking libelf1t64:arm64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../030-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../031-libicu72_72.1-5+b1_arm64.deb ... Unpacking libicu72:arm64 (72.1-5+b1) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../032-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 .../033-gettext_0.22.5-2_arm64.deb ... Unpacking gettext (0.22.5-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../034-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 .../035-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../036-debhelper_13.20_all.deb ... Unpacking debhelper (13.20) ... Selecting previously unselected package xml-core. Preparing to unpack .../037-xml-core_0.19_all.deb ... Unpacking xml-core (0.19) ... 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Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/2081948/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/2081948/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/murasaki-1.68.6/ && 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 > ../murasaki_1.68.6-14_source.changes dpkg-buildpackage: info: source package murasaki dpkg-buildpackage: info: source version 1.68.6-14 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 dh_auto_clean make -j12 clean make[1]: Entering directory '/build/reproducible-path/murasaki-1.68.6' rm -rf *.o *~ .*~ core make -C src clean make[2]: Entering directory '/build/reproducible-path/murasaki-1.68.6/src' rm -rf *.o *~ .*~ core ../murasaki ../cgr-image ../cgr-compare ../cgr-random ../cgr-sample ../testeco ../align-compare ../align-or ../geneparse ../align-and ../align-best ../align-coverage ../getsegments ../mbfa make[2]: Leaving directory '/build/reproducible-path/murasaki-1.68.6/src' make[1]: Leaving directory '/build/reproducible-path/murasaki-1.68.6' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/murasaki-1.68.6' dh_auto_build -- USE_MPI=YES make -j12 "INSTALL=install --strip-program=true" USE_MPI=YES make[2]: Entering directory '/build/reproducible-path/murasaki-1.68.6' make -C src all make[3]: Entering directory '/build/reproducible-path/murasaki-1.68.6/src' mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c murasaki.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c timing.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c dinkymath.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c sequence.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c msethash.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c options.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c ecohash.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c ecolist.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c murasaki_mpi.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c arrayhash.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c seqread.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c scoring.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c openhash.cc In file included from ecolist.h:23, from ecolist.cc:20: sequence.h:444:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 444 | struct ltRegion : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_tree.h:65, from /usr/include/c++/14/set:62, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ecolist.cc:467:26: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 467 | struct less_map : public binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ecolist.h:23, from ecohash.h:29, from ecohash.cc:26: sequence.h:444:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 444 | struct ltRegion : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_tree.h:65, from /usr/include/c++/14/set:62, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from options.h:28, from options.cc:26: sequence.h:444:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 444 | struct ltRegion : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_tree.h:65, from /usr/include/c++/14/set:62, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from murasaki.h:24, from sequence.cc:28: sequence.h:444:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 444 | struct ltRegion : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_tree.h:65, from /usr/include/c++/14/set:62, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c genopts.cc sequence.cc: In destructor 'Sequence::~Sequence()': sequence.cc:377:9: warning: 'throw' will always call 'terminate' [-Wterminate] 377 | throw MurasakiException("Couldn't mark System V IPC shared memory region for deletion for sequence "+name+strerror(errno)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sequence.cc:377:9: note: in C++11 destructors default to 'noexcept' sequence.cc: In member function 'void BitSequence::loadBinary(const SequenceBinary&)': sequence.cc:1113:9: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'ShmVector >::val_type' {aka 'struct std::pair'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1113 | memcpy(&matchRegions.front(),binseq.regions[srcMatchRegionsIdx],sizeof(SequenceBinary::Region)*binseq.regionSizes[srcMatchRegionsIdx]); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_algobase.h:64, from /usr/include/c++/14/bits/stl_tree.h:63: /usr/include/c++/14/bits/stl_pair.h:284:12: note: 'ShmVector >::val_type' {aka 'struct std::pair'} declared here 284 | struct pair | ^~~~ sequence.cc:1114:9: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'ShmVector >::val_type' {aka 'struct std::pair'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1114 | memcpy(&subSeqs.front(),binseq.regions[0],sizeof(SequenceBinary::Region)*binseq.regionSizes[0]); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_pair.h:284:12: note: 'ShmVector >::val_type' {aka 'struct std::pair'} declared here 284 | struct pair | ^~~~ sequence.cc: In destructor 'BitSequence::~BitSequence()': sequence.cc:1394:9: warning: 'throw' will always call 'terminate' [-Wterminate] 1394 | throw MurasakiException("Couldn't detach System V shared memory region for "+(seq ? seq->filename:string("(anon)"))+strerror(errno)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sequence.cc:1394:9: note: in C++11 destructors default to 'noexcept' In file included from murasaki.h:24, from murasaki_mpi.cc:33: sequence.h:444:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 444 | struct ltRegion : 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 murasaki_mpi.cc:30: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from msethash.cc:25: sequence.h:444:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 444 | struct ltRegion : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_tree.h:65, from /usr/include/c++/14/set:62, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ murasaki_mpi.cc:89:29: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 89 | struct lt_mpi_worldMemory : binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ murasaki_mpi.cc:95:29: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 95 | struct gt_mpi_worldMemory : binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ murasaki_mpi.cc: In function 'void mpi_hasher_client_mode(BitSequence*)': murasaki_mpi.cc:561:9: warning: variable 'send_done' set but not used [-Wunused-but-set-variable] 561 | int send_done; | ^~~~~~~~~ In file included from murasaki.h:24, from arrayhash.cc:28: sequence.h:444:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 444 | struct ltRegion : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_tree.h:65, from /usr/include/c++/14/set:62, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ sequence.cc: In member function 'std::pair IntervalSet::entropy() const': sequence.cc:3332:10: warning: variable 'shortest' set but not used [-Wunused-but-set-variable] 3332 | SeqPos shortest=0,shortlen=length(spaces[0]); | ^~~~~~~~ In file included from murasaki.h:24, from dinkymath.cc:27: sequence.h:444:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 444 | struct ltRegion : 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 dinkymath.h:24, from dinkymath.cc:26: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ dinkymath.cc: In function 'std::string littleEndianStr(unsigned int, int)': dinkymath.cc:40:7: warning: variable 'last' set but not used [-Wunused-but-set-variable] 40 | int last=0; | ^~~~ dinkymath.cc: In function 'std::string littleEndianPat(unsigned int, int)': dinkymath.cc:53:7: warning: variable 'last' set but not used [-Wunused-but-set-variable] 53 | int last=0; | ^~~~ In file included from sequence.cc:41: hashing.h: In instantiation of 'SBox::SBox(int) [with T = short unsigned int]': sequence.cc:162:29: required from here 162 | sbox=new SBoxT(hash_bits); | ^ hashing.h:56:21: warning: 'void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = short unsigned int*]' is deprecated: use 'std::shuffle' instead [-Wdeprecated-declarations] 56 | random_shuffle(boxes[b],boxes[b]+boxsize); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/algorithm:61, from /usr/include/boost/regex/v5/regex_workaround.hpp:23, from /usr/include/boost/regex/v5/regex.hpp:29, from /usr/include/boost/regex.hpp:34, from seqread.h:33, from binseq.hh:31, from sequence.h:32: /usr/include/c++/14/bits/stl_algo.h:4491:5: note: declared here 4491 | random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last) | ^~~~~~~~~~~~~~ In file included from murasaki.h:24, from murasaki.cc:37: sequence.h:444:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 444 | struct ltRegion : 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 murasaki.cc:29: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from sequence.h:44: shmvector.hh: In instantiation of 'void ShmVector::shmRealloc(size_t) [with T = std::pair; size_t = long unsigned int]': shmvector.hh:282:5: required from 'void ShmVector::resize(size_t) [with T = std::pair; size_t = long unsigned int]' 282 | shmRealloc(c); | ^~~~~~~~~~ sequence.cc:1110:17: required from here 1110 | subSeqs.resize(binseq.regionSizes[0]); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ shmvector.hh:225:13: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'struct std::pair' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 225 | memcpy(_data,old_data,(oldByteCapacity<_byteCapacity ? oldByteCapacity:_byteCapacity)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_pair.h:284:12: note: 'struct std::pair' declared here 284 | struct pair | ^~~~ In file included from murasaki.h:24, from scoring.cc:27: sequence.h:444:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 444 | struct ltRegion : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_tree.h:65, from /usr/include/c++/14/set:62, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ seqread.cc: In member function 'void SequenceByteReader::addRedirect(boost::cmatch)': seqread.cc:264:38: warning: 'boost::filesystem::path boost::filesystem::path::branch_path() const' is deprecated: Use path::parent_path() instead [-Wdeprecated-declarations] 264 | stitchPath=stitchfile.branch_path(); | ~~~~~~~~~~~~~~~~~~~~~~^~ In file included from seqread.cc:35: /usr/include/boost/filesystem/path.hpp:1129:10: note: declared here 1129 | path branch_path() const { return parent_path(); } | ^~~~~~~~~~~ mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c binseq.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c cgr-image.cc In file included from ecolist.h:23, from openhash.h:29, from openhash.cc:26: sequence.h:444:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 444 | struct ltRegion : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_tree.h:65, from /usr/include/c++/14/set:62, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c cgr.cc murasaki.cc: In function 'void procLocs(LocList&, std::__cxx11::list&, int, int)': murasaki.cc:1008:8: warning: variable 'revZero' set but not used [-Wunused-but-set-variable] 1008 | bool revZero=false; | ^~~~~~~ murasaki.cc: In function 'bool convertPattern(std::string&)': murasaki.cc:1287:17: warning: 'void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' is deprecated: use 'std::shuffle' instead [-Wdeprecated-declarations] 1287 | random_shuffle(randomStr.begin(),randomStr.end()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/algorithm:61, from /usr/include/boost/regex/v5/regex_workaround.hpp:23, from /usr/include/boost/regex/v5/regex.hpp:29, from /usr/include/boost/regex.hpp:34, from seqread.h:33, from binseq.hh:31, from sequence.h:32: /usr/include/c++/14/bits/stl_algo.h:4491:5: note: declared here 4491 | random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last) | ^~~~~~~~~~~~~~ mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c cgr-compare.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c cgr-random.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c cgr-sample.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c testeco.cc cgr.cc: In member function 'void Cgr::merge(Cgr&)': cgr.cc:140:7: warning: variable 'redist' set but not used [-Wunused-but-set-variable] 140 | int redist=(unsigned long)(rez*rez)<=seedcount; | ^~~~~~ cgr.cc: In member function 'bool Cgr::savePNG(std::string)': cgr.cc:288:7: warning: variable 'res' set but not used [-Wunused-but-set-variable] 288 | int res; | ^~~ cgr.cc: In member function 'int PgmBuffer::loadPGM(std::string)': cgr.cc:435:7: warning: variable 'wordwidth' set but not used [-Wunused-but-set-variable] 435 | int wordwidth=1; | ^~~~~~~~~ binseq.cc: In member function 'bool SequenceBinary::save(std::string)': binseq.cc:70:28: warning: catching polymorphic type 'class std::ios_base::failure' by value [-Wcatch-value=] 70 | }catch(ofstream::failure e){ | ^ binseq.cc: In member function 'void SequenceBinary::fillCopyVectors()': binseq.cc:158:9: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type '__gnu_cxx::__alloc_traits >, std::pair >::value_type' {aka 'struct std::pair'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 158 | memcpy(&subSeqs.front(),regions[0],regionSizes[0]*sizeof(Region)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_algobase.h:64, from /usr/include/c++/14/string:51, 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 seqread.h:30, from binseq.hh:31, from binseq.cc:21: /usr/include/c++/14/bits/stl_pair.h:284:12: note: '__gnu_cxx::__alloc_traits >, std::pair >::value_type' {aka 'struct std::pair'} declared here 284 | struct pair | ^~~~ binseq.cc:160:9: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type '__gnu_cxx::__alloc_traits >, std::pair >::value_type' {aka 'struct std::pair'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 160 | memcpy(&readableRegions.front(),regions[1],regionSizes[1]*sizeof(Region)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_pair.h:284:12: note: '__gnu_cxx::__alloc_traits >, std::pair >::value_type' {aka 'struct std::pair'} declared here 284 | struct pair | ^~~~ binseq.cc:162:9: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type '__gnu_cxx::__alloc_traits >, std::pair >::value_type' {aka 'struct std::pair'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 162 | memcpy(&unmaskedRegions.front(),regions[2],regionSizes[2]*sizeof(Region)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_pair.h:284:12: note: '__gnu_cxx::__alloc_traits >, std::pair >::value_type' {aka 'struct std::pair'} declared here 284 | struct pair | ^~~~ mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c align-compare.cc murasaki_mpi.cc: In function 'void mpi_types_init()': murasaki_mpi.cc:107:18: warning: 'msg' may be used uninitialized [-Wmaybe-uninitialized] 107 | MPI_Get_address(&msg.key,disp); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ In file included from murasaki_mpi.cc:29: /usr/lib/aarch64-linux-gnu/openmpi/include/mpi.h:1677:20: note: by argument 1 of type 'const void*' to 'int MPI_Get_address(const void*, MPI_Aint*)' declared here 1677 | OMPI_DECLSPEC int MPI_Get_address(const void *location, MPI_Aint *address); | ^~~~~~~~~~~~~~~ murasaki_mpi.cc:102:19: note: 'msg' declared here 102 | MPI_HashMessage msg; | ^~~ cgr.cc: In member function 'std::pair Cgr::sampleHighLow(double, double)': cgr.cc:339:10: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 339 | delete alt; | ^~~ cgr.cc:330:24: note: returned from 'void* operator new [](std::size_t)' 330 | pix *alt=new pix[size]; | ^ cgr.cc: In member function 'std::pair Cgr::sampleHighLow(int, int)': cgr.cc:354:10: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 354 | delete alt; | ^~~ cgr.cc:345:24: note: returned from 'void* operator new [](std::size_t)' 345 | pix *alt=new pix[size]; | ^ cgr.cc: In member function 'std::pair Cgr::findNiceRange()': cgr.cc:395:10: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 395 | delete alt; | ^~~ cgr.cc:376:24: note: returned from 'void* operator new [](std::size_t)' 376 | pix *alt=new pix[size]; | ^ mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c alignments.cc cgr-sample.cc: In function 'int main(int, char**)': cgr-sample.cc:54:8: warning: variable 'repeatmask' set but not used [-Wunused-but-set-variable] 54 | bool repeatmask=false,save=false; | ^~~~~~~~~~ mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c align-or.cc cgr.cc: In member function 'int PgmBuffer::loadBinaryPGM(std::string)': cgr.cc:557:31: warning: 'width' may be used uninitialized [-Wmaybe-uninitialized] 557 | if(data.size()<(uint)(height*width)) | ~~~~~~~^~~~~~~ cgr.cc:493:7: note: 'width' was declared here 493 | int width,height; | ^~~~~ cgr.cc:557:31: warning: 'height' may be used uninitialized [-Wmaybe-uninitialized] 557 | if(data.size()<(uint)(height*width)) | ~~~~~~~^~~~~~~ cgr.cc:493:13: note: 'height' was declared here 493 | int width,height; | ^~~~~~ In file included from ecolist.h:23, from testeco.cc:20: sequence.h:444:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 444 | struct ltRegion : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_tree.h:65, from /usr/include/c++/14/set:62, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ cgr.cc: In member function 'int PgmBuffer::loadPGM(std::string)': cgr.cc:485:31: warning: 'width' may be used uninitialized [-Wmaybe-uninitialized] 485 | if(data.size()<(uint)(height*width)) | ~~~~~~~^~~~~~~ cgr.cc:426:7: note: 'width' was declared here 426 | int width,height; | ^~~~~ cgr.cc:485:31: warning: 'height' may be used uninitialized [-Wmaybe-uninitialized] 485 | if(data.size()<(uint)(height*width)) | ~~~~~~~^~~~~~~ cgr.cc:426:13: note: 'height' was declared here 426 | int width,height; | ^~~~~~ mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c geneparse.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c align-and.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c align-best.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c align-coverage.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c getsegments.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c mbfa.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../cgr-compare cgr-compare.o cgr.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../cgr-random cgr-random.o cgr.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../testeco testeco.o ecolist.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now align-coverage.cc: In function 'int main(int, char**)': align-coverage.cc:148:10: warning: variable 'seqStats' set but not used [-Wunused-but-set-variable] 148 | bool seqStats=true; | ^~~~~~~~ getsegments.cc: In function 'size_t getSubSeqs(SequenceFileReader&, std::__cxx11::list > >&, std::string)': getsegments.cc:153:29: warning: catching polymorphic type 'class boost::bad_lexical_cast' by value [-Wcatch-value=] 153 | }catch(bad_lexical_cast e){ | ^ mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../murasaki murasaki.o timing.o dinkymath.o sequence.o msethash.o options.o ecohash.o ecolist.o murasaki_mpi.o arrayhash.o seqread.o scoring.o openhash.o genopts.o binseq.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../cgr-image cgr-image.o cgr.o dinkymath.o timing.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../cgr-sample cgr.o cgr-sample.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../geneparse geneparse.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../getsegments getsegments.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../mbfa mbfa.o dinkymath.o timing.o seqread.o binseq.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../align-compare align-compare.o dinkymath.o alignments.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../align-or align-or.o alignments.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../align-and align-and.o alignments.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../align-best align-best.o alignments.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../align-coverage align-coverage.o alignments.o dinkymath.o timing.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/build/reproducible-path/murasaki-1.68.6/src' make[2]: Leaving directory '/build/reproducible-path/murasaki-1.68.6' for bin in geneparse mbfa murasaki cgr-* testeco align-* ; do \ mv ${bin} ${bin}-mpi ; \ done make clean make[2]: Entering directory '/build/reproducible-path/murasaki-1.68.6' rm -rf *.o *~ .*~ core make -C src clean make[3]: Entering directory '/build/reproducible-path/murasaki-1.68.6/src' rm -rf *.o *~ .*~ core ../murasaki ../cgr-image ../cgr-compare ../cgr-random ../cgr-sample ../testeco ../align-compare ../align-or ../geneparse ../align-and ../align-best ../align-coverage ../getsegments ../mbfa make[3]: Leaving directory '/build/reproducible-path/murasaki-1.68.6/src' make[2]: Leaving directory '/build/reproducible-path/murasaki-1.68.6' dh_auto_build -- USE_MPI=NO make -j12 "INSTALL=install --strip-program=true" USE_MPI=NO make[2]: Entering directory '/build/reproducible-path/murasaki-1.68.6' make -C src all make[3]: Entering directory '/build/reproducible-path/murasaki-1.68.6/src' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c murasaki.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c timing.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c dinkymath.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c sequence.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c msethash.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c options.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c ecohash.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c ecolist.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c murasaki_mpi.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c arrayhash.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c seqread.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c scoring.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c openhash.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c genopts.cc In file included from murasaki.h:24, from dinkymath.cc:27: sequence.h:444:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 444 | struct ltRegion : 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 dinkymath.h:24, from dinkymath.cc:26: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ dinkymath.cc: In function 'std::string littleEndianStr(unsigned int, int)': dinkymath.cc:40:7: warning: variable 'last' set but not used [-Wunused-but-set-variable] 40 | int last=0; | ^~~~ dinkymath.cc: In function 'std::string littleEndianPat(unsigned int, int)': dinkymath.cc:53:7: warning: variable 'last' set but not used [-Wunused-but-set-variable] 53 | int last=0; | ^~~~ In file included from ecolist.h:23, from ecohash.h:29, from ecohash.cc:26: sequence.h:444:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 444 | struct ltRegion : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_tree.h:65, from /usr/include/c++/14/set:62, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from murasaki.h:24, from sequence.cc:28: sequence.h:444:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 444 | struct ltRegion : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_tree.h:65, from /usr/include/c++/14/set:62, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from murasaki.h:24, from murasaki.cc:37: sequence.h:444:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 444 | struct ltRegion : 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 murasaki.cc:29: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c binseq.cc In file included from murasaki.h:24, from arrayhash.cc:28: sequence.h:444:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 444 | struct ltRegion : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_tree.h:65, from /usr/include/c++/14/set:62, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from options.h:28, from options.cc:26: sequence.h:444:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 444 | struct ltRegion : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_tree.h:65, from /usr/include/c++/14/set:62, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ sequence.cc: In member function 'void BitSequence::loadBinary(const SequenceBinary&)': sequence.cc:1113:9: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'ShmVector >::val_type' {aka 'struct std::pair'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1113 | memcpy(&matchRegions.front(),binseq.regions[srcMatchRegionsIdx],sizeof(SequenceBinary::Region)*binseq.regionSizes[srcMatchRegionsIdx]); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_algobase.h:64, from /usr/include/c++/14/bits/stl_tree.h:63: /usr/include/c++/14/bits/stl_pair.h:284:12: note: 'ShmVector >::val_type' {aka 'struct std::pair'} declared here 284 | struct pair | ^~~~ sequence.cc:1114:9: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'ShmVector >::val_type' {aka 'struct std::pair'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1114 | memcpy(&subSeqs.front(),binseq.regions[0],sizeof(SequenceBinary::Region)*binseq.regionSizes[0]); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_pair.h:284:12: note: 'ShmVector >::val_type' {aka 'struct std::pair'} declared here 284 | struct pair | ^~~~ In file included from ecolist.h:23, from openhash.h:29, from openhash.cc:26: sequence.h:444:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 444 | struct ltRegion : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_tree.h:65, from /usr/include/c++/14/set:62, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ sequence.cc: In member function 'std::pair IntervalSet::entropy() const': sequence.cc:3332:10: warning: variable 'shortest' set but not used [-Wunused-but-set-variable] 3332 | SeqPos shortest=0,shortlen=length(spaces[0]); | ^~~~~~~~ In file included from sequence.cc:41: hashing.h: In instantiation of 'SBox::SBox(int) [with T = short unsigned int]': sequence.cc:162:29: required from here 162 | sbox=new SBoxT(hash_bits); | ^ hashing.h:56:21: warning: 'void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = short unsigned int*]' is deprecated: use 'std::shuffle' instead [-Wdeprecated-declarations] 56 | random_shuffle(boxes[b],boxes[b]+boxsize); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/algorithm:61, from /usr/include/boost/regex/v5/regex_workaround.hpp:23, from /usr/include/boost/regex/v5/regex.hpp:29, from /usr/include/boost/regex.hpp:34, from seqread.h:33, from binseq.hh:31, from sequence.h:32: /usr/include/c++/14/bits/stl_algo.h:4491:5: note: declared here 4491 | random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last) | ^~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c cgr-image.cc murasaki.cc: In function 'void procLocs(LocList&, std::__cxx11::list&, int, int)': murasaki.cc:1008:8: warning: variable 'revZero' set but not used [-Wunused-but-set-variable] 1008 | bool revZero=false; | ^~~~~~~ murasaki.cc: In function 'bool convertPattern(std::string&)': murasaki.cc:1287:17: warning: 'void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' is deprecated: use 'std::shuffle' instead [-Wdeprecated-declarations] 1287 | random_shuffle(randomStr.begin(),randomStr.end()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/algorithm:61, from /usr/include/boost/regex/v5/regex_workaround.hpp:23, from /usr/include/boost/regex/v5/regex.hpp:29, from /usr/include/boost/regex.hpp:34, from seqread.h:33, from binseq.hh:31, from sequence.h:32: /usr/include/c++/14/bits/stl_algo.h:4491:5: note: declared here 4491 | random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last) | ^~~~~~~~~~~~~~ In file included from murasaki.h:24, from scoring.cc:27: sequence.h:444:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 444 | struct ltRegion : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_tree.h:65, from /usr/include/c++/14/set:62, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ecolist.h:23, from ecolist.cc:20: sequence.h:444:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 444 | struct ltRegion : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_tree.h:65, from /usr/include/c++/14/set:62, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from sequence.h:44: shmvector.hh: In instantiation of 'void ShmVector::shmRealloc(size_t) [with T = std::pair; size_t = long unsigned int]': shmvector.hh:282:5: required from 'void ShmVector::resize(size_t) [with T = std::pair; size_t = long unsigned int]' 282 | shmRealloc(c); | ^~~~~~~~~~ sequence.cc:1110:17: required from here 1110 | subSeqs.resize(binseq.regionSizes[0]); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ shmvector.hh:225:13: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'struct std::pair' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 225 | memcpy(_data,old_data,(oldByteCapacity<_byteCapacity ? oldByteCapacity:_byteCapacity)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_pair.h:284:12: note: 'struct std::pair' declared here 284 | struct pair | ^~~~ ecolist.cc:467:26: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 467 | struct less_map : public binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c cgr.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c cgr-compare.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c cgr-random.cc In file included from msethash.cc:25: sequence.h:444:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 444 | struct ltRegion : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_tree.h:65, from /usr/include/c++/14/set:62, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c cgr-sample.cc cgr.cc: In member function 'void Cgr::merge(Cgr&)': cgr.cc:140:7: warning: variable 'redist' set but not used [-Wunused-but-set-variable] 140 | int redist=(unsigned long)(rez*rez)<=seedcount; | ^~~~~~ cgr.cc: In member function 'bool Cgr::savePNG(std::string)': cgr.cc:288:7: warning: variable 'res' set but not used [-Wunused-but-set-variable] 288 | int res; | ^~~ cgr.cc: In member function 'int PgmBuffer::loadPGM(std::string)': cgr.cc:435:7: warning: variable 'wordwidth' set but not used [-Wunused-but-set-variable] 435 | int wordwidth=1; | ^~~~~~~~~ binseq.cc: In member function 'bool SequenceBinary::save(std::string)': binseq.cc:70:28: warning: catching polymorphic type 'class std::ios_base::failure' by value [-Wcatch-value=] 70 | }catch(ofstream::failure e){ | ^ binseq.cc: In member function 'void SequenceBinary::fillCopyVectors()': binseq.cc:158:9: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type '__gnu_cxx::__alloc_traits >, std::pair >::value_type' {aka 'struct std::pair'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 158 | memcpy(&subSeqs.front(),regions[0],regionSizes[0]*sizeof(Region)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_algobase.h:64, from /usr/include/c++/14/string:51, 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 seqread.h:30, from binseq.hh:31, from binseq.cc:21: /usr/include/c++/14/bits/stl_pair.h:284:12: note: '__gnu_cxx::__alloc_traits >, std::pair >::value_type' {aka 'struct std::pair'} declared here 284 | struct pair | ^~~~ binseq.cc:160:9: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type '__gnu_cxx::__alloc_traits >, std::pair >::value_type' {aka 'struct std::pair'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 160 | memcpy(&readableRegions.front(),regions[1],regionSizes[1]*sizeof(Region)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_pair.h:284:12: note: '__gnu_cxx::__alloc_traits >, std::pair >::value_type' {aka 'struct std::pair'} declared here 284 | struct pair | ^~~~ binseq.cc:162:9: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type '__gnu_cxx::__alloc_traits >, std::pair >::value_type' {aka 'struct std::pair'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 162 | memcpy(&unmaskedRegions.front(),regions[2],regionSizes[2]*sizeof(Region)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_pair.h:284:12: note: '__gnu_cxx::__alloc_traits >, std::pair >::value_type' {aka 'struct std::pair'} declared here 284 | struct pair | ^~~~ seqread.cc: In member function 'void SequenceByteReader::addRedirect(boost::cmatch)': seqread.cc:264:38: warning: 'boost::filesystem::path boost::filesystem::path::branch_path() const' is deprecated: Use path::parent_path() instead [-Wdeprecated-declarations] 264 | stitchPath=stitchfile.branch_path(); | ~~~~~~~~~~~~~~~~~~~~~~^~ In file included from seqread.cc:35: /usr/include/boost/filesystem/path.hpp:1129:10: note: declared here 1129 | path branch_path() const { return parent_path(); } | ^~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c testeco.cc cgr.cc: In member function 'std::pair Cgr::sampleHighLow(double, double)': cgr.cc:339:10: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 339 | delete alt; | ^~~ cgr.cc:330:24: note: returned from 'void* operator new [](std::size_t)' 330 | pix *alt=new pix[size]; | ^ cgr.cc: In member function 'std::pair Cgr::sampleHighLow(int, int)': cgr.cc:354:10: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 354 | delete alt; | ^~~ cgr.cc:345:24: note: returned from 'void* operator new [](std::size_t)' 345 | pix *alt=new pix[size]; | ^ cgr.cc: In member function 'std::pair Cgr::findNiceRange()': cgr.cc:395:10: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 395 | delete alt; | ^~~ cgr.cc:376:24: note: returned from 'void* operator new [](std::size_t)' 376 | pix *alt=new pix[size]; | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c align-compare.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c alignments.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c align-or.cc cgr.cc: In member function 'int PgmBuffer::loadBinaryPGM(std::string)': cgr.cc:557:31: warning: 'width' may be used uninitialized [-Wmaybe-uninitialized] 557 | if(data.size()<(uint)(height*width)) | ~~~~~~~^~~~~~~ cgr.cc:493:7: note: 'width' was declared here 493 | int width,height; | ^~~~~ cgr.cc:557:31: warning: 'height' may be used uninitialized [-Wmaybe-uninitialized] 557 | if(data.size()<(uint)(height*width)) | ~~~~~~~^~~~~~~ cgr.cc:493:13: note: 'height' was declared here 493 | int width,height; | ^~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c geneparse.cc cgr.cc: In member function 'int PgmBuffer::loadPGM(std::string)': cgr.cc:485:31: warning: 'width' may be used uninitialized [-Wmaybe-uninitialized] 485 | if(data.size()<(uint)(height*width)) | ~~~~~~~^~~~~~~ cgr.cc:426:7: note: 'width' was declared here 426 | int width,height; | ^~~~~ cgr.cc:485:31: warning: 'height' may be used uninitialized [-Wmaybe-uninitialized] 485 | if(data.size()<(uint)(height*width)) | ~~~~~~~^~~~~~~ cgr.cc:426:13: note: 'height' was declared here 426 | int width,height; | ^~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c align-and.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c align-best.cc In file included from ecolist.h:23, from testeco.cc:20: sequence.h:444:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 444 | struct ltRegion : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_tree.h:65, from /usr/include/c++/14/set:62, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ cgr-sample.cc: In function 'int main(int, char**)': cgr-sample.cc:54:8: warning: variable 'repeatmask' set but not used [-Wunused-but-set-variable] 54 | bool repeatmask=false,save=false; | ^~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c align-coverage.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c getsegments.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c mbfa.cc align-coverage.cc: In function 'int main(int, char**)': align-coverage.cc:148:10: warning: variable 'seqStats' set but not used [-Wunused-but-set-variable] 148 | bool seqStats=true; | ^~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -o ../cgr-compare cgr-compare.o cgr.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -o ../cgr-random cgr-random.o cgr.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -o ../testeco testeco.o ecolist.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now getsegments.cc: In function 'size_t getSubSeqs(SequenceFileReader&, std::__cxx11::list > >&, std::string)': getsegments.cc:153:29: warning: catching polymorphic type 'class boost::bad_lexical_cast' by value [-Wcatch-value=] 153 | }catch(bad_lexical_cast e){ | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -o ../murasaki murasaki.o timing.o dinkymath.o sequence.o msethash.o options.o ecohash.o ecolist.o murasaki_mpi.o arrayhash.o seqread.o scoring.o openhash.o genopts.o binseq.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -o ../cgr-image cgr-image.o cgr.o dinkymath.o timing.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -o ../cgr-sample cgr.o cgr-sample.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -o ../geneparse geneparse.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -o ../getsegments getsegments.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -o ../mbfa mbfa.o dinkymath.o timing.o seqread.o binseq.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -o ../align-compare align-compare.o dinkymath.o alignments.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -o ../align-or align-or.o alignments.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -o ../align-and align-and.o alignments.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -o ../align-best align-best.o alignments.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -o ../align-coverage align-coverage.o alignments.o dinkymath.o timing.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/build/reproducible-path/murasaki-1.68.6/src' make[2]: Leaving directory '/build/reproducible-path/murasaki-1.68.6' make[1]: Leaving directory '/build/reproducible-path/murasaki-1.68.6' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install debian/rules override_dh_install-arch make[1]: Entering directory '/build/reproducible-path/murasaki-1.68.6' dh_install -a # using wildcards in install files is practical but it duplicates some files find debian/murasaki/usr -name "*-mpi" -delete make[1]: Leaving directory '/build/reproducible-path/murasaki-1.68.6' dh_install -Nmurasaki -Nmurasaki-mpi dh_installdocs dh_installchangelogs debian/rules override_dh_installman-arch make[1]: Entering directory '/build/reproducible-path/murasaki-1.68.6' dh_installman -a mkdir -p debian/murasaki-mpi/usr/share/man/man1 for man in debian/murasaki/usr/share/man/man1/*.1 ; do \ cp -a ${man} debian/murasaki-mpi/usr/share/man/man1/`basename ${man} .1`-mpi.1 ; \ done make[1]: Leaving directory '/build/reproducible-path/murasaki-1.68.6' debian/rules override_dh_installman-indep make[1]: Entering directory '/build/reproducible-path/murasaki-1.68.6' dh_installman -i # create manpages for PL files mkdir -p debian/murasaki-common/usr/share/man/man1 for pscript in debian/murasaki-common/usr/lib/debian-med/bin/* ; do \ pod2man ${pscript} > debian/murasaki-common/usr/share/man/man1/`basename ${pscript}`.1 ; \ done pod2man: unable to format debian/murasaki-common/usr/lib/debian-med/bin/anchors2maf.pl pod2man: unable to format debian/murasaki-common/usr/lib/debian-med/bin/anchors2osfinder.pl pod2man: unable to format debian/murasaki-common/usr/lib/debian-med/bin/antisense.pl debian/murasaki-common/usr/lib/debian-med/bin/chromostitch.pl around line 134: '=item' outside of any '=over' debian/murasaki-common/usr/lib/debian-med/bin/chromostitch.pl around line 141: You forgot a '=back' before '=head1' POD document had syntax errors at /usr/bin/pod2man line 69. pod2man: unable to format debian/murasaki-common/usr/lib/debian-med/bin/dna2binary.pl pod2man: unable to format debian/murasaki-common/usr/lib/debian-med/bin/dnashuffle.pl pod2man: unable to format debian/murasaki-common/usr/lib/debian-med/bin/geneparse.pl debian/murasaki-common/usr/lib/debian-med/bin/getcds.pl around line 646: '=item' outside of any '=over' debian/murasaki-common/usr/lib/debian-med/bin/getcds.pl around line 646: =over without closing =back POD document had syntax errors at /usr/bin/pod2man line 69. pod2man: unable to format debian/murasaki-common/usr/lib/debian-med/bin/humantime.pl pod2man: unable to format debian/murasaki-common/usr/lib/debian-med/bin/osfinder2anchors.pl pod2man: unable to format debian/murasaki-common/usr/lib/debian-med/bin/randpat.pl find debian/murasaki-common/usr/share/man/man1 -empty -delete make[1]: Leaving directory '/build/reproducible-path/murasaki-1.68.6' dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress debian/rules override_dh_fixperms-indep make[1]: Entering directory '/build/reproducible-path/murasaki-1.68.6' dh_fixperms -i chmod a+x debian/murasaki-common/usr/share/perl5/murasaki/config.pl make[1]: Leaving directory '/build/reproducible-path/murasaki-1.68.6' dh_fixperms -Nmurasaki-common dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dpkg-gencontrol: warning: Depends field of package murasaki-common: substitution variable ${misc:perl} used, but is not defined dpkg-gencontrol: warning: package murasaki-mpi: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package murasaki-common: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package murasaki-mpi: substitution variable ${perl:Depends} unused, but is defined dh_md5sums dh_builddeb dpkg-deb: building package 'murasaki' in '../murasaki_1.68.6-14_arm64.deb'. dpkg-deb: building package 'murasaki-mpi-dbgsym' in '../murasaki-mpi-dbgsym_1.68.6-14_arm64.deb'. dpkg-deb: building package 'murasaki-mpi' in '../murasaki-mpi_1.68.6-14_arm64.deb'. dpkg-deb: building package 'murasaki-dbgsym' in '../murasaki-dbgsym_1.68.6-14_arm64.deb'. dpkg-deb: building package 'murasaki-common' in '../murasaki-common_1.68.6-14_all.deb'. dpkg-genbuildinfo --build=binary -O../murasaki_1.68.6-14_arm64.buildinfo dpkg-genchanges --build=binary -O../murasaki_1.68.6-14_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/2081948/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/2081948/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/2081948 and its subdirectories I: Current time: Tue Jan 6 00:03:31 +14 2026 I: pbuilder-time-stamp: 1767607411