I: pbuilder: network access will be disabled during build
I: Current time: Fri Dec  6 21:14:57 +14 2024
I: pbuilder-time-stamp: 1733469297
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz]
I: copying local configuration
W: --override-config is not set; not updating apt.conf Read the manpage for details.
I: mounting /proc filesystem
I: mounting /sys filesystem
I: creating /{dev,run}/shm
I: mounting /dev/pts filesystem
I: redirecting /dev/ptmx to /dev/pts/ptmx
I: policy-rc.d already exists
I: Copying source file
I: copying [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/23325/tmp/hooks/D01_modify_environment starting
debug: Running on virt64z.
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 Dec  6 07:15 /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/23325/tmp/hooks/D01_modify_environment finished
I: user script /srv/workspace/pbuilder/23325/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]="arm-unknown-linux-gnueabihf")
  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=armhf
  DEBIAN_FRONTEND=noninteractive
  DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 '
  DIRSTACK=()
  DISTRIBUTION=trixie
  EUID=0
  FUNCNAME=([0]="Echo" [1]="main")
  GROUPS=()
  HOME=/root
  HOSTNAME=i-capture-the-hostname
  HOSTTYPE=arm
  HOST_ARCH=armhf
  IFS=' 	
  '
  INVOCATION_ID=01f69b391fba46658e27697cf1eee058
  LANG=C
  LANGUAGE=it_CH:it
  LC_ALL=C
  MACHTYPE=arm-unknown-linux-gnueabihf
  MAIL=/var/mail/root
  OPTERR=1
  OPTIND=1
  OSTYPE=linux-gnueabihf
  PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path
  PBCURRENTCOMMANDLINEOPERATION=build
  PBUILDER_OPERATION=build
  PBUILDER_PKGDATADIR=/usr/share/pbuilder
  PBUILDER_PKGLIBDIR=/usr/lib/pbuilder
  PBUILDER_SYSCONFDIR=/etc
  PIPESTATUS=([0]="0")
  POSIXLY_CORRECT=y
  PPID=23325
  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.6StvvwLx/pbuilderrc_Lzlb --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.6StvvwLx/b2 --logfile b2/build.log murasaki_1.68.6-14.dsc'
  SUDO_GID=110
  SUDO_UID=103
  SUDO_USER=jenkins
  TERM=unknown
  TZ=/usr/share/zoneinfo/Etc/GMT-14
  UID=0
  USER=root
  _='I: set'
  http_proxy=http://10.0.0.15:3142/
I: uname -a
  Linux i-capture-the-hostname 6.1.0-28-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 14:40 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/23325/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: armhf
Maintainer: Debian Pbuilder Team <pbuilder-maint@lists.alioth.debian.org>
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 ... 19683 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} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} gfortran-14{a} gfortran-14-arm-linux-gnueabihf{a} groff-base{a} hwloc-nox{a} icu-devtools{a} intltool-debian{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} libcrypto++-dev{a} libcrypto++8t64{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libgfortran-14-dev{a} libgfortran5{a} libhwloc-dev{a} libhwloc15{a} libicu-dev{a} libicu72{a} libjs-jquery{a} libltdl-dev{a} libltdl7{a} libmagic-mgc{a} libmagic1t64{a} libmpich-dev{a} libmpich12{a} libnuma-dev{a} libnuma1{a} libpipeline1{a} libpstreams-dev{a} libslurm41t64{a} libterm-readkey-perl{a} libtext-wrapper-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} mpi-default-dev{a} mpich{a} po-debconf{a} sensible-utils{a} 
The following packages are RECOMMENDED but will NOT be installed:
  curl javascript-common libarchive-cpio-perl libhwloc-plugins libmail-sendmail-perl lynx wget 
0 packages upgraded, 66 newly installed, 0 to remove and 0 not upgraded.
Need to get 61.2 MB of archives. After unpacking 363 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian trixie/main armhf sensible-utils all 0.0.24 [24.8 kB]
Get: 2 http://deb.debian.org/debian trixie/main armhf libmagic-mgc armhf 1:5.45-3+b1 [314 kB]
Get: 3 http://deb.debian.org/debian trixie/main armhf libmagic1t64 armhf 1:5.45-3+b1 [98.5 kB]
Get: 4 http://deb.debian.org/debian trixie/main armhf file armhf 1:5.45-3+b1 [42.3 kB]
Get: 5 http://deb.debian.org/debian trixie/main armhf gettext-base armhf 0.22.5-2 [195 kB]
Get: 6 http://deb.debian.org/debian trixie/main armhf libuchardet0 armhf 0.0.8-1+b2 [65.6 kB]
Get: 7 http://deb.debian.org/debian trixie/main armhf groff-base armhf 1.23.0-5 [1091 kB]
Get: 8 http://deb.debian.org/debian trixie/main armhf bsdextrautils armhf 2.40.2-11 [83.6 kB]
Get: 9 http://deb.debian.org/debian trixie/main armhf libpipeline1 armhf 1.5.8-1 [35.0 kB]
Get: 10 http://deb.debian.org/debian trixie/main armhf man-db armhf 2.13.0-1 [1382 kB]
Get: 11 http://deb.debian.org/debian trixie/main armhf m4 armhf 1.4.19-4 [264 kB]
Get: 12 http://deb.debian.org/debian trixie/main armhf autoconf all 2.72-3 [493 kB]
Get: 13 http://deb.debian.org/debian trixie/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get: 14 http://deb.debian.org/debian trixie/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get: 15 http://deb.debian.org/debian trixie/main armhf autopoint all 0.22.5-2 [723 kB]
Get: 16 http://deb.debian.org/debian trixie/main armhf libdebhelper-perl all 13.20 [89.7 kB]
Get: 17 http://deb.debian.org/debian trixie/main armhf libtool all 2.4.7-8 [517 kB]
Get: 18 http://deb.debian.org/debian trixie/main armhf dh-autoreconf all 20 [17.1 kB]
Get: 19 http://deb.debian.org/debian trixie/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get: 20 http://deb.debian.org/debian trixie/main armhf libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB]
Get: 21 http://deb.debian.org/debian trixie/main armhf dh-strip-nondeterminism all 1.14.0-1 [8448 B]
Get: 22 http://deb.debian.org/debian trixie/main armhf libelf1t64 armhf 0.192-4 [184 kB]
Get: 23 http://deb.debian.org/debian trixie/main armhf dwz armhf 0.15-1+b2 [106 kB]
Get: 24 http://deb.debian.org/debian trixie/main armhf libicu72 armhf 72.1-5+b1 [9088 kB]
Get: 25 http://deb.debian.org/debian trixie/main armhf libxml2 armhf 2.12.7+dfsg+really2.9.14-0.2+b1 [605 kB]
Get: 26 http://deb.debian.org/debian trixie/main armhf gettext armhf 0.22.5-2 [1485 kB]
Get: 27 http://deb.debian.org/debian trixie/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 28 http://deb.debian.org/debian trixie/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get: 29 http://deb.debian.org/debian trixie/main armhf debhelper all 13.20 [915 kB]
Get: 30 http://deb.debian.org/debian trixie/main armhf libgfortran5 armhf 14.2.0-8 [263 kB]
Get: 31 http://deb.debian.org/debian trixie/main armhf libgfortran-14-dev armhf 14.2.0-8 [315 kB]
Get: 32 http://deb.debian.org/debian trixie/main armhf gfortran-14-arm-linux-gnueabihf armhf 14.2.0-8 [8724 kB]
Get: 33 http://deb.debian.org/debian trixie/main armhf gfortran-14 armhf 14.2.0-8 [12.2 kB]
Get: 34 http://deb.debian.org/debian trixie/main armhf libhwloc15 armhf 2.11.2-1 [134 kB]
Get: 35 http://deb.debian.org/debian trixie/main armhf hwloc-nox armhf 2.11.2-1 [201 kB]
Get: 36 http://deb.debian.org/debian trixie/main armhf icu-devtools armhf 72.1-5+b1 [187 kB]
Get: 37 http://deb.debian.org/debian trixie/main armhf libboost1.83-dev armhf 1.83.0-3.2+b2 [10.6 MB]
Get: 38 http://deb.debian.org/debian trixie/main armhf libboost-atomic1.83.0 armhf 1.83.0-3.2+b2 [233 kB]
Get: 39 http://deb.debian.org/debian trixie/main armhf libboost-atomic1.83-dev armhf 1.83.0-3.2+b2 [234 kB]
Get: 40 http://deb.debian.org/debian trixie/main armhf libboost-filesystem1.83.0 armhf 1.83.0-3.2+b2 [271 kB]
Get: 41 http://deb.debian.org/debian trixie/main armhf libboost-system1.83.0 armhf 1.83.0-3.2+b2 [230 kB]
Get: 42 http://deb.debian.org/debian trixie/main armhf libboost-system1.83-dev armhf 1.83.0-3.2+b2 [232 kB]
Get: 43 http://deb.debian.org/debian trixie/main armhf libboost-filesystem1.83-dev armhf 1.83.0-3.2+b2 [286 kB]
Get: 44 http://deb.debian.org/debian trixie/main armhf libboost-filesystem-dev armhf 1.83.0.2+b2 [3616 B]
Get: 45 http://deb.debian.org/debian trixie/main armhf libboost-regex1.83.0 armhf 1.83.0-3.2+b2 [308 kB]
Get: 46 http://deb.debian.org/debian trixie/main armhf libicu-dev armhf 72.1-5+b1 [10.1 MB]
Get: 47 http://deb.debian.org/debian trixie/main armhf libboost-regex1.83-dev armhf 1.83.0-3.2+b2 [337 kB]
Get: 48 http://deb.debian.org/debian trixie/main armhf libboost-iostreams1.83-dev armhf 1.83.0-3.2+b2 [261 kB]
Get: 49 http://deb.debian.org/debian trixie/main armhf libboost-iostreams-dev armhf 1.83.0.2+b2 [3568 B]
Get: 50 http://deb.debian.org/debian trixie/main armhf libboost-regex-dev armhf 1.83.0.2+b2 [3856 B]
Get: 51 http://deb.debian.org/debian trixie/main armhf libcrypto++8t64 armhf 8.9.0-1.1+b1 [1062 kB]
Get: 52 http://deb.debian.org/debian trixie/main armhf libcrypto++-dev armhf 8.9.0-1.1+b1 [1941 kB]
Get: 53 http://deb.debian.org/debian trixie/main armhf libnuma1 armhf 2.0.18-1+b1 [18.9 kB]
Get: 54 http://deb.debian.org/debian trixie/main armhf libnuma-dev armhf 2.0.18-1+b1 [34.6 kB]
Get: 55 http://deb.debian.org/debian trixie/main armhf libltdl7 armhf 2.4.7-8 [390 kB]
Get: 56 http://deb.debian.org/debian trixie/main armhf libltdl-dev armhf 2.4.7-8 [162 kB]
Get: 57 http://deb.debian.org/debian trixie/main armhf libhwloc-dev armhf 2.11.2-1 [226 kB]
Get: 58 http://deb.debian.org/debian trixie/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB]
Get: 59 http://deb.debian.org/debian trixie/main armhf libmpich12 armhf 4.2.0-14 [1498 kB]
Get: 60 http://deb.debian.org/debian trixie/main armhf libslurm41t64 armhf 24.05.4-1 [683 kB]
Get: 61 http://deb.debian.org/debian trixie/main armhf mpich armhf 4.2.0-14 [223 kB]
Get: 62 http://deb.debian.org/debian trixie/main armhf libmpich-dev armhf 4.2.0-14 [2410 kB]
Get: 63 http://deb.debian.org/debian trixie/main armhf libpstreams-dev all 1.0.3-1 [134 kB]
Get: 64 http://deb.debian.org/debian trixie/main armhf libterm-readkey-perl armhf 2.38-2+b4 [23.7 kB]
Get: 65 http://deb.debian.org/debian trixie/main armhf libtext-wrapper-perl all 1.05-4 [10.3 kB]
Get: 66 http://deb.debian.org/debian trixie/main armhf mpi-default-dev armhf 1.17 [3148 B]
Fetched 61.2 MB in 1s (99.7 MB/s)
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package sensible-utils.
(Reading database ... 
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(Reading database ... 19683 files and directories currently installed.)
Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ...
Unpacking sensible-utils (0.0.24) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3+b1_armhf.deb ...
Unpacking libmagic-mgc (1:5.45-3+b1) ...
Selecting previously unselected package libmagic1t64:armhf.
Preparing to unpack .../02-libmagic1t64_1%3a5.45-3+b1_armhf.deb ...
Unpacking libmagic1t64:armhf (1:5.45-3+b1) ...
Selecting previously unselected package file.
Preparing to unpack .../03-file_1%3a5.45-3+b1_armhf.deb ...
Unpacking file (1:5.45-3+b1) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../04-gettext-base_0.22.5-2_armhf.deb ...
Unpacking gettext-base (0.22.5-2) ...
Selecting previously unselected package libuchardet0:armhf.
Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_armhf.deb ...
Unpacking libuchardet0:armhf (0.0.8-1+b2) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../06-groff-base_1.23.0-5_armhf.deb ...
Unpacking groff-base (1.23.0-5) ...
Selecting previously unselected package bsdextrautils.
Preparing to unpack .../07-bsdextrautils_2.40.2-11_armhf.deb ...
Unpacking bsdextrautils (2.40.2-11) ...
Selecting previously unselected package libpipeline1:armhf.
Preparing to unpack .../08-libpipeline1_1.5.8-1_armhf.deb ...
Unpacking libpipeline1:armhf (1.5.8-1) ...
Selecting previously unselected package man-db.
Preparing to unpack .../09-man-db_2.13.0-1_armhf.deb ...
Unpacking man-db (2.13.0-1) ...
Selecting previously unselected package m4.
Preparing to unpack .../10-m4_1.4.19-4_armhf.deb ...
Unpacking m4 (1.4.19-4) ...
Selecting previously unselected package autoconf.
Preparing to unpack .../11-autoconf_2.72-3_all.deb ...
Unpacking autoconf (2.72-3) ...
Selecting previously unselected package autotools-dev.
Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ...
Unpacking autotools-dev (20220109.1) ...
Selecting previously unselected package automake.
Preparing to unpack .../13-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 .../14-autopoint_0.22.5-2_all.deb ...
Unpacking autopoint (0.22.5-2) ...
Selecting previously unselected package libdebhelper-perl.
Preparing to unpack .../15-libdebhelper-perl_13.20_all.deb ...
Unpacking libdebhelper-perl (13.20) ...
Selecting previously unselected package libtool.
Preparing to unpack .../16-libtool_2.4.7-8_all.deb ...
Unpacking libtool (2.4.7-8) ...
Selecting previously unselected package dh-autoreconf.
Preparing to unpack .../17-dh-autoreconf_20_all.deb ...
Unpacking dh-autoreconf (20) ...
Selecting previously unselected package libarchive-zip-perl.
Preparing to unpack .../18-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 .../19-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 .../20-dh-strip-nondeterminism_1.14.0-1_all.deb ...
Unpacking dh-strip-nondeterminism (1.14.0-1) ...
Selecting previously unselected package libelf1t64:armhf.
Preparing to unpack .../21-libelf1t64_0.192-4_armhf.deb ...
Unpacking libelf1t64:armhf (0.192-4) ...
Selecting previously unselected package dwz.
Preparing to unpack .../22-dwz_0.15-1+b2_armhf.deb ...
Unpacking dwz (0.15-1+b2) ...
Selecting previously unselected package libicu72:armhf.
Preparing to unpack .../23-libicu72_72.1-5+b1_armhf.deb ...
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I: Building the package
I: user script /srv/workspace/pbuilder/23325/tmp/hooks/A99_set_merged_usr starting
Not re-configuring usrmerge for trixie
I: user script /srv/workspace/pbuilder/23325/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 <emollier@debian.org>
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
 debian/rules clean
dh clean
   dh_auto_clean
	make -j4 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 -j4 "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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c msethash.cc
In file included from murasaki.h:24,
                 from dinkymath.cc:27:
sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
      |                   ^~~~~~~~~~~~~~~
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
      |            ^~~~~~~~~~~~~~~
In file included from murasaki.h:24,
                 from murasaki.cc:37:
sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
      |                   ^~~~~~~~~~~~~~~
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
      |            ^~~~~~~~~~~~~~~
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 murasaki.h:24,
                 from sequence.cc:28:
sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
      |                   ^~~~~~~~~~~~~~~
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 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<std::pair<long int, long int> >::val_type' {aka 'struct std::pair<long int, long int>'} 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<std::pair<long int, long int> >::val_type' {aka 'struct std::pair<long int, long int>'} declared here
  284 |     struct pair
      |            ^~~~
sequence.cc:1114:9: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'ShmVector<std::pair<long int, long int> >::val_type' {aka 'struct std::pair<long int, long int>'} 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<std::pair<long int, long int> >::val_type' {aka 'struct std::pair<long int, long int>'} declared here
  284 |     struct pair
      |            ^~~~
murasaki.cc: In function 'void procLocs(LocList&, std::__cxx11::list<Location>&, int, int)':
murasaki.cc:1008:8: warning: variable 'revZero' set but not used [-Wunused-but-set-variable]
 1008 |   bool revZero=false;
      |        ^~~~~~~
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'
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<char*, __cxx11::basic_string<char> >]' 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)
      |     ^~~~~~~~~~~~~~
sequence.cc: In member function 'std::pair<double, long int> 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<T>::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 sequence.h:44:
shmvector.hh: In instantiation of 'void ShmVector<T>::shmRealloc(size_t) [with T = std::pair<long int, long int>; size_t = unsigned int]':
shmvector.hh:282:5:   required from 'void ShmVector<T>::resize(size_t) [with T = std::pair<long int, long int>; size_t = 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<long int, long int>' 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<long int, long int>' declared here
  284 |     struct pair
      |            ^~~~
mpicxx -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c options.cc
In file included from msethash.cc:25:
sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
      |                   ^~~~~~~~~~~~~~~
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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c ecohash.cc
In file included from options.h:28,
                 from options.cc:26:
sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
      |                   ^~~~~~~~~~~~~~~
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 ecohash.h:29,
                 from ecohash.cc:26:
sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
      |                   ^~~~~~~~~~~~~~~
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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c ecolist.cc
In file included from /usr/include/c++/14/bits/stl_algo.h:61:
/usr/include/c++/14/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >; _Distance = int; _Tp = HashMethod; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/14/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
  224 |     __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
      |     ^~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_heap.h: In function 'void std::__pop_heap(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/14/bits/stl_heap.h:254:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
  254 |     __pop_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
      |     ^~~~~~~~~~
/usr/include/c++/14/bits/stl_heap.h:254:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
/usr/include/c++/14/bits/stl_heap.h:254:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
/usr/include/c++/14/bits/stl_heap.h: In function 'void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/14/bits/stl_heap.h:340:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
  340 |     __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
      |     ^~~~~~~~~~~
/usr/include/c++/14/bits/stl_heap.h:340:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
/usr/include/c++/14/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/14/bits/stl_algo.h:1770:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
 1770 |     __insertion_sort(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_algo.h:1770:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
In file included from /usr/include/c++/14/vector:72,
                 from murasaki.cc:31:
/usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
  700 |     vector<_Tp, _Alloc>::
      |     ^~~~~~~~~~~~~~~~~~~
In file included from ecolist.h:23,
                 from ecolist.cc:20:
sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
      |                   ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  467 | struct less_map : public binary_function<const Ecolist::val_type&,const Ecolist::val_type&,bool> {
      |                          ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/vector:66:
In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void MurasakiRuntime::prep()' at murasaki.cc:378:26:
/usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
 1037 |           _M_fill_insert(end(), __new_size - size(), __x);
      |           ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void MurasakiRuntime::prep()' at murasaki.cc:414:25:
/usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
 1037 |           _M_fill_insert(end(), __new_size - size(), __x);
      |           ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mpicxx -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c arrayhash.cc
In file included from /usr/include/c++/14/vector:72,
                 from scoring.h:27,
                 from sequence.h:31:
/usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
  700 |     vector<_Tp, _Alloc>::
      |     ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/vector:66:
In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'double HashMethod::fitnessCheck()' at sequence.cc:1430:17:
/usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
 1037 |           _M_fill_insert(end(), __new_size - size(), __x);
      |           ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from murasaki.h:24,
                 from arrayhash.cc:28:
sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
      |                   ^~~~~~~~~~~~~~~
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_mpi.cc:33:
sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
      |                   ^~~~~~~~~~~~~~~
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
      |            ^~~~~~~~~~~~~~~
murasaki_mpi.cc:89:29: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   89 | struct lt_mpi_worldMemory : binary_function<int,int,bool> {
      |                             ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
murasaki_mpi.cc:95:29: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   95 | struct gt_mpi_worldMemory : binary_function<int,int,bool> {
      |                             ^~~~~~~~~~~~~~~
/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;
      |         ^~~~~~~~~
mpicxx -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c seqread.cc
/usr/include/c++/14/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/14/bits/stl_algo.h:1876:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
 1876 |     __introsort_loop(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_algo.h:1876:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
In function 'void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
    inlined from 'void std::__partial_sort(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/14/bits/stl_algo.h:1868:25,
    inlined from 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/14/bits/stl_algo.h:1884:27:
/usr/include/c++/14/bits/stl_algo.h:1593:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
 1593 |       std::__make_heap(__first, __middle, __comp);
      |       ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'void std::__sort_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
    inlined from 'void std::__partial_sort(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/14/bits/stl_algo.h:1869:23,
    inlined from 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/14/bits/stl_algo.h:1884:27:
/usr/include/c++/14/bits/stl_heap.h:425:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
  425 |           std::__pop_heap(__first, __last, __last, __comp);
      |           ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/14/bits/stl_algo.h:1890:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
 1890 |           std::__introsort_loop(__cut, __last, __depth_limit, __comp);
      |           ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
    inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >]' at /usr/include/c++/14/bits/stl_algo.h:4771:18,
    inlined from 'void BitSequence::compileHashFunc()' at sequence.cc:1645:7:
/usr/include/c++/14/bits/stl_algo.h:1905:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
 1905 |           std::__introsort_loop(__first, __last,
      |           ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
 1906 |                                 std::__lg(__last - __first) * 2,
      |                                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1907 |                                 __comp);
      |                                 ~~~~~~~
In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
    inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/14/bits/stl_algo.h:1908:31,
    inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >]' at /usr/include/c++/14/bits/stl_algo.h:4771:18,
    inlined from 'void BitSequence::compileHashFunc()' at sequence.cc:1645:7:
/usr/include/c++/14/bits/stl_algo.h:1817:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
 1817 |           std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
      |           ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_algo.h:1822:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
 1822 |         std::__insertion_sort(__first, __last, __comp);
      |         ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
    inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >]' at /usr/include/c++/14/bits/stl_algo.h:4771:18,
    inlined from 'void BitSequence::compileHashFunc()' at sequence.cc:1672:9:
/usr/include/c++/14/bits/stl_algo.h:1905:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
 1905 |           std::__introsort_loop(__first, __last,
      |           ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
 1906 |                                 std::__lg(__last - __first) * 2,
      |                                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1907 |                                 __comp);
      |                                 ~~~~~~~
In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
    inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/14/bits/stl_algo.h:1908:31,
    inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >]' at /usr/include/c++/14/bits/stl_algo.h:4771:18,
    inlined from 'void BitSequence::compileHashFunc()' at sequence.cc:1672:9:
/usr/include/c++/14/bits/stl_algo.h:1817:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
 1817 |           std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
      |           ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_algo.h:1822:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
 1822 |         std::__insertion_sort(__first, __last, __comp);
      |         ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c scoring.cc
In file included from /usr/include/c++/14/vector:72,
                 from scoring.h:27,
                 from sequence.h:31:
/usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
  700 |     vector<_Tp, _Alloc>::
      |     ^~~~~~~~~~~~~~~~~~~
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 /usr/lib/arm-linux-gnueabihf/mpich/include/mpi.h:958,
                 from murasaki_mpi.cc:29:
/usr/lib/arm-linux-gnueabihf/mpich/include/mpi_proto.h:324:5: note: by argument 1 of type 'const void*' to 'int MPI_Get_address(const void*, MPI_Aint*)' declared here
  324 | int MPI_Get_address(const void *location, MPI_Aint *address) MPICH_API_PUBLIC;
      |     ^~~~~~~~~~~~~~~
murasaki_mpi.cc:102:19: note: 'msg' declared here
  102 |   MPI_HashMessage msg;
      |                   ^~~
In file included from /usr/include/c++/14/vector:66:
In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'void mpi_types_init()' at murasaki_mpi.cc:120:22:
/usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
 1037 |           _M_fill_insert(end(), __new_size - size(), __x);
      |           ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from murasaki.h:24,
                 from scoring.cc:27:
sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
      |                   ^~~~~~~~~~~~~~~
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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c openhash.cc
mpicxx -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c genopts.cc
mpicxx -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
      |                   ^~~~~~~~~~~~~~~
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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c cgr.cc
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::allocator<std::pair<unsigned int, unsigned int> >, std::pair<unsigned int, unsigned int> >::value_type' {aka 'struct std::pair<unsigned int, unsigned int>'} 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::allocator<std::pair<unsigned int, unsigned int> >, std::pair<unsigned int, unsigned int> >::value_type' {aka 'struct std::pair<unsigned int, unsigned int>'} 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::allocator<std::pair<unsigned int, unsigned int> >, std::pair<unsigned int, unsigned int> >::value_type' {aka 'struct std::pair<unsigned int, unsigned int>'} 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::allocator<std::pair<unsigned int, unsigned int> >, std::pair<unsigned int, unsigned int> >::value_type' {aka 'struct std::pair<unsigned int, unsigned int>'} 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::allocator<std::pair<unsigned int, unsigned int> >, std::pair<unsigned int, unsigned int> >::value_type' {aka 'struct std::pair<unsigned int, unsigned int>'} 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::allocator<std::pair<unsigned int, unsigned int> >, std::pair<unsigned int, unsigned int> >::value_type' {aka 'struct std::pair<unsigned int, unsigned int>'} declared here
  284 |     struct pair
      |            ^~~~
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;
      |       ^~~~~~~~~
mpicxx -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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
cgr.cc: In member function 'std::pair<long unsigned int, long unsigned int> 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<long unsigned int, long unsigned int> 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<long unsigned int, long unsigned int> 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];
      |                        ^
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;
      |             ^~~~~~
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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c testeco.cc
mpicxx -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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
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;
      |        ^~~~~~~~~~
In file included from ecolist.h:23,
                 from testeco.cc:20:
sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
      |                   ^~~~~~~~~~~~~~~
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
      |            ^~~~~~~~~~~~~~~
testeco.cc: In function 'long int bigrand()':
testeco.cc:29:41: warning: left shift count >= width of type [-Wshift-count-overflow]
   29 |   return (long)(((unsigned long)(rand())<<32) + ((unsigned long)(rand())));
      |                  ~~~~~~~~~~~~~~~~~~~~~~~^~~~
mpicxx -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c alignments.cc
mpicxx -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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
mpicxx -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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
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;
      |          ^~~~~~~~
mpicxx -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c mbfa.cc
getsegments.cc: In function 'size_t getSubSeqs(SequenceFileReader&, std::__cxx11::list<std::pair<unsigned int, std::__cxx11::basic_string<char> > >&, 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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 
mpicxx -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 
mpicxx -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 
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 -j4 "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++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c murasaki.cc
g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c timing.cc
g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c dinkymath.cc
g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c sequence.cc
g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c msethash.cc
In file included from murasaki.h:24,
                 from sequence.cc:28:
sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
      |                   ^~~~~~~~~~~~~~~
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 dinkymath.cc:27:
sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
      |                   ^~~~~~~~~~~~~~~
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
      |            ^~~~~~~~~~~~~~~
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<std::pair<long int, long int> >::val_type' {aka 'struct std::pair<long int, long int>'} 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<std::pair<long int, long int> >::val_type' {aka 'struct std::pair<long int, long int>'} declared here
  284 |     struct pair
      |            ^~~~
sequence.cc:1114:9: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'ShmVector<std::pair<long int, long int> >::val_type' {aka 'struct std::pair<long int, long int>'} 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<std::pair<long int, long int> >::val_type' {aka 'struct std::pair<long int, long int>'} declared here
  284 |     struct pair
      |            ^~~~
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;
      |       ^~~~
sequence.cc: In member function 'std::pair<double, long int> 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 murasaki.cc:37:
sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
      |                   ^~~~~~~~~~~~~~~
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.cc:41:
hashing.h: In instantiation of 'SBox<T>::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 sequence.h:44:
shmvector.hh: In instantiation of 'void ShmVector<T>::shmRealloc(size_t) [with T = std::pair<long int, long int>; size_t = unsigned int]':
shmvector.hh:282:5:   required from 'void ShmVector<T>::resize(size_t) [with T = std::pair<long int, long int>; size_t = 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<long int, long int>' 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<long int, long int>' declared here
  284 |     struct pair
      |            ^~~~
murasaki.cc: In function 'void procLocs(LocList&, std::__cxx11::list<Location>&, 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<char*, __cxx11::basic_string<char> >]' 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 msethash.cc:25:
sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
      |                   ^~~~~~~~~~~~~~~
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++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c options.cc
g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c ecohash.cc
In file included from options.h:28,
                 from options.cc:26:
sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
      |                   ^~~~~~~~~~~~~~~
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 ecohash.h:29,
                 from ecohash.cc:26:
sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
      |                   ^~~~~~~~~~~~~~~
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++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c ecolist.cc
In file included from /usr/include/c++/14/bits/stl_algo.h:61:
/usr/include/c++/14/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >; _Distance = int; _Tp = HashMethod; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/14/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
  224 |     __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
      |     ^~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_heap.h: In function 'void std::__pop_heap(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/14/bits/stl_heap.h:254:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
  254 |     __pop_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
      |     ^~~~~~~~~~
/usr/include/c++/14/bits/stl_heap.h:254:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
/usr/include/c++/14/bits/stl_heap.h:254:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
/usr/include/c++/14/bits/stl_heap.h: In function 'void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/14/bits/stl_heap.h:340:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
  340 |     __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
      |     ^~~~~~~~~~~
/usr/include/c++/14/bits/stl_heap.h:340:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
/usr/include/c++/14/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/14/bits/stl_algo.h:1770:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
 1770 |     __insertion_sort(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_algo.h:1770:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
In file included from ecolist.h:23,
                 from ecolist.cc:20:
sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
      |                   ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  467 | struct less_map : public binary_function<const Ecolist::val_type&,const Ecolist::val_type&,bool> {
      |                          ^~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c murasaki_mpi.cc
g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c arrayhash.cc
g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c seqread.cc
In file included from /usr/include/c++/14/vector:72,
                 from scoring.h:27,
                 from sequence.h:31:
/usr/include/c++/14/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
  700 |     vector<_Tp, _Alloc>::
      |     ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/vector:66:
In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
    inlined from 'double HashMethod::fitnessCheck()' at sequence.cc:1430:17:
/usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
 1037 |           _M_fill_insert(end(), __new_size - size(), __x);
      |           ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from murasaki.h:24,
                 from arrayhash.cc:28:
sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
      |                   ^~~~~~~~~~~~~~~
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++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c scoring.cc
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(); }
      |          ^~~~~~~~~~~
/usr/include/c++/14/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/14/bits/stl_algo.h:1876:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
 1876 |     __introsort_loop(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_algo.h:1876:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
In function 'void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
    inlined from 'void std::__partial_sort(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/14/bits/stl_algo.h:1868:25,
    inlined from 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/14/bits/stl_algo.h:1884:27:
/usr/include/c++/14/bits/stl_algo.h:1593:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
 1593 |       std::__make_heap(__first, __middle, __comp);
      |       ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'void std::__sort_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
    inlined from 'void std::__partial_sort(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/14/bits/stl_algo.h:1869:23,
    inlined from 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/14/bits/stl_algo.h:1884:27:
/usr/include/c++/14/bits/stl_heap.h:425:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
  425 |           std::__pop_heap(__first, __last, __last, __comp);
      |           ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/14/bits/stl_algo.h:1890:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
 1890 |           std::__introsort_loop(__cut, __last, __depth_limit, __comp);
      |           ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
    inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >]' at /usr/include/c++/14/bits/stl_algo.h:4771:18,
    inlined from 'void BitSequence::compileHashFunc()' at sequence.cc:1645:7:
/usr/include/c++/14/bits/stl_algo.h:1905:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
 1905 |           std::__introsort_loop(__first, __last,
      |           ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
 1906 |                                 std::__lg(__last - __first) * 2,
      |                                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1907 |                                 __comp);
      |                                 ~~~~~~~
In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
    inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/14/bits/stl_algo.h:1908:31,
    inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >]' at /usr/include/c++/14/bits/stl_algo.h:4771:18,
    inlined from 'void BitSequence::compileHashFunc()' at sequence.cc:1645:7:
/usr/include/c++/14/bits/stl_algo.h:1817:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
 1817 |           std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
      |           ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_algo.h:1822:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
 1822 |         std::__insertion_sort(__first, __last, __comp);
      |         ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
    inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >]' at /usr/include/c++/14/bits/stl_algo.h:4771:18,
    inlined from 'void BitSequence::compileHashFunc()' at sequence.cc:1672:9:
/usr/include/c++/14/bits/stl_algo.h:1905:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
 1905 |           std::__introsort_loop(__first, __last,
      |           ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
 1906 |                                 std::__lg(__last - __first) * 2,
      |                                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1907 |                                 __comp);
      |                                 ~~~~~~~
In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
    inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/14/bits/stl_algo.h:1908:31,
    inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<HashMethod*, vector<HashMethod> >]' at /usr/include/c++/14/bits/stl_algo.h:4771:18,
    inlined from 'void BitSequence::compileHashFunc()' at sequence.cc:1672:9:
/usr/include/c++/14/bits/stl_algo.h:1817:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
 1817 |           std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
      |           ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_algo.h:1822:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<HashMethod*, std::vector<HashMethod> >' changed in GCC 7.1
 1822 |         std::__insertion_sort(__first, __last, __comp);
      |         ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from murasaki.h:24,
                 from scoring.cc:27:
sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
      |                   ^~~~~~~~~~~~~~~
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++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c openhash.cc
g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c genopts.cc
g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c binseq.cc
g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
      |                   ^~~~~~~~~~~~~~~
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++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c cgr.cc
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::allocator<std::pair<unsigned int, unsigned int> >, std::pair<unsigned int, unsigned int> >::value_type' {aka 'struct std::pair<unsigned int, unsigned int>'} 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::allocator<std::pair<unsigned int, unsigned int> >, std::pair<unsigned int, unsigned int> >::value_type' {aka 'struct std::pair<unsigned int, unsigned int>'} 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::allocator<std::pair<unsigned int, unsigned int> >, std::pair<unsigned int, unsigned int> >::value_type' {aka 'struct std::pair<unsigned int, unsigned int>'} 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::allocator<std::pair<unsigned int, unsigned int> >, std::pair<unsigned int, unsigned int> >::value_type' {aka 'struct std::pair<unsigned int, unsigned int>'} 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::allocator<std::pair<unsigned int, unsigned int> >, std::pair<unsigned int, unsigned int> >::value_type' {aka 'struct std::pair<unsigned int, unsigned int>'} 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::allocator<std::pair<unsigned int, unsigned int> >, std::pair<unsigned int, unsigned int> >::value_type' {aka 'struct std::pair<unsigned int, unsigned int>'} declared here
  284 |     struct pair
      |            ^~~~
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;
      |       ^~~~~~~~~
g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c cgr-compare.cc
cgr.cc: In member function 'std::pair<long unsigned int, long unsigned int> 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<long unsigned int, long unsigned int> 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<long unsigned int, long unsigned int> 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++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c cgr-random.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;
      |             ^~~~~~
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++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c cgr-sample.cc
g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c testeco.cc
g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c align-compare.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;
      |        ^~~~~~~~~~
In file included from ecolist.h:23,
                 from testeco.cc:20:
sequence.h:444:19: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  444 | struct ltRegion : binary_function<SeqPosPair,SeqPosPair,bool> {
      |                   ^~~~~~~~~~~~~~~
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
      |            ^~~~~~~~~~~~~~~
testeco.cc: In function 'long int bigrand()':
testeco.cc:29:41: warning: left shift count >= width of type [-Wshift-count-overflow]
   29 |   return (long)(((unsigned long)(rand())<<32) + ((unsigned long)(rand())));
      |                  ~~~~~~~~~~~~~~~~~~~~~~~^~~~
g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c alignments.cc
g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c align-or.cc
g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c geneparse.cc
g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c align-and.cc
g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c align-best.cc
g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c align-coverage.cc
g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c getsegments.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;
      |          ^~~~~~~~
getsegments.cc: In function 'size_t getSubSeqs(SequenceFileReader&, std::__cxx11::list<std::pair<unsigned int, std::__cxx11::basic_string<char> > >&, 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++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall  -DLARGESEQ_SUPPORT -c mbfa.cc
g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 
g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 
g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 
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
dpkg-shlibdeps: warning: debian/murasaki-mpi/usr/lib/murasaki/align-coverage-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki-mpi/usr/bin/geneparse-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki/usr/bin/murasaki contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki-mpi/usr/lib/murasaki/align-and-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki/usr/lib/murasaki/cgr-sample contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki-mpi/usr/lib/murasaki/cgr-compare-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki/usr/bin/mbfa contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki-mpi/usr/lib/murasaki/align-or-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki/usr/bin/geneparse contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki-mpi/usr/bin/mbfa-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki/usr/lib/murasaki/align-and contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki/usr/lib/murasaki/cgr-compare contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki-mpi/usr/lib/murasaki/cgr-image-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki/usr/lib/murasaki/align-coverage contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki-mpi/usr/lib/murasaki/align-best-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki/usr/lib/murasaki/align-or contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki-mpi/usr/lib/murasaki/align-compare-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki/usr/lib/murasaki/align-best contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki/usr/lib/murasaki/align-compare contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki-mpi/usr/lib/murasaki/cgr-sample-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki/usr/lib/murasaki/cgr-image contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/murasaki-mpi/usr/bin/murasaki-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
   dh_installdeb
   dh_gencontrol
dpkg-gencontrol: warning: Depends field of package murasaki-common: substitution variable ${misc:perl} used, but is not 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
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_armhf.deb'.
dpkg-deb: building package 'murasaki-mpi' in '../murasaki-mpi_1.68.6-14_armhf.deb'.
dpkg-deb: building package 'murasaki-common' in '../murasaki-common_1.68.6-14_all.deb'.
dpkg-deb: building package 'murasaki-dbgsym' in '../murasaki-dbgsym_1.68.6-14_armhf.deb'.
dpkg-deb: building package 'murasaki-mpi-dbgsym' in '../murasaki-mpi-dbgsym_1.68.6-14_armhf.deb'.
 dpkg-genbuildinfo --build=binary -O../murasaki_1.68.6-14_armhf.buildinfo
 dpkg-genchanges --build=binary -O../murasaki_1.68.6-14_armhf.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/23325/tmp/hooks/B01_cleanup starting
I: user script /srv/workspace/pbuilder/23325/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/23325 and its subdirectories
I: Current time: Fri Dec  6 21:21:11 +14 2024
I: pbuilder-time-stamp: 1733469671