I: pbuilder: network access will be disabled during build
I: Current time: Wed Jan 21 01:51:10 +14 2026
I: pbuilder-time-stamp: 1768909870
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz]
I: copying local configuration
W: --override-config is not set; not updating apt.conf Read the manpage for details.
I: mounting /proc filesystem
I: mounting /sys filesystem
I: creating /{dev,run}/shm
I: mounting /dev/pts filesystem
I: redirecting /dev/ptmx to /dev/pts/ptmx
I: policy-rc.d already exists
I: using eatmydata during job
I: Copying source file
I: copying [mira_4.9.6-11.dsc]
I: copying [./mira_4.9.6.orig.tar.bz2]
I: copying [./mira_4.9.6-11.debian.tar.xz]
I: Extracting source
gpgv: Signature made Tue Feb  6 11:03:20 2024 
gpgv:                using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv:                issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./mira_4.9.6-11.dsc: no acceptable signature found
dpkg-source: info: extracting mira in mira-4.9.6
dpkg-source: info: unpacking mira_4.9.6.orig.tar.bz2
dpkg-source: info: unpacking mira_4.9.6-11.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying spelling.patch
dpkg-source: info: applying sls-rrna-fix
dpkg-source: info: applying man-directory
dpkg-source: info: applying fix_buildorder.patch
dpkg-source: info: applying gcc-12.patch
dpkg-source: info: applying gcc-13.patch
dpkg-source: info: applying fix-debian-compileinfo.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/2805/tmp/hooks/D01_modify_environment starting
debug: Running on infom08-i386.
I: Changing host+domainname to test build reproducibility
I: Adding a custom variable just for the fun of it...
I: Changing /bin/sh to bash
'/bin/sh' -> '/bin/bash'
lrwxrwxrwx 1 root root 9 Jan 20 11:51 /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/2805/tmp/hooks/D01_modify_environment finished
I: user script /srv/workspace/pbuilder/2805/tmp/hooks/D02_print_environment starting
I: set
  BASH=/bin/sh
  BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath
  BASH_ALIASES=()
  BASH_ARGC=()
  BASH_ARGV=()
  BASH_CMDS=()
  BASH_LINENO=([0]="12" [1]="0")
  BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:.
  BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment")
  BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="i686-pc-linux-gnu")
  BASH_VERSION='5.2.37(1)-release'
  BUILDDIR=/build/reproducible-path
  BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other'
  BUILDUSERNAME=pbuilder2
  BUILD_ARCH=i386
  DEBIAN_FRONTEND=noninteractive
  DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=5 '
  DIRSTACK=()
  DISTRIBUTION=unstable
  EUID=0
  FUNCNAME=([0]="Echo" [1]="main")
  GROUPS=()
  HOME=/root
  HOSTNAME=i-capture-the-hostname
  HOSTTYPE=i686
  HOST_ARCH=i386
  IFS=' 	
  '
  INVOCATION_ID=2092ecd46a0e435e92031a47da667e31
  LANG=C
  LANGUAGE=de_CH:de
  LC_ALL=C
  LD_LIBRARY_PATH=/usr/lib/libeatmydata
  LD_PRELOAD=libeatmydata.so
  MACHTYPE=i686-pc-linux-gnu
  MAIL=/var/mail/root
  OPTERR=1
  OPTIND=1
  OSTYPE=linux-gnu
  PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path
  PBCURRENTCOMMANDLINEOPERATION=build
  PBUILDER_OPERATION=build
  PBUILDER_PKGDATADIR=/usr/share/pbuilder
  PBUILDER_PKGLIBDIR=/usr/lib/pbuilder
  PBUILDER_SYSCONFDIR=/etc
  PIPESTATUS=([0]="0")
  POSIXLY_CORRECT=y
  PPID=2805
  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.EORpubqv/pbuilderrc_Z4oU --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.EORpubqv/b2 --logfile b2/build.log mira_4.9.6-11.dsc'
  SUDO_GID=111
  SUDO_UID=104
  SUDO_USER=jenkins
  TERM=unknown
  TZ=/usr/share/zoneinfo/Etc/GMT-14
  UID=0
  USER=root
  _='I: set'
I: uname -a
  Linux i-capture-the-hostname 6.11.5+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.5-1~bpo12+1 (2024-11-11) x86_64 GNU/Linux
I: ls -l /bin
  lrwxrwxrwx 1 root root 7 Nov 22  2024 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/2805/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: i386
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), autoconf-archive, libbz2-dev, libexpat1-dev, libgoogle-perftools-dev, flex, libfl-dev, xxd, zlib1g-dev, libboost-thread-dev, libboost-regex-dev, libboost-filesystem-dev, libboost-system-dev, libboost-iostreams-dev, docbook-xsl, dblatex
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19952 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 autoconf-archive; however:
  Package autoconf-archive is not installed.
 pbuilder-satisfydepends-dummy depends on libbz2-dev; however:
  Package libbz2-dev is not installed.
 pbuilder-satisfydepends-dummy depends on libexpat1-dev; however:
  Package libexpat1-dev is not installed.
 pbuilder-satisfydepends-dummy depends on libgoogle-perftools-dev; however:
  Package libgoogle-perftools-dev is not installed.
 pbuilder-satisfydepends-dummy depends on flex; however:
  Package flex is not installed.
 pbuilder-satisfydepends-dummy depends on libfl-dev; however:
  Package libfl-dev is not installed.
 pbuilder-satisfydepends-dummy depends on xxd; however:
  Package xxd is not installed.
 pbuilder-satisfydepends-dummy depends on zlib1g-dev; however:
  Package zlib1g-dev is not installed.
 pbuilder-satisfydepends-dummy depends on libboost-thread-dev; however:
  Package libboost-thread-dev 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-filesystem-dev; however:
  Package libboost-filesystem-dev is not installed.
 pbuilder-satisfydepends-dummy depends on libboost-system-dev; however:
  Package libboost-system-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 docbook-xsl; however:
  Package docbook-xsl is not installed.
 pbuilder-satisfydepends-dummy depends on dblatex; however:
  Package dblatex 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} autoconf-archive{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} dblatex{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} distro-info-data{a} docbook-xml{a} docbook-xsl{a} dwz{a} file{a} flex{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} fonts-gfs-baskerville{a} fonts-gfs-porson{a} fonts-lmodern{a} gettext{a} gettext-base{a} groff-base{a} icu-devtools{a} intltool-debian{a} libapache-pom-java{a} libarchive-zip-perl{a} libbibtex-parser-perl{a} libboost-atomic1.83-dev{a} libboost-atomic1.83.0{a} libboost-chrono1.83-dev{a} libboost-chrono1.83.0t64{a} libboost-date-time1.83-dev{a} libboost-date-time1.83.0{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-serialization1.83-dev{a} libboost-serialization1.83.0{a} libboost-system-dev{a} libboost-system1.83-dev{a} libboost-system1.83.0{a} libboost-thread-dev{a} libboost-thread1.83-dev{a} libboost-thread1.83.0{a} libboost1.83-dev{a} libbrotli1{a} libbz2-dev{a} libcairo2{a} libcom-err2{a} libcommons-logging-java{a} libcommons-parent-java{a} libdatrie1{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libfile-homedir-perl{a} libfile-stripnondeterminism-perl{a} libfile-which-perl{a} libfl-dev{a} libfl2{a} libfontbox-java{a} libfontconfig1{a} libfontenc1{a} libfreetype6{a} libglib2.0-0t64{a} libgoogle-perftools-dev{a} libgoogle-perftools4t64{a} libgraphite2-3{a} libgssapi-krb5-2{a} libharfbuzz0b{a} libice6{a} libicu-dev{a} libicu72{a} libio-string-perl{a} libjs-jquery{a} libk5crypto3{a} libkeyutils1{a} libkpathsea6{a} libkrb5-3{a} libkrb5support0{a} liblatex-tounicode-perl{a} libmagic-mgc{a} libmagic1t64{a} libmime-charset-perl{a} libmpfi0{a} libnsl2{a} libpaper-utils{a} libpaper1{a} libpdfbox-java{a} libpipeline1{a} libpixman-1-0{a} libpng16-16t64{a} libpotrace0{a} libproc2-0{a} libptexenc1{a} libpython3-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libreadline8t64{a} libsm6{a} libsombok3{a} libsynctex2{a} libtcmalloc-minimal4t64{a} libteckit0{a} libtexlua53-5{a} libthai-data{a} libthai0{a} libtirpc-common{a} libtirpc3t64{a} libtool{a} libuchardet0{a} libunicode-linebreak-perl{a} libx11-6{a} libx11-data{a} libxau6{a} libxaw7{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxi6{a} libxml2{a} libxmu6{a} libxpm4{a} libxrender1{a} libxslt1.1{a} libxt6t64{a} libyaml-tiny-perl{a} libzzip-0-13t64{a} lmodern{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} preview-latex-style{a} procps{a} python-apt-common{a} python3{a} python3-apt{a} python3-minimal{a} python3.12{a} python3.12-minimal{a} readline-common{a} sensible-utils{a} sgml-base{a} sgml-data{a} t1utils{a} tex-common{a} texlive{a} texlive-base{a} texlive-bibtex-extra{a} texlive-binaries{a} texlive-extra-utils{a} texlive-fonts-recommended{a} texlive-lang-greek{a} texlive-latex-base{a} texlive-latex-extra{a} texlive-latex-recommended{a} texlive-luatex{a} texlive-pictures{a} texlive-plain-generic{a} texlive-science{a} tzdata{a} ucf{a} x11-common{a} xdg-utils{a} xfonts-encodings{a} xfonts-utils{a} xml-core{a} xsltproc{a} xxd{a} zlib1g-dev{a} 
The following packages are RECOMMENDED but will NOT be installed:
  bzip2-doc ca-certificates curl dblatex-doc default-jre dvisvgm ghostscript iso-codes javascript-common krb5-locales libarchive-cpio-perl libfile-mimeinfo-perl libglib2.0-data liblog-log4perl-perl libltdl-dev libmail-sendmail-perl libnet-dbus-perl libspreadsheet-parseexcel-perl libx11-protocol-perl libxml2-utils linux-sysctl-defaults lsb-release lynx psmisc ruby shared-mime-info tex-gyre tipa tk wget x11-utils x11-xserver-utils xdg-user-dirs 
0 packages upgraded, 183 newly installed, 0 to remove and 0 not upgraded.
Need to get 464 MB of archives. After unpacking 1279 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian unstable/main i386 autoconf-archive all 20220903-3 [775 kB]
Get: 2 http://deb.debian.org/debian unstable/main i386 m4 i386 1.4.19-4 [293 kB]
Get: 3 http://deb.debian.org/debian unstable/main i386 flex i386 2.6.4-8.2+b3 [412 kB]
Get: 4 http://deb.debian.org/debian unstable/main i386 libpython3.12-minimal i386 3.12.8-3 [816 kB]
Get: 5 http://deb.debian.org/debian unstable/main i386 libexpat1 i386 2.6.4-1 [107 kB]
Get: 6 http://deb.debian.org/debian unstable/main i386 python3.12-minimal i386 3.12.8-3 [2239 kB]
Get: 7 http://deb.debian.org/debian unstable/main i386 python3-minimal i386 3.12.7-1 [26.8 kB]
Get: 8 http://deb.debian.org/debian unstable/main i386 media-types all 10.1.0 [26.9 kB]
Get: 9 http://deb.debian.org/debian unstable/main i386 netbase all 6.4 [12.8 kB]
Get: 10 http://deb.debian.org/debian unstable/main i386 tzdata all 2024b-4 [256 kB]
Get: 11 http://deb.debian.org/debian unstable/main i386 libkrb5support0 i386 1.21.3-3 [34.9 kB]
Get: 12 http://deb.debian.org/debian unstable/main i386 libcom-err2 i386 1.47.2~rc1-2 [24.0 kB]
Get: 13 http://deb.debian.org/debian unstable/main i386 libk5crypto3 i386 1.21.3-3 [83.6 kB]
Get: 14 http://deb.debian.org/debian unstable/main i386 libkeyutils1 i386 1.6.3-4 [9600 B]
Get: 15 http://deb.debian.org/debian unstable/main i386 libkrb5-3 i386 1.21.3-3 [350 kB]
Get: 16 http://deb.debian.org/debian unstable/main i386 libgssapi-krb5-2 i386 1.21.3-3 [146 kB]
Get: 17 http://deb.debian.org/debian unstable/main i386 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB]
Get: 18 http://deb.debian.org/debian unstable/main i386 libtirpc3t64 i386 1.3.4+ds-1.3+b1 [90.5 kB]
Get: 19 http://deb.debian.org/debian unstable/main i386 libnsl2 i386 1.3.0-3+b3 [42.7 kB]
Get: 20 http://deb.debian.org/debian unstable/main i386 readline-common all 8.2-6 [69.4 kB]
Get: 21 http://deb.debian.org/debian unstable/main i386 libreadline8t64 i386 8.2-6 [173 kB]
Get: 22 http://deb.debian.org/debian unstable/main i386 libpython3.12-stdlib i386 3.12.8-3 [1968 kB]
Get: 23 http://deb.debian.org/debian unstable/main i386 python3.12 i386 3.12.8-3 [677 kB]
Get: 24 http://deb.debian.org/debian unstable/main i386 libpython3-stdlib i386 3.12.7-1 [9712 B]
Get: 25 http://deb.debian.org/debian unstable/main i386 python3 i386 3.12.7-1 [27.8 kB]
Get: 26 http://deb.debian.org/debian unstable/main i386 sgml-base all 1.31 [15.4 kB]
Get: 27 http://deb.debian.org/debian unstable/main i386 libproc2-0 i386 2:4.0.4-6 [65.7 kB]
Get: 28 http://deb.debian.org/debian unstable/main i386 procps i386 2:4.0.4-6 [876 kB]
Get: 29 http://deb.debian.org/debian unstable/main i386 sensible-utils all 0.0.24 [24.8 kB]
Get: 30 http://deb.debian.org/debian unstable/main i386 libmagic-mgc i386 1:5.45-3+b1 [314 kB]
Get: 31 http://deb.debian.org/debian unstable/main i386 libmagic1t64 i386 1:5.45-3+b1 [115 kB]
Get: 32 http://deb.debian.org/debian unstable/main i386 file i386 1:5.45-3+b1 [43.2 kB]
Get: 33 http://deb.debian.org/debian unstable/main i386 gettext-base i386 0.22.5-3 [201 kB]
Get: 34 http://deb.debian.org/debian unstable/main i386 libuchardet0 i386 0.0.8-1+b2 [69.2 kB]
Get: 35 http://deb.debian.org/debian unstable/main i386 groff-base i386 1.23.0-6 [1198 kB]
Get: 36 http://deb.debian.org/debian unstable/main i386 bsdextrautils i386 2.40.2-12 [95.9 kB]
Get: 37 http://deb.debian.org/debian unstable/main i386 libpipeline1 i386 1.5.8-1 [41.2 kB]
Get: 38 http://deb.debian.org/debian unstable/main i386 man-db i386 2.13.0-1 [1428 kB]
Get: 39 http://deb.debian.org/debian unstable/main i386 ucf all 3.0045 [45.2 kB]
Get: 40 http://deb.debian.org/debian unstable/main i386 autoconf all 2.72-3 [493 kB]
Get: 41 http://deb.debian.org/debian unstable/main i386 autotools-dev all 20220109.1 [51.6 kB]
Get: 42 http://deb.debian.org/debian unstable/main i386 automake all 1:1.16.5-1.3 [823 kB]
Get: 43 http://deb.debian.org/debian unstable/main i386 autopoint all 0.22.5-3 [723 kB]
Get: 44 http://deb.debian.org/debian unstable/main i386 xml-core all 0.19 [20.1 kB]
Get: 45 http://deb.debian.org/debian unstable/main i386 sgml-data all 2.0.11+nmu1 [179 kB]
Get: 46 http://deb.debian.org/debian unstable/main i386 docbook-xml all 4.5-13 [77.4 kB]
Get: 47 http://deb.debian.org/debian unstable/main i386 python-apt-common all 2.9.4 [68.0 kB]
Get: 48 http://deb.debian.org/debian unstable/main i386 distro-info-data all 0.63 [6408 B]
Get: 49 http://deb.debian.org/debian unstable/main i386 python3-apt i386 2.9.4 [175 kB]
Get: 50 http://deb.debian.org/debian unstable/main i386 tex-common all 6.18 [32.5 kB]
Get: 51 http://deb.debian.org/debian unstable/main i386 libpaper1 i386 1.1.29+b2 [13.0 kB]
Get: 52 http://deb.debian.org/debian unstable/main i386 libpaper-utils i386 1.1.29+b2 [9304 B]
Get: 53 http://deb.debian.org/debian unstable/main i386 libkpathsea6 i386 2024.20240313.70630+ds-5 [160 kB]
Get: 54 http://deb.debian.org/debian unstable/main i386 libptexenc1 i386 2024.20240313.70630+ds-5 [50.0 kB]
Get: 55 http://deb.debian.org/debian unstable/main i386 libsynctex2 i386 2024.20240313.70630+ds-5 [65.6 kB]
Get: 56 http://deb.debian.org/debian unstable/main i386 libtexlua53-5 i386 2024.20240313.70630+ds-5 [129 kB]
Get: 57 http://deb.debian.org/debian unstable/main i386 t1utils i386 1.41-4 [62.3 kB]
Get: 58 http://deb.debian.org/debian unstable/main i386 libbrotli1 i386 1.1.0-2+b6 [308 kB]
Get: 59 http://deb.debian.org/debian unstable/main i386 libpng16-16t64 i386 1.6.44-3 [288 kB]
Get: 60 http://deb.debian.org/debian unstable/main i386 libfreetype6 i386 2.13.3+dfsg-1 [464 kB]
Get: 61 http://deb.debian.org/debian unstable/main i386 fonts-dejavu-mono all 2.37-8 [489 kB]
Get: 62 http://deb.debian.org/debian unstable/main i386 fonts-dejavu-core all 2.37-8 [840 kB]
Get: 63 http://deb.debian.org/debian unstable/main i386 fontconfig-config i386 2.15.0-1.1+b1 [318 kB]
Get: 64 http://deb.debian.org/debian unstable/main i386 libfontconfig1 i386 2.15.0-1.1+b1 [402 kB]
Get: 65 http://deb.debian.org/debian unstable/main i386 libpixman-1-0 i386 0.44.0-3 [246 kB]
Get: 66 http://deb.debian.org/debian unstable/main i386 libxau6 i386 1:1.0.11-1 [20.7 kB]
Get: 67 http://deb.debian.org/debian unstable/main i386 libxdmcp6 i386 1:1.1.5-1 [28.2 kB]
Get: 68 http://deb.debian.org/debian unstable/main i386 libxcb1 i386 1.17.0-2+b1 [148 kB]
Get: 69 http://deb.debian.org/debian unstable/main i386 libx11-data all 2:1.8.10-2 [337 kB]
Get: 70 http://deb.debian.org/debian unstable/main i386 libx11-6 i386 2:1.8.10-2 [834 kB]
Get: 71 http://deb.debian.org/debian unstable/main i386 libxcb-render0 i386 1.17.0-2+b1 [116 kB]
Get: 72 http://deb.debian.org/debian unstable/main i386 libxcb-shm0 i386 1.17.0-2+b1 [105 kB]
Get: 73 http://deb.debian.org/debian unstable/main i386 libxext6 i386 2:1.3.4-1+b2 [52.6 kB]
Get: 74 http://deb.debian.org/debian unstable/main i386 libxrender1 i386 1:0.9.10-1.1+b3 [28.8 kB]
Get: 75 http://deb.debian.org/debian unstable/main i386 libcairo2 i386 1.18.2-2 [591 kB]
Get: 76 http://deb.debian.org/debian unstable/main i386 libgraphite2-3 i386 1.3.14-2+b1 [77.8 kB]
Get: 77 http://deb.debian.org/debian unstable/main i386 libglib2.0-0t64 i386 2.82.4-1 [1572 kB]
Get: 78 http://deb.debian.org/debian unstable/main i386 libharfbuzz0b i386 10.1.0-1 [503 kB]
Get: 79 http://deb.debian.org/debian unstable/main i386 libicu72 i386 72.1-5+b1 [9583 kB]
Get: 80 http://deb.debian.org/debian unstable/main i386 libmpfi0 i386 1.5.4+ds-4 [38.8 kB]
Get: 81 http://deb.debian.org/debian unstable/main i386 libpotrace0 i386 1.16-2+b2 [24.5 kB]
Get: 82 http://deb.debian.org/debian unstable/main i386 libteckit0 i386 2.5.12+ds1-1+b1 [285 kB]
Get: 83 http://deb.debian.org/debian unstable/main i386 x11-common all 1:7.7+23.1 [216 kB]
Get: 84 http://deb.debian.org/debian unstable/main i386 libice6 i386 2:1.1.1-1 [67.8 kB]
Get: 85 http://deb.debian.org/debian unstable/main i386 libsm6 i386 2:1.2.4-1 [35.9 kB]
Get: 86 http://deb.debian.org/debian unstable/main i386 libxt6t64 i386 1:1.2.1-1.2+b1 [193 kB]
Get: 87 http://deb.debian.org/debian unstable/main i386 libxmu6 i386 2:1.1.3-3+b3 [60.9 kB]
Get: 88 http://deb.debian.org/debian unstable/main i386 libxpm4 i386 1:3.5.17-1+b2 [58.3 kB]
Get: 89 http://deb.debian.org/debian unstable/main i386 libxaw7 i386 2:1.0.16-1 [220 kB]
Get: 90 http://deb.debian.org/debian unstable/main i386 libxi6 i386 2:1.8.2-1 [81.2 kB]
Get: 91 http://deb.debian.org/debian unstable/main i386 libzzip-0-13t64 i386 0.13.72+dfsg.1-1.3 [58.0 kB]
Get: 92 http://deb.debian.org/debian unstable/main i386 texlive-binaries i386 2024.20240313.70630+ds-5 [8368 kB]
Get: 93 http://deb.debian.org/debian unstable/main i386 xdg-utils all 1.2.1-2 [75.8 kB]
Get: 94 http://deb.debian.org/debian unstable/main i386 texlive-base all 2024.20241115-1 [22.7 MB]
Get: 95 http://deb.debian.org/debian unstable/main i386 texlive-fonts-recommended all 2024.20241115-1 [4991 kB]
Get: 96 http://deb.debian.org/debian unstable/main i386 fonts-lmodern all 2.005-1 [4540 kB]
Get: 97 http://deb.debian.org/debian unstable/main i386 texlive-latex-base all 2024.20241115-1 [1278 kB]
Get: 98 http://deb.debian.org/debian unstable/main i386 texlive-latex-recommended all 2024.20241115-1 [8757 kB]
Get: 99 http://deb.debian.org/debian unstable/main i386 texlive all 2024.20241115-1 [18.6 kB]
Get: 100 http://deb.debian.org/debian unstable/main i386 libio-string-perl all 1.08-4 [12.1 kB]
Get: 101 http://deb.debian.org/debian unstable/main i386 liblatex-tounicode-perl all 0.55-1 [28.8 kB]
Get: 102 http://deb.debian.org/debian unstable/main i386 libbibtex-parser-perl all 1.05+dfsg-1 [17.4 kB]
Get: 103 http://deb.debian.org/debian unstable/main i386 texlive-bibtex-extra all 2024.20241115-1 [80.0 MB]
Get: 104 http://deb.debian.org/debian unstable/main i386 libfile-which-perl all 1.27-2 [15.1 kB]
Get: 105 http://deb.debian.org/debian unstable/main i386 libfile-homedir-perl all 1.006-2 [42.4 kB]
Get: 106 http://deb.debian.org/debian unstable/main i386 libthai-data all 0.1.29-2 [168 kB]
Get: 107 http://deb.debian.org/debian unstable/main i386 libdatrie1 i386 0.2.13-3+b1 [39.9 kB]
Get: 108 http://deb.debian.org/debian unstable/main i386 libthai0 i386 0.1.29-2+b1 [50.3 kB]
Get: 109 http://deb.debian.org/debian unstable/main i386 libsombok3 i386 2.4.0-2+b2 [33.6 kB]
Get: 110 http://deb.debian.org/debian unstable/main i386 libmime-charset-perl all 1.013.1-2 [34.0 kB]
Get: 111 http://deb.debian.org/debian unstable/main i386 libunicode-linebreak-perl i386 0.0.20190101-1+b7 [97.5 kB]
Get: 112 http://deb.debian.org/debian unstable/main i386 libyaml-tiny-perl all 1.74-1 [30.7 kB]
Get: 113 http://deb.debian.org/debian unstable/main i386 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB]
Get: 114 http://deb.debian.org/debian unstable/main i386 libfontenc1 i386 1:1.1.8-1+b1 [23.4 kB]
Get: 115 http://deb.debian.org/debian unstable/main i386 xfonts-encodings all 1:1.0.4-2.2 [577 kB]
Get: 116 http://deb.debian.org/debian unstable/main i386 xfonts-utils i386 1:7.7+7 [95.1 kB]
Get: 117 http://deb.debian.org/debian unstable/main i386 lmodern all 2.005-1 [9480 kB]
Get: 118 http://deb.debian.org/debian unstable/main i386 texlive-luatex all 2024.20241115-1 [27.8 MB]
Get: 119 http://deb.debian.org/debian unstable/main i386 texlive-plain-generic all 2024.20241115-1 [28.6 MB]
Get: 120 http://deb.debian.org/debian unstable/main i386 texlive-extra-utils all 2024.20241115-1 [64.6 MB]
Get: 121 http://deb.debian.org/debian unstable/main i386 libapache-pom-java all 33-2 [5852 B]
Get: 122 http://deb.debian.org/debian unstable/main i386 libcommons-parent-java all 56-1 [10.8 kB]
Get: 123 http://deb.debian.org/debian unstable/main i386 libcommons-logging-java all 1.3.0-1 [68.6 kB]
Get: 124 http://deb.debian.org/debian unstable/main i386 libfontbox-java all 1:1.8.16-5 [211 kB]
Get: 125 http://deb.debian.org/debian unstable/main i386 libpdfbox-java all 1:1.8.16-5 [5527 kB]
Get: 126 http://deb.debian.org/debian unstable/main i386 preview-latex-style all 13.2-1 [350 kB]
Get: 127 http://deb.debian.org/debian unstable/main i386 texlive-pictures all 2024.20241115-1 [17.0 MB]
Get: 128 http://deb.debian.org/debian unstable/main i386 texlive-latex-extra all 2024.20241115-1 [24.6 MB]
Get: 129 http://deb.debian.org/debian unstable/main i386 fonts-gfs-baskerville all 1.1-6 [43.7 kB]
Get: 130 http://deb.debian.org/debian unstable/main i386 fonts-gfs-porson all 1.1-7 [33.8 kB]
Get: 131 http://deb.debian.org/debian unstable/main i386 texlive-lang-greek all 2024.20241115-1 [79.2 MB]
Get: 132 http://deb.debian.org/debian unstable/main i386 texlive-science all 2024.20241115-1 [3876 kB]
Get: 133 http://deb.debian.org/debian unstable/main i386 libxml2 i386 2.12.7+dfsg+really2.9.14-0.2+b1 [734 kB]
Get: 134 http://deb.debian.org/debian unstable/main i386 libxslt1.1 i386 1.1.35-1.1+b1 [243 kB]
Get: 135 http://deb.debian.org/debian unstable/main i386 xsltproc i386 1.1.35-1.1+b1 [115 kB]
Get: 136 http://deb.debian.org/debian unstable/main i386 dblatex all 0.3.12py3-4 [359 kB]
Get: 137 http://deb.debian.org/debian unstable/main i386 libdebhelper-perl all 13.21 [88.9 kB]
Get: 138 http://deb.debian.org/debian unstable/main i386 libtool all 2.4.7-8 [517 kB]
Get: 139 http://deb.debian.org/debian unstable/main i386 dh-autoreconf all 20 [17.1 kB]
Get: 140 http://deb.debian.org/debian unstable/main i386 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 141 http://deb.debian.org/debian unstable/main i386 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB]
Get: 142 http://deb.debian.org/debian unstable/main i386 dh-strip-nondeterminism all 1.14.0-1 [8448 B]
Get: 143 http://deb.debian.org/debian unstable/main i386 libelf1t64 i386 0.192-4 [195 kB]
Get: 144 http://deb.debian.org/debian unstable/main i386 dwz i386 0.15-1+b1 [116 kB]
Get: 145 http://deb.debian.org/debian unstable/main i386 gettext i386 0.22.5-3 [1631 kB]
Get: 146 http://deb.debian.org/debian unstable/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 147 http://deb.debian.org/debian unstable/main i386 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 148 http://deb.debian.org/debian unstable/main i386 debhelper all 13.21 [919 kB]
Get: 149 http://deb.debian.org/debian unstable/main i386 docbook-xsl all 1.79.2+dfsg-7 [1221 kB]
Get: 150 http://deb.debian.org/debian unstable/main i386 icu-devtools i386 72.1-5+b1 [218 kB]
Get: 151 http://deb.debian.org/debian unstable/main i386 libboost1.83-dev i386 1.83.0-4 [10.6 MB]
Get: 152 http://deb.debian.org/debian unstable/main i386 libboost-atomic1.83.0 i386 1.83.0-4 [234 kB]
Get: 153 http://deb.debian.org/debian unstable/main i386 libboost-atomic1.83-dev i386 1.83.0-4 [235 kB]
Get: 154 http://deb.debian.org/debian unstable/main i386 libboost-chrono1.83.0t64 i386 1.83.0-4 [241 kB]
Get: 155 http://deb.debian.org/debian unstable/main i386 libboost-chrono1.83-dev i386 1.83.0-4 [247 kB]
Get: 156 http://deb.debian.org/debian unstable/main i386 libboost-date-time1.83.0 i386 1.83.0-4 [230 kB]
Get: 157 http://deb.debian.org/debian unstable/main i386 libboost-serialization1.83.0 i386 1.83.0-4 [343 kB]
Get: 158 http://deb.debian.org/debian unstable/main i386 libboost-serialization1.83-dev i386 1.83.0-4 [386 kB]
Get: 159 http://deb.debian.org/debian unstable/main i386 libboost-date-time1.83-dev i386 1.83.0-4 [239 kB]
Get: 160 http://deb.debian.org/debian unstable/main i386 libboost-filesystem1.83.0 i386 1.83.0-4 [287 kB]
Get: 161 http://deb.debian.org/debian unstable/main i386 libboost-system1.83.0 i386 1.83.0-4 [230 kB]
Get: 162 http://deb.debian.org/debian unstable/main i386 libboost-system1.83-dev i386 1.83.0-4 [231 kB]
Get: 163 http://deb.debian.org/debian unstable/main i386 libboost-filesystem1.83-dev i386 1.83.0-4 [305 kB]
Get: 164 http://deb.debian.org/debian unstable/main i386 libboost-filesystem-dev i386 1.83.0.2+b2 [3640 B]
Get: 165 http://deb.debian.org/debian unstable/main i386 libboost-regex1.83.0 i386 1.83.0-4 [329 kB]
Get: 166 http://deb.debian.org/debian unstable/main i386 libicu-dev i386 72.1-5+b1 [10.6 MB]
Get: 167 http://deb.debian.org/debian unstable/main i386 libboost-regex1.83-dev i386 1.83.0-4 [347 kB]
Get: 168 http://deb.debian.org/debian unstable/main i386 libboost-iostreams1.83-dev i386 1.83.0-4 [264 kB]
Get: 169 http://deb.debian.org/debian unstable/main i386 libboost-iostreams-dev i386 1.83.0.2+b2 [3588 B]
Get: 170 http://deb.debian.org/debian unstable/main i386 libboost-regex-dev i386 1.83.0.2+b2 [3872 B]
Get: 171 http://deb.debian.org/debian unstable/main i386 libboost-system-dev i386 1.83.0.2+b2 [3740 B]
Get: 172 http://deb.debian.org/debian unstable/main i386 libboost-thread1.83.0 i386 1.83.0-4 [271 kB]
Get: 173 http://deb.debian.org/debian unstable/main i386 libboost-thread1.83-dev i386 1.83.0-4 [279 kB]
Get: 174 http://deb.debian.org/debian unstable/main i386 libboost-thread-dev i386 1.83.0.2+b2 [3632 B]
Get: 175 http://deb.debian.org/debian unstable/main i386 libbz2-dev i386 1.0.8-6 [32.1 kB]
Get: 176 http://deb.debian.org/debian unstable/main i386 libexpat1-dev i386 2.6.4-1 [165 kB]
Get: 177 http://deb.debian.org/debian unstable/main i386 libfl2 i386 2.6.4-8.2+b3 [84.3 kB]
Get: 178 http://deb.debian.org/debian unstable/main i386 libfl-dev i386 2.6.4-8.2+b3 [85.7 kB]
Get: 179 http://deb.debian.org/debian unstable/main i386 libtcmalloc-minimal4t64 i386 2.16-1 [91.4 kB]
Get: 180 http://deb.debian.org/debian unstable/main i386 libgoogle-perftools4t64 i386 2.16-1 [196 kB]
Get: 181 http://deb.debian.org/debian unstable/main i386 libgoogle-perftools-dev i386 2.16-1 [478 kB]
Get: 182 http://deb.debian.org/debian unstable/main i386 xxd i386 2:9.1.0861-1 [98.2 kB]
Get: 183 http://deb.debian.org/debian unstable/main i386 zlib1g-dev i386 1:1.3.dfsg+really1.3.1-1+b1 [916 kB]
Fetched 464 MB in 5s (96.2 MB/s)
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package autoconf-archive.
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Preparing to unpack .../0-autoconf-archive_20220903-3_all.deb ...
Unpacking autoconf-archive (20220903-3) ...
Selecting previously unselected package m4.
Preparing to unpack .../1-m4_1.4.19-4_i386.deb ...
Unpacking m4 (1.4.19-4) ...
Selecting previously unselected package flex.
Preparing to unpack .../2-flex_2.6.4-8.2+b3_i386.deb ...
Unpacking flex (2.6.4-8.2+b3) ...
Selecting previously unselected package libpython3.12-minimal:i386.
Preparing to unpack .../3-libpython3.12-minimal_3.12.8-3_i386.deb ...
Unpacking libpython3.12-minimal:i386 (3.12.8-3) ...
Selecting previously unselected package libexpat1:i386.
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Unpacking libexpat1:i386 (2.6.4-1) ...
Selecting previously unselected package python3.12-minimal.
Preparing to unpack .../5-python3.12-minimal_3.12.8-3_i386.deb ...
Unpacking python3.12-minimal (3.12.8-3) ...
Setting up libpython3.12-minimal:i386 (3.12.8-3) ...
Setting up libexpat1:i386 (2.6.4-1) ...
Setting up python3.12-minimal (3.12.8-3) ...
Selecting previously unselected package python3-minimal.
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Unpacking python3-minimal (3.12.7-1) ...
Selecting previously unselected package media-types.
Preparing to unpack .../01-media-types_10.1.0_all.deb ...
Unpacking media-types (10.1.0) ...
Selecting previously unselected package netbase.
Preparing to unpack .../02-netbase_6.4_all.deb ...
Unpacking netbase (6.4) ...
Selecting previously unselected package tzdata.
Preparing to unpack .../03-tzdata_2024b-4_all.deb ...
Unpacking tzdata (2024b-4) ...
Selecting previously unselected package libkrb5support0:i386.
Preparing to unpack .../04-libkrb5support0_1.21.3-3_i386.deb ...
Unpacking libkrb5support0:i386 (1.21.3-3) ...
Selecting previously unselected package libcom-err2:i386.
Preparing to unpack .../05-libcom-err2_1.47.2~rc1-2_i386.deb ...
Unpacking libcom-err2:i386 (1.47.2~rc1-2) ...
Selecting previously unselected package libk5crypto3:i386.
Preparing to unpack .../06-libk5crypto3_1.21.3-3_i386.deb ...
Unpacking libk5crypto3:i386 (1.21.3-3) ...
Selecting previously unselected package libkeyutils1:i386.
Preparing to unpack .../07-libkeyutils1_1.6.3-4_i386.deb ...
Unpacking libkeyutils1:i386 (1.6.3-4) ...
Selecting previously unselected package libkrb5-3:i386.
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Unpacking libkrb5-3:i386 (1.21.3-3) ...
Selecting previously unselected package libgssapi-krb5-2:i386.
Preparing to unpack .../09-libgssapi-krb5-2_1.21.3-3_i386.deb ...
Unpacking libgssapi-krb5-2:i386 (1.21.3-3) ...
Selecting previously unselected package libtirpc-common.
Preparing to unpack .../10-libtirpc-common_1.3.4+ds-1.3_all.deb ...
Unpacking libtirpc-common (1.3.4+ds-1.3) ...
Selecting previously unselected package libtirpc3t64:i386.
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Adding 'diversion of /lib/i386-linux-gnu/libtirpc.so.3 to /lib/i386-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64'
Adding 'diversion of /lib/i386-linux-gnu/libtirpc.so.3.0.0 to /lib/i386-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64'
Unpacking libtirpc3t64:i386 (1.3.4+ds-1.3+b1) ...
Selecting previously unselected package libnsl2:i386.
Preparing to unpack .../12-libnsl2_1.3.0-3+b3_i386.deb ...
Unpacking libnsl2:i386 (1.3.0-3+b3) ...
Selecting previously unselected package readline-common.
Preparing to unpack .../13-readline-common_8.2-6_all.deb ...
Unpacking readline-common (8.2-6) ...
Selecting previously unselected package libreadline8t64:i386.
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Adding 'diversion of /lib/i386-linux-gnu/libhistory.so.8 to /lib/i386-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/i386-linux-gnu/libhistory.so.8.2 to /lib/i386-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/i386-linux-gnu/libreadline.so.8 to /lib/i386-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/i386-linux-gnu/libreadline.so.8.2 to /lib/i386-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64'
Unpacking libreadline8t64:i386 (8.2-6) ...
Selecting previously unselected package libpython3.12-stdlib:i386.
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Unpacking libpython3.12-stdlib:i386 (3.12.8-3) ...
Selecting previously unselected package python3.12.
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Unpacking python3.12 (3.12.8-3) ...
Selecting previously unselected package libpython3-stdlib:i386.
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Unpacking libpython3-stdlib:i386 (3.12.7-1) ...
Setting up python3-minimal (3.12.7-1) ...
Selecting previously unselected package python3.
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Unpacking file (1:5.45-3+b1) ...
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Unpacking gettext-base (0.22.5-3) ...
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Unpacking groff-base (1.23.0-6) ...
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Unpacking bsdextrautils (2.40.2-12) ...
Selecting previously unselected package libpipeline1:i386.
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Unpacking libpipeline1:i386 (1.5.8-1) ...
Selecting previously unselected package man-db.
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Unpacking man-db (2.13.0-1) ...
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Moving old data out of the way
Unpacking ucf (3.0045) ...
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Unpacking autoconf (2.72-3) ...
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Unpacking autotools-dev (20220109.1) ...
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Unpacking docbook-xml (4.5-13) ...
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Unpacking libboost-filesystem1.83-dev:i386 (1.83.0-4) ...
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Unpacking libboost-filesystem-dev:i386 (1.83.0.2+b2) ...
Selecting previously unselected package libboost-regex1.83.0:i386.
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Unpacking libboost-regex1.83.0:i386 (1.83.0-4) ...
Selecting previously unselected package libicu-dev:i386.
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Unpacking libicu-dev:i386 (72.1-5+b1) ...
Selecting previously unselected package libboost-regex1.83-dev:i386.
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Unpacking libboost-regex1.83-dev:i386 (1.83.0-4) ...
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Unpacking libboost-regex-dev:i386 (1.83.0.2+b2) ...
Selecting previously unselected package libboost-system-dev:i386.
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Unpacking libboost-system-dev:i386 (1.83.0.2+b2) ...
Selecting previously unselected package libboost-thread1.83.0:i386.
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Unpacking libboost-thread1.83.0:i386 (1.83.0-4) ...
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Unpacking libboost-thread1.83-dev:i386 (1.83.0-4) ...
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Unpacking libboost-thread-dev:i386 (1.83.0.2+b2) ...
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Unpacking libbz2-dev:i386 (1.0.8-6) ...
Selecting previously unselected package libexpat1-dev:i386.
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Unpacking libexpat1-dev:i386 (2.6.4-1) ...
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Unpacking libfl2:i386 (2.6.4-8.2+b3) ...
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Unpacking libfl-dev:i386 (2.6.4-8.2+b3) ...
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Unpacking libtcmalloc-minimal4t64:i386 (2.16-1) ...
Selecting previously unselected package libgoogle-perftools4t64:i386.
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Unpacking xxd (2:9.1.0861-1) ...
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Unpacking zlib1g-dev:i386 (1:1.3.dfsg+really1.3.1-1+b1) ...
Setting up media-types (10.1.0) ...
Setting up libpipeline1:i386 (1.5.8-1) ...
Setting up libgraphite2-3:i386 (1.3.14-2+b1) ...
Setting up libpixman-1-0:i386 (0.44.0-3) ...
Setting up libfile-which-perl (1.27-2) ...
Setting up libxau6:i386 (1:1.0.11-1) ...
Setting up libxdmcp6:i386 (1:1.1.5-1) ...
Setting up libkeyutils1:i386 (1.6.3-4) ...
Setting up libboost1.83-dev:i386 (1.83.0-4) ...
Setting up libxcb1:i386 (1.17.0-2+b1) ...
Setting up libicu72:i386 (72.1-5+b1) ...
Setting up bsdextrautils (2.40.2-12) ...
Setting up fonts-gfs-porson (1.1-7) ...
Setting up libboost-date-time1.83.0:i386 (1.83.0-4) ...
Setting up libdatrie1:i386 (0.2.13-3+b1) ...
Setting up libmagic-mgc (1:5.45-3+b1) ...
Setting up libxcb-render0:i386 (1.17.0-2+b1) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up distro-info-data (0.63) ...
Setting up libtirpc-common (1.3.4+ds-1.3) ...
Setting up libboost-regex1.83.0:i386 (1.83.0-4) ...
Setting up libdebhelper-perl (13.21) ...
Setting up libbrotli1:i386 (1.1.0-2+b6) ...
Setting up libfontbox-java (1:1.8.16-5) ...
Setting up liblatex-tounicode-perl (0.55-1) ...
Setting up libboost-system1.83.0:i386 (1.83.0-4) ...
Setting up libmagic1t64:i386 (1:5.45-3+b1) ...
Setting up x11-common (1:7.7+23.1) ...
invoke-rc.d: could not determine current runlevel
Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix.
Setting up libboost-thread1.83.0:i386 (1.83.0-4) ...
Setting up gettext-base (0.22.5-3) ...
Setting up m4 (1.4.19-4) ...
Setting up autoconf-archive (20220903-3) ...
Setting up libxcb-shm0:i386 (1.17.0-2+b1) ...
Setting up libcom-err2:i386 (1.47.2~rc1-2) ...
Setting up file (1:5.45-3+b1) ...
Setting up libboost-filesystem1.83.0:i386 (1.83.0-4) ...
Setting up libyaml-tiny-perl (1.74-1) ...
Setting up xxd (2:9.1.0861-1) ...
Setting up libelf1t64:i386 (0.192-4) ...
Setting up libkrb5support0:i386 (1.21.3-3) ...
Setting up tzdata (2024b-4) ...

Current default time zone: 'Etc/UTC'
Local time is now:      Tue Jan 20 11:52:03 UTC 2026.
Universal Time is now:  Tue Jan 20 11:52:03 UTC 2026.
Run 'dpkg-reconfigure tzdata' if you wish to change it.

Setting up libboost-atomic1.83.0:i386 (1.83.0-4) ...
Setting up libboost-serialization1.83.0:i386 (1.83.0-4) ...
Setting up libio-string-perl (1.08-4) ...
Setting up libfontenc1:i386 (1:1.1.8-1+b1) ...
Setting up autotools-dev (20220109.1) ...
Setting up libglib2.0-0t64:i386 (2.82.4-1) ...
No schema files found: doing nothing.
Setting up libexpat1-dev:i386 (2.6.4-1) ...
Setting up libzzip-0-13t64:i386 (0.13.72+dfsg.1-1.3) ...
Setting up libx11-data (2:1.8.10-2) ...
Setting up libboost-chrono1.83.0t64:i386 (1.83.0-4) ...
Setting up libteckit0:i386 (2.5.12+ds1-1+b1) ...
Setting up libapache-pom-java (33-2) ...
Setting up xfonts-encodings (1:1.0.4-2.2) ...
Setting up t1utils (1.41-4) ...
Setting up libtexlua53-5:i386 (2024.20240313.70630+ds-5) ...
Setting up libproc2-0:i386 (2:4.0.4-6) ...
Setting up fonts-dejavu-mono (2.37-8) ...
Setting up libpng16-16t64:i386 (1.6.44-3) ...
Setting up autopoint (0.22.5-3) ...
Setting up libmpfi0:i386 (1.5.4+ds-4) ...
Setting up libtcmalloc-minimal4t64:i386 (2.16-1) ...
Setting up icu-devtools (72.1-5+b1) ...
Setting up fonts-dejavu-core (2.37-8) ...
Setting up libfl2:i386 (2.6.4-8.2+b3) ...
Setting up libk5crypto3:i386 (1.21.3-3) ...
Setting up libkpathsea6:i386 (2024.20240313.70630+ds-5) ...
Setting up libboost-atomic1.83-dev:i386 (1.83.0-4) ...
Setting up autoconf (2.72-3) ...
Setting up zlib1g-dev:i386 (1:1.3.dfsg+really1.3.1-1+b1) ...
Setting up dwz (0.15-1+b1) ...
Setting up python-apt-common (2.9.4) ...
Setting up fonts-gfs-baskerville (1.1-6) ...
Setting up sensible-utils (0.0.24) ...
Setting up libmime-charset-perl (1.013.1-2) ...
Setting up libuchardet0:i386 (0.0.8-1+b2) ...
Setting up procps (2:4.0.4-6) ...
Setting up fonts-lmodern (2.005-1) ...
Setting up libx11-6:i386 (2:1.8.10-2) ...
Setting up libthai-data (0.1.29-2) ...
Setting up netbase (6.4) ...
Setting up sgml-base (1.31) ...
Setting up libkrb5-3:i386 (1.21.3-3) ...
Setting up libboost-system1.83-dev:i386 (1.83.0-4) ...
Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ...
Setting up libfile-homedir-perl (1.006-2) ...
Setting up readline-common (8.2-6) ...
Setting up libicu-dev:i386 (72.1-5+b1) ...
Setting up libxml2:i386 (2.12.7+dfsg+really2.9.14-0.2+b1) ...
Setting up xdg-utils (1.2.1-2) ...
update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode
Setting up libsynctex2:i386 (2024.20240313.70630+ds-5) ...
Setting up libbz2-dev:i386 (1.0.8-6) ...
Setting up libpotrace0:i386 (1.16-2+b2) ...
Setting up automake (1:1.16.5-1.3) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libfile-stripnondeterminism-perl (1.14.0-1) ...
Setting up libice6:i386 (2:1.1.1-1) ...
Setting up flex (2.6.4-8.2+b3) ...
Setting up gettext (0.22.5-3) ...
Setting up libpdfbox-java (1:1.8.16-5) ...
Setting up libboost-chrono1.83-dev:i386 (1.83.0-4) ...
Setting up libxpm4:i386 (1:3.5.17-1+b2) ...
Setting up libgoogle-perftools4t64:i386 (2.16-1) ...
Setting up libxrender1:i386 (1:0.9.10-1.1+b3) ...
Setting up libtool (2.4.7-8) ...
Setting up fontconfig-config (2.15.0-1.1+b1) ...
Setting up libgoogle-perftools-dev:i386 (2.16-1) ...
Setting up libboost-system-dev:i386 (1.83.0.2+b2) ...
Setting up libcommons-parent-java (56-1) ...
Setting up libboost-serialization1.83-dev:i386 (1.83.0-4) ...
Setting up libcommons-logging-java (1.3.0-1) ...
Setting up libxext6:i386 (2:1.3.4-1+b2) ...
Setting up libboost-filesystem1.83-dev:i386 (1.83.0-4) ...
Setting up libbibtex-parser-perl (1.05+dfsg-1) ...
Setting up libfl-dev:i386 (2.6.4-8.2+b3) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up dh-autoreconf (20) ...
Setting up libthai0:i386 (0.1.29-2+b1) ...
Setting up libptexenc1:i386 (2024.20240313.70630+ds-5) ...
Setting up libfreetype6:i386 (2.13.3+dfsg-1) ...
Setting up libboost-date-time1.83-dev:i386 (1.83.0-4) ...
Setting up libgssapi-krb5-2:i386 (1.21.3-3) ...
Setting up libboost-regex1.83-dev:i386 (1.83.0-4) ...
Setting up ucf (3.0045) ...
Setting up libreadline8t64:i386 (8.2-6) ...
Setting up dh-strip-nondeterminism (1.14.0-1) ...
Setting up groff-base (1.23.0-6) ...
Setting up xml-core (0.19) ...
Setting up libxslt1.1:i386 (1.1.35-1.1+b1) ...
Setting up libharfbuzz0b:i386 (10.1.0-1) ...
Setting up libfontconfig1:i386 (2.15.0-1.1+b1) ...
Setting up libboost-regex-dev:i386 (1.83.0.2+b2) ...
Setting up libsm6:i386 (2:1.2.4-1) ...
Setting up libboost-filesystem-dev:i386 (1.83.0.2+b2) ...
Setting up libboost-thread1.83-dev:i386 (1.83.0-4) ...
Setting up libpaper1:i386 (1.1.29+b2) ...
Creating config file /etc/papersize with new version
Setting up libxi6:i386 (2:1.8.2-1) ...
Setting up libtirpc3t64:i386 (1.3.4+ds-1.3+b1) ...
Setting up libsombok3:i386 (2.4.0-2+b2) ...
Setting up libboost-iostreams1.83-dev:i386 (1.83.0-4) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up xsltproc (1.1.35-1.1+b1) ...
Setting up libpaper-utils (1.1.29+b2) ...
Setting up libboost-iostreams-dev:i386 (1.83.0.2+b2) ...
Setting up xfonts-utils (1:7.7+7) ...
Setting up man-db (2.13.0-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libcairo2:i386 (1.18.2-2) ...
Setting up tex-common (6.18) ...
update-language: texlive-base not installed and configured, doing nothing!
Setting up libunicode-linebreak-perl (0.0.20190101-1+b7) ...
Setting up libxt6t64:i386 (1:1.2.1-1.2+b1) ...
Setting up lmodern (2.005-1) ...
Setting up libnsl2:i386 (1.3.0-3+b3) ...
Setting up libboost-thread-dev:i386 (1.83.0.2+b2) ...
Setting up libxmu6:i386 (2:1.1.3-3+b3) ...
Setting up libpython3.12-stdlib:i386 (3.12.8-3) ...
Setting up preview-latex-style (13.2-1) ...
Setting up python3.12 (3.12.8-3) ...
Setting up debhelper (13.21) ...
Setting up libxaw7:i386 (2:1.0.16-1) ...
Setting up texlive-binaries (2024.20240313.70630+ds-5) ...
update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode
update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode
Setting up texlive-base (2024.20241115-1) ...
tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps
tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg
tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper
tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/tex-ini-files/pdftexconfig.tex
Setting up libpython3-stdlib:i386 (3.12.7-1) ...
Setting up texlive-luatex (2024.20241115-1) ...
Setting up texlive-plain-generic (2024.20241115-1) ...
Setting up python3 (3.12.7-1) ...
Setting up texlive-lang-greek (2024.20241115-1) ...
Setting up texlive-latex-base (2024.20241115-1) ...
Setting up texlive-extra-utils (2024.20241115-1) ...
Setting up texlive-latex-recommended (2024.20241115-1) ...
Setting up texlive-pictures (2024.20241115-1) ...
Setting up texlive-fonts-recommended (2024.20241115-1) ...
Setting up texlive (2024.20241115-1) ...
Setting up python3-apt (2.9.4) ...
Setting up texlive-science (2024.20241115-1) ...
Setting up texlive-latex-extra (2024.20241115-1) ...
Setting up texlive-bibtex-extra (2024.20241115-1) ...
Processing triggers for libc-bin (2.40-4) ...
Processing triggers for sgml-base (1.31) ...
Setting up docbook-xsl (1.79.2+dfsg-7) ...
Setting up sgml-data (2.0.11+nmu1) ...
Processing triggers for sgml-base (1.31) ...
Setting up docbook-xml (4.5-13) ...
Processing triggers for sgml-base (1.31) ...
Setting up dblatex (0.3.12py3-4) ...
Processing triggers for tex-common (6.18) ...
Running updmap-sys. This may take some time... done.
Running mktexlsr /var/lib/texmf ... done.
Building format(s) --all.
	This may take some time... done.
Reading package lists...
Building dependency tree...
Reading state information...
Reading extended state information...
Initializing package states...
Writing extended state information...
Building tag database...
 -> Finished parsing the build-deps
I: Building the package
I: user script /srv/workspace/pbuilder/2805/tmp/hooks/A99_set_merged_usr starting
Not re-configuring usrmerge for unstable
I: user script /srv/workspace/pbuilder/2805/tmp/hooks/A99_set_merged_usr finished
hostname: Name or service not known
I: Running cd /build/reproducible-path/mira-4.9.6/ && 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  > ../mira_4.9.6-11_source.changes
dpkg-buildpackage: info: source package mira
dpkg-buildpackage: info: source version 4.9.6-11
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Andreas Tille <tille@debian.org>
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture i386
 debian/rules clean
dh clean
   debian/rules override_dh_auto_clean
make[1]: Entering directory '/build/reproducible-path/mira-4.9.6'
( cd doc ; make clean ) || true
make[2]: Entering directory '/build/reproducible-path/mira-4.9.6/doc'
cd .. && make  am--refresh
make[3]: Entering directory '/build/reproducible-path/mira-4.9.6'
make[3]: *** No rule to make target 'am--refresh'.  Stop.
make[3]: Leaving directory '/build/reproducible-path/mira-4.9.6'
make[2]: *** [Makefile:263: ../config.status] Error 2
make[2]: Leaving directory '/build/reproducible-path/mira-4.9.6/doc'
dh_auto_clean || true
find * -name Makefile -exec rm '{}' ';'
find * -name '*.xxd.H' -exec rm '{}' ';'
find * -name '*.par.H' -exec rm '{}' ';'
find * -name 'compileinfo.*' -exec rm '{}' ';'
if [ -f .version.bak ] ; then mv .version.bak .version; fi
make[1]: Leaving directory '/build/reproducible-path/mira-4.9.6'
   dh_clean
	rm -f debian/debhelper-build-stamp
	rm -rf debian/.debhelper/
	rm -f -- debian/mira-assembler.substvars debian/mira-rfam-12s-rrna.substvars debian/mira-doc.substvars debian/files
	rm -fr -- debian/mira-assembler/ debian/tmp/ debian/mira-rfam-12s-rrna/ debian/mira-doc/
	find .  \( \( \
		\( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \
	        \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
		 -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
		 -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
		 -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \
		\) -exec rm -f {} + \) -o \
		\( -type d -a \( -name autom4te.cache -o -name __pycache__ \) -prune -exec rm -rf {} + \) \)
 debian/rules binary
dh binary
   dh_update_autotools_config
	cp -an --reflink=auto config.guess debian/.debhelper/bucket/files/9be3de218833c076786b919dc34aab691611f4cd73316e7705f2673e2c41921b.tmp
	mv debian/.debhelper/bucket/files/9be3de218833c076786b919dc34aab691611f4cd73316e7705f2673e2c41921b.tmp debian/.debhelper/bucket/files/9be3de218833c076786b919dc34aab691611f4cd73316e7705f2673e2c41921b
	cp -f /usr/share/misc/config.guess ./config.guess
	cp -an --reflink=auto config.sub debian/.debhelper/bucket/files/e308ae7f7f524bd790f8d4457c7c0a30f8403ffff4dd0b7d4388daca24275db4.tmp
	mv debian/.debhelper/bucket/files/e308ae7f7f524bd790f8d4457c7c0a30f8403ffff4dd0b7d4388daca24275db4.tmp debian/.debhelper/bucket/files/e308ae7f7f524bd790f8d4457c7c0a30f8403ffff4dd0b7d4388daca24275db4
	cp -f /usr/share/misc/config.sub ./config.sub
   dh_autoreconf
	find ! -ipath "./debian/*" -a ! \( -path '*/.git/*' -o -path '*/.hg/*' -o -path '*/.bzr/*' -o -path '*/.svn/*' -o -path '*/CVS/*' \) -a  -type f -exec md5sum {} + -o -type l -printf "symlink  %p
" > debian/autoreconf.before
	grep -q ^XDT_ configure.ac
	autoreconf -f -i
libtoolize: putting auxiliary files in '.'.
libtoolize: copying file './ltmain.sh'
libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'.
libtoolize: copying file 'm4/libtool.m4'
libtoolize: copying file 'm4/ltoptions.m4'
libtoolize: copying file 'm4/ltsugar.m4'
libtoolize: copying file 'm4/ltversion.m4'
libtoolize: copying file 'm4/lt~obsolete.m4'
configure.ac:38: warning: The macro 'AC_HELP_STRING' is obsolete.
configure.ac:38: You should run autoupdate.
./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from...
configure.ac:38: the top level
configure.ac:46: warning: The macro 'AC_HELP_STRING' is obsolete.
configure.ac:46: You should run autoupdate.
./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from...
configure.ac:46: the top level
configure.ac:190: warning: The macro 'AC_HELP_STRING' is obsolete.
configure.ac:190: You should run autoupdate.
./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from...
configure.ac:190: the top level
configure.ac:328: warning: The macro 'AC_TRY_COMPILE' is obsolete.
configure.ac:328: You should run autoupdate.
./lib/autoconf/general.m4:2845: AC_TRY_COMPILE is expanded from...
configure.ac:328: the top level
configure.ac:419: warning: The macro 'AC_HELP_STRING' is obsolete.
configure.ac:419: You should run autoupdate.
./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from...
configure.ac:419: the top level
configure.ac:423: warning: The macro 'AC_HELP_STRING' is obsolete.
configure.ac:423: You should run autoupdate.
./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from...
configure.ac:423: the top level
configure.ac:663: warning: AC_PROG_LEX without either yywrap or noyywrap is obsolete
./lib/autoconf/programs.m4:743: _AC_PROG_LEX is expanded from...
./lib/autoconf/programs.m4:736: AC_PROG_LEX is expanded from...
configure.ac:663: the top level
configure.ac:670: warning: The macro 'AC_HEADER_STDC' is obsolete.
configure.ac:670: You should run autoupdate.
./lib/autoconf/headers.m4:663: AC_HEADER_STDC is expanded from...
configure.ac:670: the top level
configure.ac:715: warning: The macro 'AC_TRY_LINK' is obsolete.
configure.ac:715: You should run autoupdate.
./lib/autoconf/general.m4:2918: AC_TRY_LINK is expanded from...
lib/m4sugar/m4sh.m4:690: _AS_IF_ELSE is expanded from...
lib/m4sugar/m4sh.m4:697: AS_IF is expanded from...
./lib/autoconf/general.m4:2249: AC_CACHE_VAL is expanded from...
./lib/autoconf/general.m4:2270: AC_CACHE_CHECK is expanded from...
configure.ac:702: SUDO_FUNC_ISBLANK is expanded from...
configure.ac:715: the top level
configure.ac:1033: warning: The macro 'AC_LANG_C' is obsolete.
configure.ac:1033: You should run autoupdate.
./lib/autoconf/c.m4:72: AC_LANG_C is expanded from...
m4/ax_check_zlib.m4:63: AX_CHECK_ZLIB is expanded from...
configure.ac:1033: the top level
configure.ac:1045: warning: The macro 'AC_LANG_C' is obsolete.
configure.ac:1045: You should run autoupdate.
./lib/autoconf/c.m4:72: AC_LANG_C is expanded from...
configure.ac:1045: the top level
configure.ac:1134: warning: The macro 'AC_HELP_STRING' is obsolete.
configure.ac:1134: You should run autoupdate.
./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from...
configure.ac:1134: the top level
configure.ac:1143: warning: The macro 'AC_HELP_STRING' is obsolete.
configure.ac:1143: You should run autoupdate.
./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from...
configure.ac:1143: the top level
configure.ac:1154: warning: The macro 'AC_HELP_STRING' is obsolete.
configure.ac:1154: You should run autoupdate.
./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from...
configure.ac:1154: the top level
configure.ac:1197: warning: The macro 'AC_HELP_STRING' is obsolete.
configure.ac:1197: You should run autoupdate.
./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from...
configure.ac:1197: the top level
configure.ac:1248: warning: The macro 'AC_HELP_STRING' is obsolete.
configure.ac:1248: You should run autoupdate.
./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from...
configure.ac:1248: the top level
configure.ac:1347: warning: The macro 'AC_HELP_STRING' is obsolete.
configure.ac:1347: You should run autoupdate.
./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from...
configure.ac:1347: the top level
configure.ac:1366: warning: The macro 'AC_HELP_STRING' is obsolete.
configure.ac:1366: You should run autoupdate.
./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from...
configure.ac:1366: the top level
configure.ac:1383: warning: The macro 'AC_HELP_STRING' is obsolete.
configure.ac:1383: You should run autoupdate.
./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from...
configure.ac:1383: the top level
configure.ac:1401: warning: The macro 'AC_HELP_STRING' is obsolete.
configure.ac:1401: You should run autoupdate.
./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from...
configure.ac:1401: the top level
configure.ac:1417: warning: The macro 'AC_HELP_STRING' is obsolete.
configure.ac:1417: You should run autoupdate.
./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from...
configure.ac:1417: the top level
configure.ac:1428: warning: The macro 'AC_HELP_STRING' is obsolete.
configure.ac:1428: You should run autoupdate.
./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from...
configure.ac:1428: the top level
configure.ac:1466: warning: AC_OUTPUT should be used without arguments.
configure.ac:1466: You should run autoupdate.
configure.ac:103: installing './compile'
configure.ac:9: installing './missing'
doc/docbook/Makefile.am:22: warning: '%'-style pattern rules are a GNU make extension
src/caf/Makefile.am: installing './depcomp'
src/io/Makefile.am:12: warning: '%'-style pattern rules are a GNU make extension
src/mira/Makefile.am:10: warning: '%'-style pattern rules are a GNU make extension
	find ! -ipath "./debian/*" -a ! \( -path '*/.git/*' -o -path '*/.hg/*' -o -path '*/.bzr/*' -o -path '*/.svn/*' -o -path '*/CVS/*' \) -a  -type f -exec md5sum {} + -o -type l -printf "symlink  %p
" > debian/autoreconf.after
   debian/rules override_dh_auto_configure
make[1]: Entering directory '/build/reproducible-path/mira-4.9.6'
cp -a .version .version.bak
dh_auto_configure -- --with-boost-libdir=/usr/lib/i386-linux-gnu	--with-boost=/usr
	./configure --build=i686-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/i386-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-boost-libdir=/usr/lib/i386-linux-gnu --with-boost=/usr
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a race-free mkdir -p... /usr/bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether UID '2222' is supported by ustar format... yes
checking whether GID '2222' is supported by ustar format... yes
checking how to create a ustar tar archive... gnutar
checking for a sed that does not truncate output... /usr/bin/sed
checking whether to add --prefix as include path... yes

+++++++++++++++++++++++++++++++++++++
systemuname: Linux
CFLAGS now: -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include
CXXFLAGS now: -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include
LDFLAGS now: -Wl,-z,relro -Wl,-z,now -L/usr/lib
+++++++++++++++++++++++++++++++++++++
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... none needed
checking whether gcc understands -c and -o together... yes
checking whether make supports the include directive... yes (GNU style)
checking dependency style of gcc... none
checking for g++... g++
checking whether the compiler supports GNU C++... yes
checking whether g++ accepts -g... yes
checking for g++ option to enable C++11 features... none needed
checking dependency style of g++... none
checking for OpenMP flag of C compiler... -fopenmp
Rescuing C++ flags for OpenMP
+++++++++++++++++++++++++++++++++++++
OpenMP CFLAGS: -fopenmp
OpenMP CXXFLAGS: -fopenmp
+++++++++++++++++++++++++++++++++++++

+++++++++++++++++++++++++++++++++++++
systemuname: Linux
CFLAGS now: -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include
CXXFLAGS now: -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include
LDFLAGS now: -Wl,-z,relro -Wl,-z,now -L/usr/lib
+++++++++++++++++++++++++++++++++++++
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for int64_t... yes

+++++++++++++++++++++++++++++++++++++
CFLAGS now: -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include
CXXFLAGS now: -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include
LDFLAGS now: -Wl,-z,relro -Wl,-z,now -L/usr/lib
+++++++++++++++++++++++++++++++++++++
checking whether long has 64bit... no
checking whether enabling 64bit compilation support... no
checking build system type... i686-pc-linux-gnu
checking for compiler optimisation settings... -O3 -funroll-loops

+++++++++++++++++++++++++++++++++++++
CFLAGS now: -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops
CXXFLAGS now: -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops
LDFLAGS now: -Wl,-z,relro -Wl,-z,now -L/usr/lib
+++++++++++++++++++++++++++++++++++++
checking host system type... i686-pc-linux-gnu
checking how to print strings... printf
checking for a sed that does not truncate output... (cached) /usr/bin/sed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for fgrep... /usr/bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking how to convert i686-pc-linux-gnu file names to i686-pc-linux-gnu format... func_convert_file_noop
checking how to convert i686-pc-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for file... file
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for a working dd... /usr/bin/dd
checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1
checking for mt... no
checking if : is a manifest tool... no
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking how to run the C++ preprocessor... g++ -E
checking for ld used by g++... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes
checking for g++ option to produce PIC... -fPIC -DPIC
checking if g++ PIC flag -fPIC -DPIC works... yes
checking if g++ static flag -static works... yes
checking if g++ supports -c -o file.o... yes
checking if g++ supports -c -o file.o... (cached) yes
checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether make sets $(MAKE)... (cached) yes
checking whether ln -s works... yes
checking for flex... yes
checking for flex... flex
checking for lex output file root... lex.yy
checking for lex library... none needed
checking for library containing yywrap... -ll
checking whether yytext is a pointer... yes
checking for flex++... yes
checking for xxd... yes
checking for egrep... (cached) /usr/bin/grep -E
checking for _Bool... yes
checking for stdbool.h that conforms to C99 or later... yes
checking for an ANSI C-conforming const... yes
checking for inline... inline
checking for C/C++ restrict keyword... __restrict__
checking whether struct tm is in sys/time.h or time.h... time.h
checking for GNU libc compatible malloc... yes
checking for GNU libc compatible realloc... yes
checking whether lstat correctly handles trailing slash... yes
checking whether stat accepts an empty string... no
checking for strftime... yes
checking for floor... no
checking for memset... yes
checking for pow... no
checking for sqrt... no
checking for gcc option to enable large file support... -D_FILE_OFFSET_BITS=64
checking for declarations of fseeko and ftello... yes
checking for isblank... yes

+++++++++++++++++++++++++++++++++++++
CFLAGS now: -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops
CXXFLAGS now: -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops
LDFLAGS now: -Wl,-z,relro -Wl,-z,now -L/usr/lib
+++++++++++++++++++++++++++++++++++++
checking for boostlib >= 1.48.0... yes

+++++++++++++++++++++++++++++++++++++
 BOOST_CPPFLAGS:    -I/usr/include
 BOOST LDFLAGS:     -L/usr/lib/i386-linux-gnu
 ac_boost_path:     /usr
 ac_boost_lib_path: /usr/lib/i386-linux-gnu
CFLAGS now: -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops
CXXFLAGS now: -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops
LDFLAGS now: -Wl,-z,relro -Wl,-z,now -L/usr/lib
+++++++++++++++++++++++++++++++++++++

+++++++++++++++++++++++++++++++++++++
 BOOST_CPPFLAGS:    -I/usr/include
 BOOST LDFLAGS:     -L/usr/lib/i386-linux-gnu
CFLAGS now: -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -Wl,-rpath,/usr/lib/i386-linux-gnu
CXXFLAGS now: -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops
LDFLAGS now: -Wl,-z,relro -Wl,-z,now -L/usr/lib
+++++++++++++++++++++++++++++++++++++
checking whether the Boost::Thread library is available... yes
checking for exit in -lboost_thread... yes

+++++++++++++++++++++++++++++++++++++
 BOOST_CPPFLAGS:    -pthread -I/usr/include
 BOOST LDFLAGS:     -L/usr/lib/i386-linux-gnu
 ac_boost_path:     /usr
 ac_boost_lib_path: /usr/lib/i386-linux-gnu
 BOOST_THREAD_LIB:  -lboost_thread
CFLAGS now: -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -Wl,-rpath,/usr/lib/i386-linux-gnu
CXXFLAGS now: -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops
LDFLAGS now: -Wl,-z,relro -Wl,-z,now -L/usr/lib
+++++++++++++++++++++++++++++++++++++
+++++++++++++++++++++++++++++++++++++
 BOOST_CPPFLAGS:    -pthread -I/usr/include
 BOOST LDFLAGS:     -L/usr/lib/i386-linux-gnu
 ac_boost_path:     /usr
 ac_boost_lib_path: /usr/lib/i386-linux-gnu
 BOOST_THREAD_LIB:  -lboost_thread

CFLAGS now: -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -Wl,-rpath,/usr/lib/i386-linux-gnu
CXXFLAGS now: -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include
LDFLAGS now: -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/i386-linux-gnu
LIBS now:  -lboost_thread
+++++++++++++++++++++++++++++++++++++
checking whether the Boost::Regex library is available... yes
checking for exit in -lboost_regex... yes
+++++++++++++++++++++++++++++++++++++
 BOOST_CPPFLAGS:    -pthread -I/usr/include
 BOOST LDFLAGS:     -L/usr/lib/i386-linux-gnu
 ac_boost_path:     /usr
 ac_boost_lib_path: /usr/lib/i386-linux-gnu
 BOOST_REGEX_LIB:   -lboost_regex

CFLAGS now: -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -Wl,-rpath,/usr/lib/i386-linux-gnu
CXXFLAGS now: -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include
LIBS now:  -lboost_thread -lboost_regex
+++++++++++++++++++++++++++++++++++++
checking whether the Boost::System library is available... yes
checking for exit in -lboost_system... yes
+++++++++++++++++++++++++++++++++++++
 BOOST_CPPFLAGS:    -pthread -I/usr/include
 BOOST LDFLAGS:     -L/usr/lib/i386-linux-gnu
 ac_boost_path:     /usr
 ac_boost_lib_path: /usr/lib/i386-linux-gnu
 BOOST_SYSTEM_LIB:   -lboost_system

CFLAGS now: -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -Wl,-rpath,/usr/lib/i386-linux-gnu
CXXFLAGS now: -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include
LIBS now:  -lboost_thread -lboost_regex -lboost_system
+++++++++++++++++++++++++++++++++++++
checking whether the Boost::Filesystem library is available... yes
checking for exit in -lboost_filesystem... yes
+++++++++++++++++++++++++++++++++++++
 BOOST_CPPFLAGS:    -pthread -I/usr/include
 BOOST LDFLAGS:     -L/usr/lib/i386-linux-gnu
 ac_boost_path:     /usr
 ac_boost_lib_path: /usr/lib/i386-linux-gnu
 BOOST_FILESYSTEM_LIB:   -lboost_filesystem

CFLAGS now: -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -Wl,-rpath,/usr/lib/i386-linux-gnu
CXXFLAGS now: -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include
LIBS now:  -lboost_thread -lboost_regex -lboost_system -lboost_filesystem
+++++++++++++++++++++++++++++++++++++
checking whether the Boost::IOStreams library is available... yes
checking for exit in -lboost_iostreams... yes
+++++++++++++++++++++++++++++++++++++
 BOOST_CPPFLAGS:    -pthread -I/usr/include
 BOOST LDFLAGS:     -L/usr/lib/i386-linux-gnu
 ac_boost_path:     /usr
 ac_boost_lib_path: /usr/lib/i386-linux-gnu
 BOOST_IOSTREAMS_LIB:   -lboost_iostreams

CFLAGS now: -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -Wl,-rpath,/usr/lib/i386-linux-gnu
CXXFLAGS now: -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include
LIBS now:  -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams
+++++++++++++++++++++++++++++++++++++
checking for clock_gettime in -lrt... yes
+++++++++++++++++++++++++++++++++++++
Need to specifically use rt library
LIBS now:  -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt
+++++++++++++++++++++++++++++++++++++
BOOST is through, yay.
+++++++++++++++++++++++++++++++++++++
CFLAGS now: -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops
CXXFLAGS now: -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include
LDFLAGS now: -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/i386-linux-gnu
LIBS now:  -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt
+++++++++++++++++++++++++++++++++++++
checking for Expat XML Parser headers in /usr/include... found
checking for Expat XML Parser libraries... found
checking for Expat XML Parser... yes

+++++++++++++++++++++++++++++++++++++
CFLAGS now: -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -I/usr/include
CXXFLAGS now: -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include
LDFLAGS now: -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/i386-linux-gnu -L/usr/lib
LIBS now:  -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt -lexpat
+++++++++++++++++++++++++++++++++++++
checking if zlib is wanted... yes

+++++++++++++++++++++++++++++++++++++
CFLAGS now: -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -I/usr/include
CXXFLAGS now: -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include
LDFLAGS now: -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/i386-linux-gnu -L/usr/lib
LIBS now:  -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt -lexpat -lm -lz
+++++++++++++++++++++++++++++++++++++
checking for gzoffset in -lz... yes
checking for BZ2_bzRead in -lbz2... yes
checking for flex version compatible with MIRA... yes
checking for profiling settings... no
checking for purify... no
checking whether mira should compile in public quiet mode... yes
checking whether mira should compile with bound tracking... yes
checking whether mira should compile with bug tracking... yes
checking whether mira should compile with extended bug tracking... no
checking whether mira should compile with function trace... no
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating src/other/Makefile
config.status: creating src/other/sls/Makefile
config.status: creating src/other/sls/mira-createsls/Makefile
config.status: creating src/other/sls/mira-createsls/bin/Makefile
config.status: creating src/stdinc/Makefile
config.status: creating src/debuggersupport/Makefile
config.status: creating src/memorc/Makefile
config.status: creating src/errorhandling/Makefile
config.status: creating src/util/Makefile
config.status: creating src/io/Makefile
config.status: creating src/mira/Makefile
config.status: creating src/caf/Makefile
config.status: creating src/support/Makefile
config.status: creating src/scripts/Makefile
config.status: creating src/modules/Makefile
config.status: creating src/version/Makefile
config.status: creating src/progs/Makefile
config.status: creating man/Makefile
config.status: creating doc/Makefile
config.status: creating doc/docbook/Makefile
config.status: creating distribution/Makefile
config.status: executing depfiles commands
config.status: executing libtool commands

--------------------------------------------------------------------------------
                       Summary of MIRA configuration
--------------------------------------------------------------------------------


Building version ................................. 4.9.6_linux-gnu_i686_32_dynamic

We are building on ............................... Linux
CPU supports 64 bit? ............................. no
Compiler family .................................. gcc
Compiler optimisation flags used ................. -O3 -funroll-loops
Building completely static? ...................... no
BOOST expected to compile and link? .............. yes
Have OpenMP? ..................................... yes
Have complete zlib support? ...................... yes

Can MIRA be built on this system? ................ yes

Using CFLAGS   : -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -I/usr/include -Werror=uninitialized -Werror=return-type  -fopenmp
Using CXXFLAGS : -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp
Using LDFLAGS  : -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/i386-linux-gnu -L/usr/lib
Using LIBS     :  -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt -lexpat -lm -lz -lbz2

Looks good, we do not expect compilation problems.
--------------------------------------------------------------------------------

Type 'make' to make the binaries
and then 'make install' to install binaries and man pages.
Type 'make docinstall' to install extensive documentation as HTML and PDF.
make[1]: Leaving directory '/build/reproducible-path/mira-4.9.6'
	rm -f debian/mira-assembler.debhelper.log debian/mira-doc.debhelper.log debian/mira-rfam-12s-rrna.debhelper.log
   debian/rules override_dh_auto_build-arch
make[1]: Entering directory '/build/reproducible-path/mira-4.9.6'
# some *.cc files are created by old flex version which breaks the build
# see bug #812681
find -name '*.ll' | sed -e 's/[.]ll$/.cc/' | xargs rm -f
dh_auto_build
	make -j5
make[2]: Entering directory '/build/reproducible-path/mira-4.9.6'
make  all-recursive
make[3]: Entering directory '/build/reproducible-path/mira-4.9.6'
Making all in man
make[4]: Entering directory '/build/reproducible-path/mira-4.9.6/man'
make[4]: Nothing to be done for 'all'.
make[4]: Leaving directory '/build/reproducible-path/mira-4.9.6/man'
Making all in src
make[4]: Entering directory '/build/reproducible-path/mira-4.9.6/src'
Making all in debuggersupport
make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/debuggersupport'
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2  -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o dbgsupport.o dbgsupport.C
rm -f libmiradebuggersupport.a
ar cru libmiradebuggersupport.a dbgsupport.o 
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libmiradebuggersupport.a
make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/debuggersupport'
Making all in io
make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/io'
Making .H out of .xxd mira_ft_set.xxd.H
Making .H out of .xxd gap4_ft_so_map.xxd.H
Reducing so.obo for smaller so.obo.xxd
Making .H out of .xxd so2xgap4map.xxd.H
Making .H out of .xxd oldso2so.xxd.H
Making .H out of .xxd so.obo.xxd.H
make  all-am
make[6]: Entering directory '/build/reproducible-path/mira-4.9.6/src/io'
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2  -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o annotationmappings.o annotationmappings.C
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2  -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o exp.o exp.C
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2  -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o generalio.o generalio.C
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2  -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o fasta.o fasta.C
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2  -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o fastq-mira.o fastq-mira.C
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2  -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o phd.o phd.C
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2  -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o scf.o scf.C
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2  -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o ncbiinfoxml.o ncbiinfoxml.C
/bin/sh ../../ylwrap exp_flexer.ll lex.yy.c exp_flexer.cc -- flex  
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2  -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o exp_flexer.o exp_flexer.cc
rm -f libmirafio.a
ar cru libmirafio.a annotationmappings.o exp.o generalio.o fasta.o fastq-mira.o phd.o scf.o ncbiinfoxml.o exp_flexer.o  
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libmirafio.a
make[6]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/io'
make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/io'
Making all in stdinc
make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/stdinc'
make[5]: Nothing to be done for 'all'.
make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/stdinc'
Making all in errorhandling
make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/errorhandling'
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2  -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o errorhandling.o errorhandling.C
rm -f libmiraerrorhandling.a
ar cru libmiraerrorhandling.a errorhandling.o 
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libmiraerrorhandling.a
make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/errorhandling'
Making all in util
make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/util'
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2  -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o machineinfo.o machineinfo.C
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2  -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o fileanddisk.o fileanddisk.C
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2  -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o misc.o misc.C
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2  -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o dptools.o dptools.C
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2  -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o fmttext.o fmttext.C
rm -f libmirafmttext.a
ar cru libmirafmttext.a fmttext.o 
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libmirafmttext.a
fileanddisk.C: In function 'int64 myGZRead(gzFile_s*&, void*, uint64)':
fileanddisk.C:173:19: warning: ignoring return value of 'char* strerror_r(int, char*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result]
  173 |         strerror_r(errno,buf,1024);
      |         ~~~~~~~~~~^~~~~~~~~~~~~~~~
rm -f libmiradptools.a
ar cru libmiradptools.a dptools.o 
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libmiradptools.a
rm -f libmirautil.a
ar cru libmirautil.a machineinfo.o fileanddisk.o misc.o 
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libmirautil.a
make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/util'
Making all in mira
make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/mira'
Making .H out of .xxd adaptorsforclip.454.xxd.H
Making .H out of .xxd adaptorsforclip.solexa.xxd.H
Making .H out of .xxd adaptorsforclip.iontor.xxd.H
Making .H out of .xxd adaptorsregex.solexa.xxd.H
Making .H out of .xxd adaptorsregex.iontor.xxd.H
Making .H out of .xxd seqforfilter_phix174.solexa.xxd.H
make  all-am
make[6]: Entering directory '/build/reproducible-path/mira-4.9.6/src/mira'
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2  -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o estassembly.o estassembly.C
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2  -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o hashstats_sdbg.o hashstats_sdbg.C
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2  -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o hashstats.o hashstats.C
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2  -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o skim.o skim.C
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2  -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o assembly.o assembly.C
hashstats.C:1088:9: warning: "CEBUG" redefined
 1088 | #define CEBUG(bla)   {cout << bla; cout.flush();}
      |         ^~~~~
hashstats.C:83:9: note: this is the location of the previous definition
   83 | #define CEBUG(bla)
      |         ^~~~~
hashstats.C:1197:9: warning: "CEBUG" redefined
 1197 | #define CEBUG(bla)
      |         ^~~~~
hashstats.C:1088:9: note: this is the location of the previous definition
 1088 | #define CEBUG(bla)   {cout << bla; cout.flush();}
      |         ^~~~~
In file included from /usr/include/boost/system/detail/requires_cxx11.hpp:9,
                 from /usr/include/boost/system/detail/config.hpp:11,
                 from /usr/include/boost/system/detail/error_category.hpp:13,
                 from /usr/include/boost/system/detail/error_code.hpp:14,
                 from /usr/include/boost/system/errc.hpp:14,
                 from /usr/include/boost/system/system_error.hpp:9,
                 from /usr/include/boost/thread/exceptions.hpp:22,
                 from /usr/include/boost/thread/pthread/thread_data.hpp:10,
                 from /usr/include/boost/thread/thread_only.hpp:17,
                 from /usr/include/boost/thread/thread.hpp:12,
                 from hashstats.C:24:
/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.'
   36 | BOOST_PRAGMA_MESSAGE(
      | ^~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/boost/container_hash/detail/requires_cxx11.hpp:9,
                 from /usr/include/boost/container_hash/hash.hpp:14,
                 from /usr/include/boost/functional/hash/hash.hpp:6,
                 from /usr/include/boost/bimap/relation/mutant_relation.hpp:29,
                 from /usr/include/boost/bimap/detail/bimap_core.hpp:38,
                 from /usr/include/boost/bimap/bimap.hpp:61,
                 from /usr/include/boost/bimap.hpp:13,
                 from ../../src/io/annotationmappings.H:36,
                 from ../../src/mira/multitag.H:39,
                 from ../../src/mira/read.H:38,
                 from ../../src/mira/readpool.H:41,
                 from ../../src/mira/pcrcontainer.H:30,
                 from ../../src/mira/contig.H:42,
                 from ../../src/mira/assembly_info.H:33,
                 from assembly.H:33,
                 from estassembly.C:25:
/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.'
   36 | BOOST_PRAGMA_MESSAGE(
      | ^~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/boost/container_hash/detail/requires_cxx11.hpp:9,
                 from /usr/include/boost/container_hash/hash.hpp:14,
                 from /usr/include/boost/functional/hash/hash.hpp:6,
                 from /usr/include/boost/bimap/relation/mutant_relation.hpp:29,
                 from /usr/include/boost/bimap/detail/bimap_core.hpp:38,
                 from /usr/include/boost/bimap/bimap.hpp:61,
                 from /usr/include/boost/bimap.hpp:13,
                 from ../../src/io/annotationmappings.H:36,
                 from ../../src/mira/multitag.H:39,
                 from ../../src/mira/read.H:38,
                 from ../../src/mira/readpool.H:41,
                 from ../../src/mira/pcrcontainer.H:30,
                 from ../../src/mira/contig.H:42,
                 from ../../src/mira/assembly_info.H:33,
                 from assembly.H:33,
                 from assembly.C:28:
/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.'
   36 | BOOST_PRAGMA_MESSAGE(
      | ^~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/boost/system/detail/requires_cxx11.hpp:9,
                 from /usr/include/boost/system/detail/config.hpp:11,
                 from /usr/include/boost/system/detail/error_category.hpp:13,
                 from /usr/include/boost/system/detail/error_code.hpp:14,
                 from /usr/include/boost/system/errc.hpp:14,
                 from /usr/include/boost/system/system_error.hpp:9,
                 from /usr/include/boost/thread/exceptions.hpp:22,
                 from /usr/include/boost/thread/pthread/mutex.hpp:14,
                 from /usr/include/boost/thread/mutex.hpp:16,
                 from ../../src/mira/hashstats.H:27,
                 from hashstats_sdbg.C:43:
/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.'
   36 | BOOST_PRAGMA_MESSAGE(
      | ^~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/boost/function/detail/requires_cxx11.hpp:9,
                 from /usr/include/boost/function/detail/prologue.hpp:12,
                 from /usr/include/boost/function.hpp:30,
                 from ../../src/mira/skim.H:25,
                 from skim.C:23:
/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.'
   36 | BOOST_PRAGMA_MESSAGE(
      | ^~~~~~~~~~~~~~~~~~~~
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2  -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o contig.o contig.C
In file included from /usr/include/boost/container_hash/detail/requires_cxx11.hpp:9,
                 from /usr/include/boost/container_hash/hash.hpp:14,
                 from /usr/include/boost/functional/hash/hash.hpp:6,
                 from /usr/include/boost/bimap/relation/mutant_relation.hpp:29,
                 from /usr/include/boost/bimap/detail/bimap_core.hpp:38,
                 from /usr/include/boost/bimap/bimap.hpp:61,
                 from /usr/include/boost/bimap.hpp:13,
                 from ../../src/io/annotationmappings.H:36,
                 from ../../src/mira/multitag.H:39,
                 from ../../src/mira/read.H:38,
                 from ../../src/mira/readpool.H:41,
                 from ../../src/mira/pcrcontainer.H:30,
                 from contig.H:42,
                 from contig.C:28:
/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.'
   36 | BOOST_PRAGMA_MESSAGE(
      | ^~~~~~~~~~~~~~~~~~~~
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2  -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o read.o read.C
In file included from /usr/include/boost/container_hash/detail/requires_cxx11.hpp:9,
                 from /usr/include/boost/container_hash/hash.hpp:14,
                 from /usr/include/boost/functional/hash/hash.hpp:6,
                 from /usr/include/boost/bimap/relation/mutant_relation.hpp:29,
                 from /usr/include/boost/bimap/detail/bimap_core.hpp:38,
                 from /usr/include/boost/bimap/bimap.hpp:61,
                 from /usr/include/boost/bimap.hpp:13,
                 from ../../src/io/annotationmappings.H:36,
                 from ../../src/mira/multitag.H:39,
                 from ../../src/mira/read.H:38,
                 from read.C:28:
/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.'
   36 | BOOST_PRAGMA_MESSAGE(
      | ^~~~~~~~~~~~~~~~~~~~
read.C: In member function 'void Read::dumpAsReadname(std::ostream&)':
read.C:1242:25: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'Read*' [-Wformat=]
 1242 |       sprintf(buffer, "%x", this) ;
      |                        ~^   ~~~~
      |                         |   |
      |                         |   Read*
      |                         unsigned int
read.C: In member function 'void Read::dumpAsFASTA(std::ostream&, bool, bool, bool)':
read.C:1273:25: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'Read*' [-Wformat=]
 1273 |       sprintf(buffer, "%x", this) ;
      |                        ~^   ~~~~
      |                         |   |
      |                         |   Read*
      |                         unsigned int
read.C: In member function 'void Read::dumpAsFASTQ(std::ostream&, bool, bool, bool)':
read.C:1357:25: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'Read*' [-Wformat=]
 1357 |       sprintf(buffer, "%x", this) ;
      |                        ~^   ~~~~
      |                         |   |
      |                         |   Read*
      |                         unsigned int
read.C: In member function 'void Read::dumpAsFASTAQual(std::ostream&, bool, bool, bool)':
read.C:1458:25: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'Read*' [-Wformat=]
 1458 |       sprintf(buffer, "%x", this) ;
      |                        ~^   ~~~~
      |                         |   |
      |                         |   Read*
      |                         unsigned int
read.C: In member function 'void Read::dumpAsCAF(std::ostream&)':
read.C:1530:25: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'Read*' [-Wformat=]
 1530 |       sprintf(buffer, "%x", this) ;
      |                        ~^   ~~~~
      |                         |   |
      |                         |   Read*
      |                         unsigned int
read.C: In member function 'void Read::dumpAsMAF(std::ostream&)':
read.C:1945:25: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'Read*' [-Wformat=]
 1945 |       sprintf(buffer, "%x", this) ;
      |                        ~^   ~~~~
      |                         |   |
      |                         |   Read*
      |                         unsigned int
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2  -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o contig_analysis.o contig_analysis.C
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2  -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o ads.o ads.C
In file included from /usr/include/boost/container_hash/detail/requires_cxx11.hpp:9,
                 from /usr/include/boost/container_hash/hash.hpp:14,
                 from /usr/include/boost/functional/hash/hash.hpp:6,
                 from /usr/include/boost/bimap/relation/mutant_relation.hpp:29,
                 from /usr/include/boost/bimap/detail/bimap_core.hpp:38,
                 from /usr/include/boost/bimap/bimap.hpp:61,
                 from /usr/include/boost/bimap.hpp:13,
                 from ../../src/io/annotationmappings.H:36,
                 from ../../src/mira/multitag.H:39,
                 from ../../src/mira/read.H:38,
                 from ../../src/mira/readpool.H:41,
                 from ../../src/mira/pcrcontainer.H:30,
                 from ../../src/mira/contig.H:42,
                 from contig_analysis.C:28:
/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.'
   36 | BOOST_PRAGMA_MESSAGE(
      | ^~~~~~~~~~~~~~~~~~~~
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2  -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o adsfacts.o adsfacts.C
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2  -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o align.o align.C
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2  -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o assembly_info.o assembly_info.C
In file included from /usr/include/boost/container_hash/detail/requires_cxx11.hpp:9,
                 from /usr/include/boost/container_hash/hash.hpp:14,
                 from /usr/include/boost/functional/hash/hash.hpp:6,
                 from /usr/include/boost/bimap/relation/mutant_relation.hpp:29,
                 from /usr/include/boost/bimap/detail/bimap_core.hpp:38,
                 from /usr/include/boost/bimap/bimap.hpp:61,
                 from /usr/include/boost/bimap.hpp:13,
                 from ../../src/io/annotationmappings.H:36,
                 from ../../src/mira/multitag.H:39,
                 from ../../src/mira/read.H:38,
                 from ../../src/mira/readpool.H:41,
                 from ../../src/mira/pcrcontainer.H:30,
                 from ../../src/mira/contig.H:42,
                 from ../../src/mira/assembly_info.H:33,
                 from assembly_info.C:28:
/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.'
   36 | BOOST_PRAGMA_MESSAGE(
      | ^~~~~~~~~~~~~~~~~~~~
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2  -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o assembly_buildcontigs.o assembly_buildcontigs.C
assembly_buildcontigs.C:80:9: warning: "CEBUG" redefined
   80 | #define CEBUG(bla)   {cout << bla; cout.flush(); }
      |         ^~~~~
assembly_buildcontigs.C:55:9: note: this is the location of the previous definition
   55 | #define CEBUG(bla)
      |         ^~~~~
assembly_buildcontigs.C:1251:9: warning: "CEBUG" redefined
 1251 | #define CEBUG(bla)
      |         ^~~~~
assembly_buildcontigs.C:80:9: note: this is the location of the previous definition
   80 | #define CEBUG(bla)   {cout << bla; cout.flush(); }
      |         ^~~~~
assembly_buildcontigs.C:1332:9: warning: "CEBUG" redefined
 1332 | #define CEBUG(bla)   {cout << bla; cout.flush(); }
      |         ^~~~~
assembly_buildcontigs.C:1251:9: note: this is the location of the previous definition
 1251 | #define CEBUG(bla)
      |         ^~~~~
assembly_buildcontigs.C:1485:9: warning: "CEBUG" redefined
 1485 | #define CEBUG(bla)
      |         ^~~~~
assembly_buildcontigs.C:1332:9: note: this is the location of the previous definition
 1332 | #define CEBUG(bla)   {cout << bla; cout.flush(); }
      |         ^~~~~
assembly_buildcontigs.C:1496:9: warning: "CEBUG" redefined
 1496 | #define CEBUG(bla)   {cout << bla; cout.flush(); }
      |         ^~~~~
assembly_buildcontigs.C:1485:9: note: this is the location of the previous definition
 1485 | #define CEBUG(bla)
      |         ^~~~~
assembly_buildcontigs.C:1621:9: warning: "CEBUG" redefined
 1621 | #define CEBUG(bla)
      |         ^~~~~
assembly_buildcontigs.C:1496:9: note: this is the location of the previous definition
 1496 | #define CEBUG(bla)   {cout << bla; cout.flush(); }
      |         ^~~~~
assembly_buildcontigs.C:2304:9: warning: "VCOUT" redefined
 2304 | #define VCOUT(bla)
      |         ^~~~~
assembly_buildcontigs.C:2043:9: note: this is the location of the previous definition
 2043 | #define VCOUT(bla)   {if(verbose) {cout << bla;} }
      |         ^~~~~
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2  -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o assembly_io.o assembly_io.C
In file included from /usr/include/boost/container_hash/detail/requires_cxx11.hpp:9,
                 from /usr/include/boost/container_hash/hash.hpp:14,
                 from /usr/include/boost/functional/hash/hash.hpp:6,
                 from /usr/include/boost/bimap/relation/mutant_relation.hpp:29,
                 from /usr/include/boost/bimap/detail/bimap_core.hpp:38,
                 from /usr/include/boost/bimap/bimap.hpp:61,
                 from /usr/include/boost/bimap.hpp:13,
                 from ../../src/io/annotationmappings.H:36,
                 from ../../src/mira/multitag.H:39,
                 from ../../src/mira/read.H:38,
                 from ../../src/mira/readpool.H:41,
                 from ../../src/mira/pcrcontainer.H:30,
                 from ../../src/mira/contig.H:42,
                 from ../../src/mira/assembly_info.H:33,
                 from ../../src/mira/assembly.H:33,
                 from assembly_buildcontigs.C:28:
/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.'
   36 | BOOST_PRAGMA_MESSAGE(
      | ^~~~~~~~~~~~~~~~~~~~
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2  -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o assembly_misc.o assembly_misc.C
In file included from /usr/include/boost/lexical_cast.hpp:26,
                 from ../../src/util/fileanddisk.H:43,
                 from assembly_io.C:28:
/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.'
   36 | BOOST_PRAGMA_MESSAGE(
      | ^~~~~~~~~~~~~~~~~~~~
assembly_misc.C:1871:9: warning: "CEBUG" redefined
 1871 | #define CEBUG(bla)   {cout << bla; cout.flush();}
      |         ^~~~~
assembly_misc.C:55:9: note: this is the location of the previous definition
   55 | #define CEBUG(bla)
      |         ^~~~~
assembly_misc.C:1905:9: warning: "CEBUG" redefined
 1905 | #define CEBUG(bla)
      |         ^~~~~
assembly_misc.C:1871:9: note: this is the location of the previous definition
 1871 | #define CEBUG(bla)   {cout << bla; cout.flush();}
      |         ^~~~~
In file included from /usr/include/boost/system/detail/requires_cxx11.hpp:9,
                 from /usr/include/boost/system/detail/config.hpp:11,
                 from /usr/include/boost/system/detail/error_category.hpp:13,
                 from /usr/include/boost/system/error_category.hpp:10,
                 from /usr/include/boost/filesystem/detail/path_traits.hpp:25,
                 from /usr/include/boost/filesystem/path.hpp:21,
                 from /usr/include/boost/filesystem.hpp:16,
                 from assembly_misc.C:32:
/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.'
   36 | BOOST_PRAGMA_MESSAGE(
      | ^~~~~~~~~~~~~~~~~~~~
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2  -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o assembly_output.o assembly_output.C
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2  -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o assembly_pbcorrect.o assembly_pbcorrect.C
In file included from /usr/include/boost/container_hash/detail/requires_cxx11.hpp:9,
                 from /usr/include/boost/container_hash/hash.hpp:14,
                 from /usr/include/boost/functional/hash/hash.hpp:6,
                 from /usr/include/boost/bimap/relation/mutant_relation.hpp:29,
                 from /usr/include/boost/bimap/detail/bimap_core.hpp:38,
                 from /usr/include/boost/bimap/bimap.hpp:61,
                 from /usr/include/boost/bimap.hpp:13,
                 from ../../src/io/annotationmappings.H:36,
                 from ../../src/mira/multitag.H:39,
                 from ../../src/mira/read.H:38,
                 from ../../src/mira/readpool.H:41,
                 from ../../src/mira/pcrcontainer.H:30,
                 from ../../src/mira/contig.H:42,
                 from ../../src/mira/assembly_info.H:33,
                 from ../../src/mira/assembly_output.H:32,
                 from assembly_output.C:33:
/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.'
   36 | BOOST_PRAGMA_MESSAGE(
      | ^~~~~~~~~~~~~~~~~~~~
assembly_pbcorrect.C:59:9: warning: "CEBUG" redefined
   59 | #define CEBUG(bla) { if(docebug) {cout << bla; cout.flush();}}
      |         ^~~~~
assembly_pbcorrect.C:45:9: note: this is the location of the previous definition
   45 | #define CEBUG(bla)
      |         ^~~~~
In file included from /usr/include/boost/container_hash/detail/requires_cxx11.hpp:9,
                 from /usr/include/boost/container_hash/hash.hpp:14,
                 from /usr/include/boost/functional/hash/hash.hpp:6,
                 from /usr/include/boost/bimap/relation/mutant_relation.hpp:29,
                 from /usr/include/boost/bimap/detail/bimap_core.hpp:38,
                 from /usr/include/boost/bimap/bimap.hpp:61,
                 from /usr/include/boost/bimap.hpp:13,
                 from ../../src/io/annotationmappings.H:36,
                 from ../../src/mira/multitag.H:39,
                 from ../../src/mira/read.H:38,
                 from ../../src/mira/readpool.H:41,
                 from ../../src/mira/pcrcontainer.H:30,
                 from ../../src/mira/contig.H:42,
                 from ../../src/mira/assembly_info.H:33,
                 from ../../src/mira/assembly.H:33,
                 from assembly_pbcorrect.C:26:
/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.'
   36 | BOOST_PRAGMA_MESSAGE(
      | ^~~~~~~~~~~~~~~~~~~~
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2  -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o assembly_reduceskimhits.o assembly_reduceskimhits.C
assembly_reduceskimhits.C:1111:9: warning: "CEBUG" redefined
 1111 | #define CEBUG(bla)   {cout << bla; cout.flush();}
      |         ^~~~~
assembly_reduceskimhits.C:878:9: note: this is the location of the previous definition
  878 | #define CEBUG(bla)
      |         ^~~~~
assembly_reduceskimhits.C:1151:9: warning: "CEBUG" redefined
 1151 | #define CEBUG(bla)
      |         ^~~~~
assembly_reduceskimhits.C:1111:9: note: this is the location of the previous definition
 1111 | #define CEBUG(bla)   {cout << bla; cout.flush();}
      |         ^~~~~
assembly_reduceskimhits.C:2742:9: warning: "CEBUG" redefined
 2742 | #define CEBUG(bla)   {cout << bla; cout.flush();}
      |         ^~~~~
assembly_reduceskimhits.C:1151:9: note: this is the location of the previous definition
 1151 | #define CEBUG(bla)
      |         ^~~~~
assembly_reduceskimhits.C:2760:9: warning: "CEBUG" redefined
 2760 | #define CEBUG(bla)
      |         ^~~~~
assembly_reduceskimhits.C:2742:9: note: this is the location of the previous definition
 2742 | #define CEBUG(bla)   {cout << bla; cout.flush();}
      |         ^~~~~
assembly_reduceskimhits.C:2764:9: warning: "CEBUG" redefined
 2764 | #define CEBUG(bla)   {cout << bla; cout.flush();}
      |         ^~~~~
assembly_reduceskimhits.C:2760:9: note: this is the location of the previous definition
 2760 | #define CEBUG(bla)
      |         ^~~~~
assembly_reduceskimhits.C:2803:9: warning: "CEBUG" redefined
 2803 | #define CEBUG(bla)
      |         ^~~~~
assembly_reduceskimhits.C:2764:9: note: this is the location of the previous definition
 2764 | #define CEBUG(bla)   {cout << bla; cout.flush();}
      |         ^~~~~
assembly_reduceskimhits.C:2808:9: warning: "CEBUG" redefined
 2808 | #define CEBUG(bla)   {cout << bla; cout.flush();}
      |         ^~~~~
assembly_reduceskimhits.C:2803:9: note: this is the location of the previous definition
 2803 | #define CEBUG(bla)
      |         ^~~~~
assembly_reduceskimhits.C:2887:9: warning: "CEBUG" redefined
 2887 | #define CEBUG(bla)
      |         ^~~~~
assembly_reduceskimhits.C:2808:9: note: this is the location of the previous definition
 2808 | #define CEBUG(bla)   {cout << bla; cout.flush();}
      |         ^~~~~
In file included from /usr/include/boost/container_hash/detail/requires_cxx11.hpp:9,
                 from /usr/include/boost/container_hash/hash.hpp:14,
                 from /usr/include/boost/functional/hash/hash.hpp:6,
                 from /usr/include/boost/bimap/relation/mutant_relation.hpp:29,
                 from /usr/include/boost/bimap/detail/bimap_core.hpp:38,
                 from /usr/include/boost/bimap/bimap.hpp:61,
                 from /usr/include/boost/bimap.hpp:13,
                 from ../../src/io/annotationmappings.H:36,
                 from ../../src/mira/multitag.H:39,
                 from ../../src/mira/read.H:38,
                 from ../../src/mira/readpool.H:41,
                 from ../../src/mira/pcrcontainer.H:30,
                 from ../../src/mira/contig.H:42,
                 from ../../src/mira/assembly_info.H:33,
                 from assembly.H:33,
                 from assembly_reduceskimhits.C:27:
/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.'
   36 | BOOST_PRAGMA_MESSAGE(
      | ^~~~~~~~~~~~~~~~~~~~
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2  -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o assembly_swalign.o assembly_swalign.C
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2  -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o contig_consensus.o contig_consensus.C
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2  -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o contig_covanalysis.o contig_covanalysis.C
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2  -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o contig_edit.o contig_edit.C
In file included from /usr/include/boost/container_hash/detail/requires_cxx11.hpp:9,
                 from /usr/include/boost/container_hash/hash.hpp:14,
                 from /usr/include/boost/functional/hash/hash.hpp:6,
                 from /usr/include/boost/bimap/relation/mutant_relation.hpp:29,
                 from /usr/include/boost/bimap/detail/bimap_core.hpp:38,
                 from /usr/include/boost/bimap/bimap.hpp:61,
                 from /usr/include/boost/bimap.hpp:13,
                 from ../../src/io/annotationmappings.H:36,
                 from ../../src/mira/multitag.H:39,
                 from ../../src/mira/read.H:38,
                 from ../../src/mira/readpool.H:41,
                 from ../../src/mira/pcrcontainer.H:30,
                 from ../../src/mira/contig.H:42,
                 from ../../src/mira/assembly_info.H:33,
                 from ../../src/mira/assembly.H:33,
                 from assembly_swalign.C:28:
/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.'
   36 | BOOST_PRAGMA_MESSAGE(
      | ^~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/boost/container_hash/detail/requires_cxx11.hpp:9,
                 from /usr/include/boost/container_hash/hash.hpp:14,
                 from /usr/include/boost/functional/hash/hash.hpp:6,
                 from /usr/include/boost/bimap/relation/mutant_relation.hpp:29,
                 from /usr/include/boost/bimap/detail/bimap_core.hpp:38,
                 from /usr/include/boost/bimap/bimap.hpp:61,
                 from /usr/include/boost/bimap.hpp:13,
                 from ../../src/io/annotationmappings.H:36,
                 from ../../src/mira/multitag.H:39,
                 from ../../src/mira/read.H:38,
                 from ../../src/mira/readpool.H:41,
                 from ../../src/mira/pcrcontainer.H:30,
                 from contig.H:42,
                 from contig_consensus.C:27:
/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.'
   36 | BOOST_PRAGMA_MESSAGE(
      | ^~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/boost/container_hash/detail/requires_cxx11.hpp:9,
                 from /usr/include/boost/container_hash/hash.hpp:14,
                 from /usr/include/boost/functional/hash/hash.hpp:6,
                 from /usr/include/boost/bimap/relation/mutant_relation.hpp:29,
                 from /usr/include/boost/bimap/detail/bimap_core.hpp:38,
                 from /usr/include/boost/bimap/bimap.hpp:61,
                 from /usr/include/boost/bimap.hpp:13,
                 from ../../src/io/annotationmappings.H:36,
                 from ../../src/mira/multitag.H:39,
                 from ../../src/mira/read.H:38,
                 from ../../src/mira/readpool.H:41,
                 from ../../src/mira/pcrcontainer.H:30,
                 from ../../src/mira/contig.H:42,
                 from contig_covanalysis.C:26:
/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.'
   36 | BOOST_PRAGMA_MESSAGE(
      | ^~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/boost/container_hash/detail/requires_cxx11.hpp:9,
                 from /usr/include/boost/container_hash/hash.hpp:14,
                 from /usr/include/boost/functional/hash/hash.hpp:6,
                 from /usr/include/boost/bimap/relation/mutant_relation.hpp:29,
                 from /usr/include/boost/bimap/detail/bimap_core.hpp:38,
                 from /usr/include/boost/bimap/bimap.hpp:61,
                 from /usr/include/boost/bimap.hpp:13,
                 from ../../src/io/annotationmappings.H:36,
                 from ../../src/mira/multitag.H:39,
                 from ../../src/mira/read.H:38,
                 from ../../src/mira/readpool.H:41,
                 from ../../src/mira/pcrcontainer.H:30,
                 from contig.H:42,
                 from contig_edit.C:25:
/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.'
   36 | BOOST_PRAGMA_MESSAGE(
      | ^~~~~~~~~~~~~~~~~~~~
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2  -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o contig_featureinfo.o contig_featureinfo.C
contig_featureinfo.C:512:9: warning: "CEBUGF2" redefined
  512 | #define CEBUGF2
      |         ^~~~~~~
contig_featureinfo.C:473:9: note: this is the location of the previous definition
  473 | #define CEBUGF2(bla)
      |         ^~~~~~~
In file included from /usr/include/boost/container_hash/detail/requires_cxx11.hpp:9,
                 from /usr/include/boost/container_hash/hash.hpp:14,
                 from /usr/include/boost/functional/hash/hash.hpp:6,
                 from /usr/include/boost/bimap/relation/mutant_relation.hpp:29,
                 from /usr/include/boost/bimap/detail/bimap_core.hpp:38,
                 from /usr/include/boost/bimap/bimap.hpp:61,
                 from /usr/include/boost/bimap.hpp:13,
                 from ../../src/io/annotationmappings.H:36,
                 from ../../src/mira/multitag.H:39,
                 from ../../src/mira/read.H:38,
                 from ../../src/mira/readpool.H:41,
                 from ../../src/mira/pcrcontainer.H:30,
                 from contig.H:42,
                 from contig_featureinfo.C:28:
/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.'
   36 | BOOST_PRAGMA_MESSAGE(
      | ^~~~~~~~~~~~~~~~~~~~
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2  -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o contig_output.o contig_output.C
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2  -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o contig_pairconsistency.o contig_pairconsistency.C
contig_pairconsistency.C:313:9: warning: "CEBUG" redefined
  313 | #define CEBUG(bla)
      |         ^~~~~
contig_pairconsistency.C:34:9: note: this is the location of the previous definition
   34 | #define CEBUG(bla)   {cout << bla; cout.flush();}
      |         ^~~~~
contig_pairconsistency.C:315:9: warning: "CEBUG" redefined
  315 | #define CEBUG(bla)   {cout << bla; cout.flush();}
      |         ^~~~~
contig_pairconsistency.C:313:9: note: this is the location of the previous definition
  313 | #define CEBUG(bla)
      |         ^~~~~
contig_pairconsistency.C:399:9: warning: "CEBUG" redefined
  399 | #define CEBUG(bla)
      |         ^~~~~
contig_pairconsistency.C:315:9: note: this is the location of the previous definition
  315 | #define CEBUG(bla)   {cout << bla; cout.flush();}
      |         ^~~~~
In file included from /usr/include/boost/container_hash/detail/requires_cxx11.hpp:9,
                 from /usr/include/boost/container_hash/hash.hpp:14,
                 from /usr/include/boost/functional/hash/hash.hpp:6,
                 from /usr/include/boost/bimap/relation/mutant_relation.hpp:29,
                 from /usr/include/boost/bimap/detail/bimap_core.hpp:38,
                 from /usr/include/boost/bimap/bimap.hpp:61,
                 from /usr/include/boost/bimap.hpp:13,
                 from ../../src/io/annotationmappings.H:36,
                 from ../../src/mira/multitag.H:39,
                 from ../../src/mira/read.H:38,
                 from ../../src/mira/readpool.H:41,
                 from ../../src/mira/pcrcontainer.H:30,
                 from ../../src/mira/contig.H:42,
                 from contig_output.C:28:
/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.'
   36 | BOOST_PRAGMA_MESSAGE(
      | ^~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/boost/container_hash/detail/requires_cxx11.hpp:9,
                 from /usr/include/boost/container_hash/hash.hpp:14,
                 from /usr/include/boost/functional/hash/hash.hpp:6,
                 from /usr/include/boost/bimap/relation/mutant_relation.hpp:29,
                 from /usr/include/boost/bimap/detail/bimap_core.hpp:38,
                 from /usr/include/boost/bimap/bimap.hpp:61,
                 from /usr/include/boost/bimap.hpp:13,
                 from ../../src/io/annotationmappings.H:36,
                 from ../../src/mira/multitag.H:39,
                 from ../../src/mira/read.H:38,
                 from ../../src/mira/readpool.H:41,
                 from ../../src/mira/pcrcontainer.H:30,
                 from contig.H:42,
                 from contig_pairconsistency.C:26:
/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.'
   36 | BOOST_PRAGMA_MESSAGE(
      | ^~~~~~~~~~~~~~~~~~~~
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2  -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o dataprocessing.o dataprocessing.C
In file included from /usr/include/boost/system/detail/requires_cxx11.hpp:9,
                 from /usr/include/boost/system/detail/config.hpp:11,
                 from /usr/include/boost/system/detail/error_category.hpp:13,
                 from /usr/include/boost/system/detail/error_code.hpp:14,
                 from /usr/include/boost/system/errc.hpp:14,
                 from /usr/include/boost/system/system_error.hpp:9,
                 from /usr/include/boost/thread/exceptions.hpp:22,
                 from /usr/include/boost/thread/pthread/mutex.hpp:14,
                 from /usr/include/boost/thread/mutex.hpp:16,
                 from ../../src/mira/hashstats.H:27,
                 from ../../src/mira/dataprocessing.H:33,
                 from dataprocessing.C:31:
/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.'
   36 | BOOST_PRAGMA_MESSAGE(
      | ^~~~~~~~~~~~~~~~~~~~
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2  -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o dynamic.o dynamic.C
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2  -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o gbf_parse.o gbf_parse.C
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2  -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o gff_parse.o gff_parse.C
In file included from /usr/include/boost/function/detail/requires_cxx11.hpp:9,
                 from /usr/include/boost/function/detail/prologue.hpp:12,
                 from /usr/include/boost/function.hpp:30,
                 from /usr/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from /usr/include/boost/algorithm/string/find_iterator.hpp:24,
                 from /usr/include/boost/algorithm/string/iter_find.hpp:27,
                 from /usr/include/boost/algorithm/string/split.hpp:16,
                 from /usr/include/boost/algorithm/string.hpp:23,
                 from gbf_parse.C:25:
/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.'
   36 | BOOST_PRAGMA_MESSAGE(
      | ^~~~~~~~~~~~~~~~~~~~
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2  -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o gff_save.o gff_save.C
In file included from /usr/include/boost/function/detail/requires_cxx11.hpp:9,
                 from /usr/include/boost/function/detail/prologue.hpp:12,
                 from /usr/include/boost/function.hpp:30,
                 from /usr/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from /usr/include/boost/algorithm/string/find_iterator.hpp:24,
                 from /usr/include/boost/algorithm/string/iter_find.hpp:27,
                 from /usr/include/boost/algorithm/string/split.hpp:16,
                 from /usr/include/boost/algorithm/string.hpp:23,
                 from gff_parse.C:26:
/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.'
   36 | BOOST_PRAGMA_MESSAGE(
      | ^~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/boost/container_hash/detail/requires_cxx11.hpp:9,
                 from /usr/include/boost/container_hash/hash.hpp:14,
                 from /usr/include/boost/functional/hash/hash.hpp:6,
                 from /usr/include/boost/bimap/relation/mutant_relation.hpp:29,
                 from /usr/include/boost/bimap/detail/bimap_core.hpp:38,
                 from /usr/include/boost/bimap/bimap.hpp:61,
                 from /usr/include/boost/bimap.hpp:13,
                 from ../../src/io/annotationmappings.H:36,
                 from ../../src/mira/multitag.H:39,
                 from ../../src/mira/read.H:38,
                 from ../../src/mira/readpool.H:41,
                 from ../../src/mira/pcrcontainer.H:30,
                 from ../../src/mira/contig.H:42,
                 from gff_save.C:31:
/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.'
   36 | BOOST_PRAGMA_MESSAGE(
      | ^~~~~~~~~~~~~~~~~~~~
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2  -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o maf_parse.o maf_parse.C
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2  -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o manifest.o manifest.C
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2  -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o multitag.o multitag.C
In file included from /usr/include/boost/container_hash/detail/requires_cxx11.hpp:9,
                 from /usr/include/boost/container_hash/hash.hpp:14,
                 from /usr/include/boost/functional/hash/hash.hpp:6,
                 from /usr/include/boost/bimap/relation/mutant_relation.hpp:29,
                 from /usr/include/boost/bimap/detail/bimap_core.hpp:38,
                 from /usr/include/boost/bimap/bimap.hpp:61,
                 from /usr/include/boost/bimap.hpp:13,
                 from ../../src/io/annotationmappings.H:36,
                 from ../../src/mira/multitag.H:39,
                 from ../../src/mira/read.H:38,
                 from ../../src/mira/readpool.H:41,
                 from ../../src/mira/pcrcontainer.H:30,
                 from ../../src/mira/contig.H:42,
                 from ../../src/mira/maf_parse.H:38,
                 from maf_parse.C:27:
/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.'
   36 | BOOST_PRAGMA_MESSAGE(
      | ^~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/boost/container_hash/detail/requires_cxx11.hpp:9,
                 from /usr/include/boost/container_hash/hash.hpp:14,
                 from /usr/include/boost/functional/hash/hash.hpp:6,
                 from /usr/include/boost/bimap/relation/mutant_relation.hpp:29,
                 from /usr/include/boost/bimap/detail/bimap_core.hpp:38,
                 from /usr/include/boost/bimap/bimap.hpp:61,
                 from /usr/include/boost/bimap.hpp:13,
                 from ../../src/io/annotationmappings.H:36,
                 from multitag.C:28:
/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.'
   36 | BOOST_PRAGMA_MESSAGE(
      | ^~~~~~~~~~~~~~~~~~~~
/bin/sh ../../ylwrap parameters_flexer.ll lex.yy.c parameters_flexer.cc -- flex  
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2  -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o parameters.o parameters.C
In file included from /usr/include/boost/function/detail/requires_cxx11.hpp:9,
                 from /usr/include/boost/function/detail/prologue.hpp:12,
                 from /usr/include/boost/function.hpp:30,
                 from /usr/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from /usr/include/boost/algorithm/string/find_iterator.hpp:24,
                 from /usr/include/boost/algorithm/string/iter_find.hpp:27,
                 from /usr/include/boost/algorithm/string/split.hpp:16,
                 from /usr/include/boost/algorithm/string.hpp:23,
                 from parameters.C:30:
/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.'
   36 | BOOST_PRAGMA_MESSAGE(
      | ^~~~~~~~~~~~~~~~~~~~
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2  -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o pcrcontainer.o pcrcontainer.C
In file included from /usr/include/boost/container_hash/detail/requires_cxx11.hpp:9,
                 from /usr/include/boost/container_hash/hash.hpp:14,
                 from /usr/include/boost/functional/hash/hash.hpp:6,
                 from /usr/include/boost/bimap/relation/mutant_relation.hpp:29,
                 from /usr/include/boost/bimap/detail/bimap_core.hpp:38,
                 from /usr/include/boost/bimap/bimap.hpp:61,
                 from /usr/include/boost/bimap.hpp:13,
                 from ../../src/io/annotationmappings.H:36,
                 from ../../src/mira/multitag.H:39,
                 from ../../src/mira/read.H:38,
                 from ../../src/mira/readpool.H:41,
                 from ../../src/mira/pcrcontainer.H:30,
                 from pcrcontainer.C:27:
/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.'
   36 | BOOST_PRAGMA_MESSAGE(
      | ^~~~~~~~~~~~~~~~~~~~
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2  -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o ppathfinder.o ppathfinder.C
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2  -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o preventinitfiasco.o preventinitfiasco.C
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2  -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o readgrouplib.o readgrouplib.C
In file included from /usr/include/boost/container_hash/detail/requires_cxx11.hpp:9,
                 from /usr/include/boost/container_hash/hash.hpp:14,
                 from /usr/include/boost/functional/hash/hash.hpp:6,
                 from /usr/include/boost/bimap/relation/mutant_relation.hpp:29,
                 from /usr/include/boost/bimap/detail/bimap_core.hpp:38,
                 from /usr/include/boost/bimap/bimap.hpp:61,
                 from /usr/include/boost/bimap.hpp:13,
                 from ../../src/io/annotationmappings.H:36,
                 from ../../src/mira/multitag.H:39,
                 from ../../src/mira/read.H:38,
                 from ../../src/mira/readpool.H:41,
                 from ../../src/mira/pcrcontainer.H:30,
                 from ../../src/mira/contig.H:42,
                 from ../../src/mira/ppathfinder.H:35,
                 from ppathfinder.C:25:
/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.'
   36 | BOOST_PRAGMA_MESSAGE(
      | ^~~~~~~~~~~~~~~~~~~~
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2  -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o readlotstat.o readlotstat.C
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2  -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o readpool.o readpool.C
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2  -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o readpool_io.o readpool_io.C
In file included from /usr/include/boost/container_hash/detail/requires_cxx11.hpp:9,
                 from /usr/include/boost/container_hash/hash.hpp:14,
                 from /usr/include/boost/functional/hash/hash.hpp:6,
                 from /usr/include/boost/bimap/relation/mutant_relation.hpp:29,
                 from /usr/include/boost/bimap/detail/bimap_core.hpp:38,
                 from /usr/include/boost/bimap/bimap.hpp:61,
                 from /usr/include/boost/bimap.hpp:13,
                 from ../../src/io/annotationmappings.H:36,
                 from preventinitfiasco.C:30:
/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.'
   36 | BOOST_PRAGMA_MESSAGE(
      | ^~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/boost/container_hash/detail/requires_cxx11.hpp:9,
                 from /usr/include/boost/container_hash/hash.hpp:14,
                 from /usr/include/boost/functional/hash/hash.hpp:6,
                 from /usr/include/boost/bimap/relation/mutant_relation.hpp:29,
                 from /usr/include/boost/bimap/detail/bimap_core.hpp:38,
                 from /usr/include/boost/bimap/bimap.hpp:61,
                 from /usr/include/boost/bimap.hpp:13,
                 from ../../src/io/annotationmappings.H:36,
                 from ../../src/mira/multitag.H:39,
                 from ../../src/mira/read.H:38,
                 from ../../src/mira/readpool.H:41,
                 from readpool.C:29:
/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.'
   36 | BOOST_PRAGMA_MESSAGE(
      | ^~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/boost/function/detail/requires_cxx11.hpp:9,
                 from /usr/include/boost/function/detail/prologue.hpp:12,
                 from /usr/include/boost/function.hpp:30,
                 from /usr/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from /usr/include/boost/algorithm/string/find_iterator.hpp:24,
                 from /usr/include/boost/algorithm/string/iter_find.hpp:27,
                 from /usr/include/boost/algorithm/string/split.hpp:16,
                 from /usr/include/boost/algorithm/string.hpp:23,
                 from readpool_io.C:25:
/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.'
   36 | BOOST_PRAGMA_MESSAGE(
      | ^~~~~~~~~~~~~~~~~~~~
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2  -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o sam_collect.o sam_collect.C
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2  -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o scaffolder.o scaffolder.C
In file included from /usr/include/boost/container_hash/detail/requires_cxx11.hpp:9,
                 from /usr/include/boost/container_hash/hash.hpp:14,
                 from /usr/include/boost/functional/hash/hash.hpp:6,
                 from /usr/include/boost/bimap/relation/mutant_relation.hpp:29,
                 from /usr/include/boost/bimap/detail/bimap_core.hpp:38,
                 from /usr/include/boost/bimap/bimap.hpp:61,
                 from /usr/include/boost/bimap.hpp:13,
                 from ../../src/io/annotationmappings.H:36,
                 from ../../src/mira/multitag.H:39,
                 from ../../src/mira/read.H:38,
                 from ../../src/mira/readpool.H:41,
                 from ../../src/mira/pcrcontainer.H:30,
                 from ../../src/mira/contig.H:42,
                 from ../../src/mira/maf_parse.H:38,
                 from sam_collect.C:31:
/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.'
   36 | BOOST_PRAGMA_MESSAGE(
      | ^~~~~~~~~~~~~~~~~~~~
scaffolder.C:203:9: warning: "CEBUG" redefined
  203 | #define CEBUG(bla)
      |         ^~~~~
scaffolder.C:84:9: note: this is the location of the previous definition
   84 | #define CEBUG(bla)   {cout << bla; cout.flush(); }
      |         ^~~~~
In file included from /usr/include/boost/container_hash/detail/requires_cxx11.hpp:9,
                 from /usr/include/boost/container_hash/hash.hpp:14,
                 from /usr/include/boost/functional/hash/hash.hpp:6,
                 from /usr/include/boost/bimap/relation/mutant_relation.hpp:29,
                 from /usr/include/boost/bimap/detail/bimap_core.hpp:38,
                 from /usr/include/boost/bimap/bimap.hpp:61,
                 from /usr/include/boost/bimap.hpp:13,
                 from ../../src/io/annotationmappings.H:36,
                 from ../../src/mira/multitag.H:39,
                 from ../../src/mira/read.H:38,
                 from ../../src/mira/readpool.H:41,
                 from ../../src/mira/pcrcontainer.H:30,
                 from ../../src/mira/contig.H:42,
                 from scaffolder.C:28:
/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.'
   36 | BOOST_PRAGMA_MESSAGE(
      | ^~~~~~~~~~~~~~~~~~~~
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2  -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o seqtohash.o seqtohash.C
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2  -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o simplebloomfilter.o simplebloomfilter.C
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2  -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o skim_lowbph.o skim_lowbph.C
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2  -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o warnings.o warnings.C
rm -f libmiraestass.a
ar cru libmiraestass.a estassembly.o 
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libmiraestass.a
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2  -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o parameters_flexer.o parameters_flexer.cc
In file included from /usr/include/boost/function/detail/requires_cxx11.hpp:9,
                 from /usr/include/boost/function/detail/prologue.hpp:12,
                 from /usr/include/boost/function.hpp:30,
                 from skim.H:25,
                 from skim_lowbph.C:23:
/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.'
   36 | BOOST_PRAGMA_MESSAGE(
      | ^~~~~~~~~~~~~~~~~~~~
rm -f libmira.a
ar cru libmira.a  hashstats_sdbg.o hashstats.o skim.o assembly.o contig.o read.o contig_analysis.o ads.o adsfacts.o align.o assembly_info.o assembly_buildcontigs.o assembly_io.o assembly_misc.o assembly_output.o assembly_pbcorrect.o assembly_reduceskimhits.o assembly_swalign.o contig_consensus.o contig_covanalysis.o contig_edit.o contig_featureinfo.o contig_output.o contig_pairconsistency.o dataprocessing.o dynamic.o gbf_parse.o gff_parse.o gff_save.o maf_parse.o manifest.o multitag.o parameters_flexer.o parameters.o pcrcontainer.o ppathfinder.o preventinitfiasco.o readgrouplib.o readlotstat.o readpool.o readpool_io.o sam_collect.o scaffolder.o seqtohash.o simplebloomfilter.o skim_lowbph.o warnings.o  
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libmira.a
make[6]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/mira'
make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/mira'
Making all in caf
make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/caf'
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2  -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o caf.o caf.C
/bin/sh ../../ylwrap caf_flexer.ll lex.yy.c caf_flexer.cc -- flex  
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2  -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o caf_flexer.o caf_flexer.cc
In file included from /usr/include/boost/lexical_cast.hpp:26,
                 from ../../src/util/fileanddisk.H:43,
                 from ../../src/caf/caf.H:43,
                 from caf.C:50:
/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.'
   36 | BOOST_PRAGMA_MESSAGE(
      | ^~~~~~~~~~~~~~~~~~~~
rm -f libmiracaf.a
ar cru libmiracaf.a caf.o caf_flexer.o 
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libmiracaf.a
make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/caf'
Making all in memorc
make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/memorc'
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2  -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o memorc.o memorc.C
memorc.C: In static member function 'static void MemORC::statistics()':
memorc.C:155:39: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 2 has type 'std::map<void*, MemORC::memblockinfo_t>::size_type' {aka 'unsigned int'} [-Wformat=]
  155 |   printf("Num. memory blocks     : %llu\n", MOC_memblocks.size());
      |                                    ~~~^     ~~~~~~~~~~~~~~~~~~~~
      |                                       |                       |
      |                                       long long unsigned int  std::map<void*, MemORC::memblockinfo_t>::size_type {aka unsigned int}
      |                                    %u
memorc.C:156:39: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 2 has type 'std::map<void*, MemORC::memblockinfo_t>::size_type' {aka 'unsigned int'} [-Wformat=]
  156 |   printf("Num. active hot blocks : %llu\n", MOC_hotblocks.size());
      |                                    ~~~^     ~~~~~~~~~~~~~~~~~~~~
      |                                       |                       |
      |                                       long long unsigned int  std::map<void*, MemORC::memblockinfo_t>::size_type {aka unsigned int}
      |                                    %u
memorc.C:157:39: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 2 has type 'std::vector<long long unsigned int>::size_type' {aka 'unsigned int'} [-Wformat=]
  157 |   printf("Num. pending hot blocks: %llu\n", MOC_hotaidsrequested.size());
      |                                    ~~~^     ~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                       |                              |
      |                                       long long unsigned int         std::vector<long long unsigned int>::size_type {aka unsigned int}
      |                                    %u
memorc.C:158:39: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 2 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
  158 |   printf("Total mem reqested     : %llu\n", MOC_reqmemalloc);
      |                                    ~~~^     ~~~~~~~~~~~~~~~
      |                                       |     |
      |                                       |     size_t {aka unsigned int}
      |                                       long long unsigned int
      |                                    %u
memorc.C:159:39: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 2 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
  159 |   printf("Total mem allocated    : %llu (including pads and fences)\n", MOC_totalmemalloc);
      |                                    ~~~^                                 ~~~~~~~~~~~~~~~~~
      |                                       |                                 |
      |                                       long long unsigned int            size_t {aka unsigned int}
      |                                    %u
memorc.C: In static member function 'static void* MemORC::newMemBlock(size_t)':
memorc.C:225:51: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 2 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
  225 |       printf("Used malloc()\nTried to allocate %llu byte.\nSorry, memory allocation failed. Bailing out.\n", totaln);
      |                                                ~~~^                                                          ~~~~~~
      |                                                   |                                                          |
      |                                                   long long unsigned int                                     size_t {aka unsigned int}
      |                                                %u
memorc.C: In static member function 'static void MemORC::deleteMemBlock(void*)':
memorc.C:311:42: warning: format '%d' expects argument of type 'int', but argument 2 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
  311 |         printf("Nearest memblock above (%d):\t",reinterpret_cast<uint64>(mbI->first)-reinterpret_cast<uint64>(usraddr));
      |                                         ~^      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                          |                                          |
      |                                          int                                        uint64 {aka long long unsigned int}
      |                                         %lld
memorc.C:318:43: warning: format '%d' expects argument of type 'int', but argument 2 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=]
  318 |         printf("Nearest memblock below (-%d):\t",reinterpret_cast<uint64>(usraddr)-reinterpret_cast<uint64>(mbI->first));
      |                                          ~^      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                           |                                       |
      |                                           int                                     uint64 {aka long long unsigned int}
      |                                          %lld
memorc.C: In static member function 'static bool MemORC::checkMemBlock(std::map<void*, memblockinfo_t>::iterator)':
memorc.C:500:22: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 2 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
  500 |     printf("Size: %llu\n", mbI->second.size);
      |                   ~~~^     ~~~~~~~~~~~~~~~~
      |                      |                 |
      |                      |                 size_t {aka unsigned int}
      |                      long long unsigned int
      |                   %u
memorc.C: In static member function 'static void MemORC::printMemBlockInfo(std::map<void*, memblockinfo_t>::iterator)':
memorc.C:558:18: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
  558 |   printf("%p\t%llu\t",mbI->first,mbI->second.size);
      |               ~~~^               ~~~~~~~~~~~~~~~~
      |                  |                           |
      |                  long long unsigned int      size_t {aka unsigned int}
      |               %u
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2  -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o main.o main.C
rm -f libmemorc.a
ar cru libmemorc.a memorc.o 
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libmemorc.a
/bin/sh ../../libtool  --tag=CXX   --mode=link g++  -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -L../io/ -L../util/ -L../errorhandling/ -L../mira -L../caf/ -L/usr/lib/i386-linux-gnu -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/i386-linux-gnu -L/usr/lib -o main main.o  -lmiraerrorhandling -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt -lexpat -lm -lz -lbz2
libtool: link: g++ -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -Wl,-z -Wl,relro -Wl,-z -Wl,now -o main main.o  -L../io/ -L../util/ -L../errorhandling/ -L../mira -L../caf/ -L/usr/lib/i386-linux-gnu -L/usr/lib -lmiraerrorhandling -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt -lexpat -lm -lz -lbz2 -fopenmp -pthread
make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/memorc'
Making all in modules
make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/modules'
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2  -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o mod_sigconex.o mod_sigconex.C
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2  -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o mod_scaffold.o mod_scaffold.C
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2  -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o mod_bait.o mod_bait.C
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2  -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o mod_dbgreplay.o mod_dbgreplay.C
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2  -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o mod_diff.o mod_diff.C
In file included from /usr/include/boost/container_hash/detail/requires_cxx11.hpp:9,
                 from /usr/include/boost/container_hash/hash.hpp:14,
                 from /usr/include/boost/functional/hash/hash.hpp:6,
                 from /usr/include/boost/bimap/relation/mutant_relation.hpp:29,
                 from /usr/include/boost/bimap/detail/bimap_core.hpp:38,
                 from /usr/include/boost/bimap/bimap.hpp:61,
                 from /usr/include/boost/bimap.hpp:13,
                 from ../../src/io/annotationmappings.H:36,
                 from ../../src/mira/multitag.H:39,
                 from ../../src/mira/read.H:38,
                 from ../../src/mira/readpool.H:41,
                 from ../../src/mira/pcrcontainer.H:30,
                 from ../../src/mira/contig.H:42,
                 from mod_scaffold.C:32:
/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.'
   36 | BOOST_PRAGMA_MESSAGE(
      | ^~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/boost/container_hash/detail/requires_cxx11.hpp:9,
                 from /usr/include/boost/container_hash/hash.hpp:14,
                 from /usr/include/boost/functional/hash/hash.hpp:6,
                 from /usr/include/boost/bimap/relation/mutant_relation.hpp:29,
                 from /usr/include/boost/bimap/detail/bimap_core.hpp:38,
                 from /usr/include/boost/bimap/bimap.hpp:61,
                 from /usr/include/boost/bimap.hpp:13,
                 from ../../src/io/annotationmappings.H:36,
                 from ../../src/mira/multitag.H:39,
                 from ../../src/mira/read.H:38,
                 from ../../src/mira/readpool.H:41,
                 from ../../src/mira/pcrcontainer.H:30,
                 from ../../src/mira/contig.H:42,
                 from ../../src/mira/assembly_info.H:33,
                 from ../../src/mira/assembly.H:33,
                 from mod_dbgreplay.C:4:
/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.'
   36 | BOOST_PRAGMA_MESSAGE(
      | ^~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/boost/container_hash/detail/requires_cxx11.hpp:9,
                 from /usr/include/boost/container_hash/hash.hpp:14,
                 from /usr/include/boost/functional/hash/hash.hpp:6,
                 from /usr/include/boost/bimap/relation/mutant_relation.hpp:29,
                 from /usr/include/boost/bimap/detail/bimap_core.hpp:38,
                 from /usr/include/boost/bimap/bimap.hpp:61,
                 from /usr/include/boost/bimap.hpp:13,
                 from ../../src/io/annotationmappings.H:36,
                 from ../../src/mira/multitag.H:39,
                 from ../../src/mira/read.H:38,
                 from ../../src/mira/readpool.H:41,
                 from ../../src/mira/pcrcontainer.H:30,
                 from ../../src/mira/contig.H:42,
                 from ../../src/mira/assembly_info.H:33,
                 from ../../src/mira/assembly.H:33,
                 from ../../src/modules/mod_diff.H:34,
                 from mod_diff.C:29:
/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.'
   36 | BOOST_PRAGMA_MESSAGE(
      | ^~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/boost/container_hash/detail/requires_cxx11.hpp:9,
                 from /usr/include/boost/container_hash/hash.hpp:14,
                 from /usr/include/boost/functional/hash/hash.hpp:6,
                 from /usr/include/boost/bimap/relation/mutant_relation.hpp:29,
                 from /usr/include/boost/bimap/detail/bimap_core.hpp:38,
                 from /usr/include/boost/bimap/bimap.hpp:61,
                 from /usr/include/boost/bimap.hpp:13,
                 from ../../src/io/annotationmappings.H:36,
                 from ../../src/mira/multitag.H:39,
                 from ../../src/mira/read.H:38,
                 from ../../src/mira/readpool.H:41,
                 from ../../src/mira/readpool_io.H:45,
                 from ../../src/modules/mod_sigconex.H:35,
                 from mod_sigconex.C:27:
/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.'
   36 | BOOST_PRAGMA_MESSAGE(
      | ^~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/boost/system/detail/requires_cxx11.hpp:9,
                 from /usr/include/boost/system/detail/config.hpp:11,
                 from /usr/include/boost/system/detail/error_category.hpp:13,
                 from /usr/include/boost/system/detail/error_code.hpp:14,
                 from /usr/include/boost/system/errc.hpp:14,
                 from /usr/include/boost/system/system_error.hpp:9,
                 from /usr/include/boost/thread/exceptions.hpp:22,
                 from /usr/include/boost/thread/pthread/mutex.hpp:14,
                 from /usr/include/boost/thread/mutex.hpp:16,
                 from mod_bait.C:35:
/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.'
   36 | BOOST_PRAGMA_MESSAGE(
      | ^~~~~~~~~~~~~~~~~~~~
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2  -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o mod_mer.o mod_mer.C
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2  -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o mod_mira.o mod_mira.C
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2  -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o mod_convert.o mod_convert.C
In file included from /usr/include/boost/container_hash/detail/requires_cxx11.hpp:9,
                 from /usr/include/boost/container_hash/hash.hpp:14,
                 from /usr/include/boost/functional/hash/hash.hpp:6,
                 from /usr/include/boost/bimap/relation/mutant_relation.hpp:29,
                 from /usr/include/boost/bimap/detail/bimap_core.hpp:38,
                 from /usr/include/boost/bimap/bimap.hpp:61,
                 from /usr/include/boost/bimap.hpp:13,
                 from ../../src/io/annotationmappings.H:36,
                 from ../../src/mira/multitag.H:39,
                 from ../../src/mira/read.H:38,
                 from ../../src/mira/readpool.H:41,
                 from ../../src/mira/readpool_io.H:45,
                 from ../../src/modules/mod_mer.H:35,
                 from mod_mer.C:27:
/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.'
   36 | BOOST_PRAGMA_MESSAGE(
      | ^~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/boost/system/detail/requires_cxx11.hpp:9,
                 from /usr/include/boost/system/detail/config.hpp:11,
                 from /usr/include/boost/system/detail/error_category.hpp:13,
                 from /usr/include/boost/system/error_category.hpp:10,
                 from /usr/include/boost/filesystem/detail/path_traits.hpp:25,
                 from /usr/include/boost/filesystem/path.hpp:21,
                 from /usr/include/boost/filesystem/operations.hpp:20,
                 from mod_mira.C:37:
/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.'
   36 | BOOST_PRAGMA_MESSAGE(
      | ^~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/boost/container_hash/detail/requires_cxx11.hpp:9,
                 from /usr/include/boost/container_hash/hash.hpp:14,
                 from /usr/include/boost/functional/hash/hash.hpp:6,
                 from /usr/include/boost/bimap/relation/mutant_relation.hpp:29,
                 from /usr/include/boost/bimap/detail/bimap_core.hpp:38,
                 from /usr/include/boost/bimap/bimap.hpp:61,
                 from /usr/include/boost/bimap.hpp:13,
                 from ../../src/io/annotationmappings.H:36,
                 from ../../src/mira/multitag.H:39,
                 from ../../src/mira/read.H:38,
                 from ../../src/mira/readpool.H:41,
                 from ../../src/modules/mod_convert.H:34,
                 from mod_convert.C:29:
/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.'
   36 | BOOST_PRAGMA_MESSAGE(
      | ^~~~~~~~~~~~~~~~~~~~
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2  -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o mod_memestim.o mod_memestim.C
mod_mira.C: In function 'void miraMain_extractContigs(int, char**)':
mod_mira.C:414:10: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  414 |     chdir("../..");
      |     ~~~~~^~~~~~~~~
mod_mira.C:439:10: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  439 |     chdir("../..");
      |     ~~~~~^~~~~~~~~
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2  -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o mod_tagsnp.o mod_tagsnp.C
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2  -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o misc.o misc.C
In file included from /usr/include/boost/container_hash/detail/requires_cxx11.hpp:9,
                 from /usr/include/boost/container_hash/hash.hpp:14,
                 from /usr/include/boost/functional/hash/hash.hpp:6,
                 from /usr/include/boost/bimap/relation/mutant_relation.hpp:29,
                 from /usr/include/boost/bimap/detail/bimap_core.hpp:38,
                 from /usr/include/boost/bimap/bimap.hpp:61,
                 from /usr/include/boost/bimap.hpp:13,
                 from ../../src/io/annotationmappings.H:36,
                 from ../../src/mira/multitag.H:39,
                 from ../../src/mira/read.H:38,
                 from ../../src/mira/readpool.H:41,
                 from ../../src/mira/pcrcontainer.H:30,
                 from ../../src/mira/contig.H:42,
                 from ../../src/mira/assembly_info.H:33,
                 from ../../src/mira/assembly.H:33,
                 from mod_memestim.C:36:
/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.'
   36 | BOOST_PRAGMA_MESSAGE(
      | ^~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/boost/lexical_cast.hpp:26,
                 from ../../src/util/fileanddisk.H:43,
                 from ../../src/caf/caf.H:43,
                 from mod_tagsnp.C:29:
/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.'
   36 | BOOST_PRAGMA_MESSAGE(
      | ^~~~~~~~~~~~~~~~~~~~
rm -f libmiramodules.a
ar cru libmiramodules.a mod_sigconex.o mod_scaffold.o mod_bait.o mod_dbgreplay.o mod_diff.o mod_mer.o mod_mira.o mod_convert.o mod_memestim.o mod_tagsnp.o misc.o 
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libmiramodules.a
make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/modules'
Making all in support
make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/support'
make[5]: Nothing to be done for 'all'.
make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/support'
Making all in scripts
make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/scripts'
make[5]: Nothing to be done for 'all'.
make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/scripts'
Making all in version
make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/version'
make  all-am
make[6]: Entering directory '/build/reproducible-path/mira-4.9.6/src/version'
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.   -Wdate-time -D_FORTIFY_SOURCE=2  -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o mversion.o mversion.C
rm -f libmiraversion.a
ar cru libmiraversion.a mversion.o 
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libmiraversion.a
make[6]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/version'
make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/version'
Making all in progs
make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/progs'
Making .C out of .xxd compileinfo.itxt
make  all-am
make[6]: Entering directory '/build/reproducible-path/mira-4.9.6/src/progs'
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o mira.o mira.C
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o quirks.o quirks.C
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o miratest.o miratest.C
Making .C out of .xxd compileinfo.itxt
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o compileinfo.itxt.xxd.o compileinfo.itxt.xxd.C
In file included from /usr/include/boost/function/detail/requires_cxx11.hpp:9,
                 from /usr/include/boost/function/detail/prologue.hpp:12,
                 from /usr/include/boost/function.hpp:30,
                 from /usr/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from /usr/include/boost/algorithm/string/find_iterator.hpp:24,
                 from /usr/include/boost/algorithm/string/iter_find.hpp:27,
                 from /usr/include/boost/algorithm/string/split.hpp:16,
                 from /usr/include/boost/algorithm/string.hpp:23,
                 from mira.C:34:
/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.'
   36 | BOOST_PRAGMA_MESSAGE(
      | ^~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/boost/smart_ptr/detail/requires_cxx11.hpp:9,
                 from /usr/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /usr/include/boost/shared_ptr.hpp:17,
                 from /usr/include/boost/iostreams/chain.hpp:36,
                 from /usr/include/boost/iostreams/filtering_streambuf.hpp:17,
                 from /usr/include/boost/iostreams/filtering_stream.hpp:22,
                 from ../../src/io/fastq-mira.H:31,
                 from miratest.C:12:
/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.'
   36 | BOOST_PRAGMA_MESSAGE(
      | ^~~~~~~~~~~~~~~~~~~~
/bin/sh ../../libtool  --tag=CXX   --mode=link g++ -pthread -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -L../version -L../modules -L../debuggersupport -L../memorc -L../io/ -L../util/ -L../errorhandling/ -L../mira -L../caf -L/usr/lib/i386-linux-gnu -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/i386-linux-gnu -L/usr/lib -o mira mira.o quirks.o compileinfo.itxt.xxd.o -lmiraversion -lmiramodules -lmiradebuggersupport  -lmira -lmiraestass -lmiracaf -lmirautil -lmiradptools -lmirafio -lmiraerrorhandling -lmiradebuggersupport -lmirafmttext -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt -lexpat -lm -lz -lbz2
/bin/sh ../../libtool  --tag=CXX   --mode=link g++ -pthread -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -L../version -L../modules -L../debuggersupport -L../memorc -L../io/ -L../util/ -L../errorhandling/ -L../mira -L../caf -L/usr/lib/i386-linux-gnu -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/i386-linux-gnu -L/usr/lib -o miratest miratest.o compileinfo.itxt.xxd.o -lmiraversion -lmiramodules -lmiradebuggersupport  -lmira -lmiraestass -lmiracaf -lmirautil -lmiradptools -lmirafio -lmiraerrorhandling -lmiradebuggersupport -lmirafmttext -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt -lexpat -lm -lz -lbz2
libtool: link: g++ -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -Wl,-z -Wl,relro -Wl,-z -Wl,now -o mira mira.o quirks.o compileinfo.itxt.xxd.o  -L../version -L../modules -L../debuggersupport -L../memorc -L../io/ -L../util/ -L../errorhandling/ -L../mira -L../caf -L/usr/lib/i386-linux-gnu -L/usr/lib -lmiraversion -lmiramodules -lmira -lmiraestass -lmiracaf -lmirautil -lmiradptools -lmirafio -lmiraerrorhandling -lmiradebuggersupport -lmirafmttext -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt -lexpat -lm -lz -lbz2 -fopenmp -pthread
libtool: link: g++ -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -Wl,-z -Wl,relro -Wl,-z -Wl,now -o miratest miratest.o compileinfo.itxt.xxd.o  -L../version -L../modules -L../debuggersupport -L../memorc -L../io/ -L../util/ -L../errorhandling/ -L../mira -L../caf -L/usr/lib/i386-linux-gnu -L/usr/lib -lmiraversion -lmiramodules -lmira -lmiraestass -lmiracaf -lmirautil -lmiradptools -lmirafio -lmiraerrorhandling -lmiradebuggersupport -lmirafmttext -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt -lexpat -lm -lz -lbz2 -fopenmp -pthread
make[6]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/progs'
make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/progs'
Making all in other
make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/other'
Making all in sls
make[6]: Entering directory '/build/reproducible-path/mira-4.9.6/src/other/sls'
Making all in mira-createsls
make[7]: Entering directory '/build/reproducible-path/mira-4.9.6/src/other/sls/mira-createsls'
Making all in bin
make[8]: Entering directory '/build/reproducible-path/mira-4.9.6/src/other/sls/mira-createsls/bin'
make[8]: Nothing to be done for 'all'.
make[8]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/other/sls/mira-createsls/bin'
make[8]: Entering directory '/build/reproducible-path/mira-4.9.6/src/other/sls/mira-createsls'
make[8]: Nothing to be done for 'all-am'.
make[8]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/other/sls/mira-createsls'
make[7]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/other/sls/mira-createsls'
make[7]: Entering directory '/build/reproducible-path/mira-4.9.6/src/other/sls'
make[7]: Nothing to be done for 'all-am'.
make[7]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/other/sls'
make[6]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/other/sls'
make[6]: Entering directory '/build/reproducible-path/mira-4.9.6/src/other'
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	rm -f debian/mira-assembler.debhelper.log
   debian/rules override_dh_auto_build-indep
make[1]: Entering directory '/build/reproducible-path/mira-4.9.6'
dh_auto_build --sourcedir=doc
	cd doc && make -j5 "INSTALL=install --strip-program=true"
make[2]: Entering directory '/build/reproducible-path/mira-4.9.6/doc'
Making all in docbook
make[3]: Entering directory '/build/reproducible-path/mira-4.9.6/doc/docbook'
Making versionfile
xsltproc --nonet --xinclude --output DefinitiveGuideToMIRA.html ../../doc/docbook/book.xsl ../../doc/docbook/book_definitiveguide.xml
xsltproc --nonet --xinclude --output 3rdparty_MIRA.html ../../doc/docbook/book.xsl ../../doc/docbook/book_3rdparty.xml
dblatex --xslt-opts=--nonet --output=DefinitiveGuideToMIRA.pdf ../../doc/docbook/book_definitiveguide.xml
dblatex --xslt-opts=--nonet --output=3rdparty_MIRA.pdf ../../doc/docbook/book_3rdparty.xml
Making .html out of _part.xml chap_bitsandpieces_part.html
Build the book set list...
Build the book set list...
Making .html out of _part.xml chap_mirautils_part.html
Making .html out of _part.xml chap_est_part.html
ERROR: xref linking to chap_dataprep has no generated link text.
Error: no ID for constraint linkend: "chap_dataprep".
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ERROR: xref linking to sect_res_looking_at_results has no generated link text.
Error: no ID for constraint linkend: "sect_res_looking_at_results".
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Error: no ID for constraint linkend: "sect_res_filtering_of_results".
ERROR: xref linking to sect_res_places_of_importance_in_a_de_novo_assembly has no generated link text.
Error: no ID for constraint linkend: "sect_res_places_of_importance_in_a_de_novo_assembly".
ERROR: xref linking to chap_reference has no generated link text.
Error: no ID for constraint linkend: "chap_reference".
ERROR: xref linking to sect_ref_manifest_basics has no generated link text.
Error: no ID for constraint linkend: "sect_ref_manifest_basics".
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Error: no ID for constraint linkend: "sect_ref_manifest_readgroups".
ERROR: xref linking to sect_ref_manifest_parameters has no generated link text.
Error: no ID for constraint linkend: "sect_ref_manifest_parameters".
Making .html out of _part.xml chap_faq_part.html
Making .html out of _part.xml chap_hard_part.html
Build the listings...
Making .html out of _part.xml chap_logfiles_part.html
Making .html out of _part.xml chap_maf_part.html
XSLT stylesheets DocBook - LaTeX 2e (0.3.12)
===================================================
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Build book_3rdparty.pdf
Making .html out of _part.xml chap_reference_part.html
Making .html out of _part.xml chap_installation_part.html
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Making .html out of _part.xml chap_intro_part.html
Making .html out of _part.xml chap_results_part.html
Making .html out of _part.xml chap_sra_part.html
Making .html out of _part.xml chap_seqadvice_part.html
Making .html out of _part.xml chap_bonus_part.html
Element emph in namespace '' encountered in note, but no template matches.
Making .html out of _part.xml chap_preface_part.html
Build the listings...
'3rdparty_MIRA.pdf' successfully built
XSLT stylesheets DocBook - LaTeX 2e (0.3.12)
===================================================
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Build book_definitiveguide.pdf
'DefinitiveGuideToMIRA.pdf' successfully built
make[3]: Leaving directory '/build/reproducible-path/mira-4.9.6/doc/docbook'
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	rm -f debian/mira-doc.debhelper.log debian/mira-rfam-12s-rrna.debhelper.log
   debian/rules override_dh_auto_test-arch
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make check
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Making .C out of .xxd compileinfo.itxt
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o compileinfo.itxt.xxd.o compileinfo.itxt.xxd.C
/bin/sh ../../libtool  --tag=CXX   --mode=link g++ -pthread -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -L../version -L../modules -L../debuggersupport -L../memorc -L../io/ -L../util/ -L../errorhandling/ -L../mira -L../caf -L/usr/lib/i386-linux-gnu -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/i386-linux-gnu -L/usr/lib -o mira mira.o quirks.o compileinfo.itxt.xxd.o -lmiraversion -lmiramodules -lmiradebuggersupport  -lmira -lmiraestass -lmiracaf -lmirautil -lmiradptools -lmirafio -lmiraerrorhandling -lmiradebuggersupport -lmirafmttext -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt -lexpat -lm -lz -lbz2
libtool: link: g++ -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -Wl,-z -Wl,relro -Wl,-z -Wl,now -o mira mira.o quirks.o compileinfo.itxt.xxd.o  -L../version -L../modules -L../debuggersupport -L../memorc -L../io/ -L../util/ -L../errorhandling/ -L../mira -L../caf -L/usr/lib/i386-linux-gnu -L/usr/lib -lmiraversion -lmiramodules -lmira -lmiraestass -lmiracaf -lmirautil -lmiradptools -lmirafio -lmiraerrorhandling -lmiradebuggersupport -lmirafmttext -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt -lexpat -lm -lz -lbz2 -fopenmp -pthread
/bin/sh ../../libtool  --tag=CXX   --mode=link g++ -pthread -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -L../version -L../modules -L../debuggersupport -L../memorc -L../io/ -L../util/ -L../errorhandling/ -L../mira -L../caf -L/usr/lib/i386-linux-gnu -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/i386-linux-gnu -L/usr/lib -o miratest miratest.o compileinfo.itxt.xxd.o -lmiraversion -lmiramodules -lmiradebuggersupport  -lmira -lmiraestass -lmiracaf -lmirautil -lmiradptools -lmirafio -lmiraerrorhandling -lmiradebuggersupport -lmirafmttext -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt -lexpat -lm -lz -lbz2
libtool: link: g++ -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -Wl,-z -Wl,relro -Wl,-z -Wl,now -o miratest miratest.o compileinfo.itxt.xxd.o  -L../version -L../modules -L../debuggersupport -L../memorc -L../io/ -L../util/ -L../errorhandling/ -L../mira -L../caf -L/usr/lib/i386-linux-gnu -L/usr/lib -lmiraversion -lmiramodules -lmira -lmiraestass -lmiracaf -lmirautil -lmiradptools -lmirafio -lmiraerrorhandling -lmiradebuggersupport -lmirafmttext -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt -lexpat -lm -lz -lbz2 -fopenmp -pthread
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make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src'
make[5]: Nothing to be done for 'check-am'.
make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src'
make[4]: Leaving directory '/build/reproducible-path/mira-4.9.6/src'
make[4]: Entering directory '/build/reproducible-path/mira-4.9.6'
make[4]: Nothing to be done for 'check-am'.
make[4]: Leaving directory '/build/reproducible-path/mira-4.9.6'
make[3]: Leaving directory '/build/reproducible-path/mira-4.9.6'
make[2]: Leaving directory '/build/reproducible-path/mira-4.9.6'
make[1]: Leaving directory '/build/reproducible-path/mira-4.9.6'
   debian/rules override_dh_auto_test-indep
make[1]: Entering directory '/build/reproducible-path/mira-4.9.6'
echo no tests for -indep
no tests for -indep
make[1]: Leaving directory '/build/reproducible-path/mira-4.9.6'
   create-stamp debian/debhelper-build-stamp
   dh_prep
	rm -f -- debian/mira-assembler.substvars debian/mira-rfam-12s-rrna.substvars debian/mira-doc.substvars
	rm -fr -- debian/.debhelper/generated/mira-assembler/ debian/mira-assembler/ debian/tmp/ debian/.debhelper/generated/mira-rfam-12s-rrna/ debian/mira-rfam-12s-rrna/ debian/.debhelper/generated/mira-doc/ debian/mira-doc/
   debian/rules override_dh_auto_install-arch
make[1]: Entering directory '/build/reproducible-path/mira-4.9.6'
make install DESTDIR=/build/reproducible-path/mira-4.9.6/debian/mira-assembler
make[2]: Entering directory '/build/reproducible-path/mira-4.9.6'
make  install-recursive
make[3]: Entering directory '/build/reproducible-path/mira-4.9.6'
Making install in man
make[4]: Entering directory '/build/reproducible-path/mira-4.9.6/man'
make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/man'
make[5]: Nothing to be done for 'install-exec-am'.
 /usr/bin/mkdir -p '/build/reproducible-path/mira-4.9.6/debian/mira-assembler/usr/share/man/man1'
 /usr/bin/install -c -m 644 mirabait.1 miradiff.1 miramer.1 mira.1 miraconvert.1 miramem.1 '/build/reproducible-path/mira-4.9.6/debian/mira-assembler/usr/share/man/man1'
make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/man'
make[4]: Leaving directory '/build/reproducible-path/mira-4.9.6/man'
Making install in src
make[4]: Entering directory '/build/reproducible-path/mira-4.9.6/src'
Making install in debuggersupport
make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/debuggersupport'
make[6]: Entering directory '/build/reproducible-path/mira-4.9.6/src/debuggersupport'
make[6]: Nothing to be done for 'install-exec-am'.
make[6]: Nothing to be done for 'install-data-am'.
make[6]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/debuggersupport'
make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/debuggersupport'
Making install in io
make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/io'
make  install-am
make[6]: Entering directory '/build/reproducible-path/mira-4.9.6/src/io'
make[7]: Entering directory '/build/reproducible-path/mira-4.9.6/src/io'
make[7]: Nothing to be done for 'install-exec-am'.
make[7]: Nothing to be done for 'install-data-am'.
make[7]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/io'
make[6]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/io'
make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/io'
Making install in stdinc
make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/stdinc'
make[6]: Entering directory '/build/reproducible-path/mira-4.9.6/src/stdinc'
make[6]: Nothing to be done for 'install-exec-am'.
make[6]: Nothing to be done for 'install-data-am'.
make[6]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/stdinc'
make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/stdinc'
Making install in errorhandling
make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/errorhandling'
make[6]: Entering directory '/build/reproducible-path/mira-4.9.6/src/errorhandling'
make[6]: Nothing to be done for 'install-exec-am'.
make[6]: Nothing to be done for 'install-data-am'.
make[6]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/errorhandling'
make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/errorhandling'
Making install in util
make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/util'
make[6]: Entering directory '/build/reproducible-path/mira-4.9.6/src/util'
make[6]: Nothing to be done for 'install-exec-am'.
make[6]: Nothing to be done for 'install-data-am'.
make[6]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/util'
make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/util'
Making install in mira
make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/mira'
make  install-am
make[6]: Entering directory '/build/reproducible-path/mira-4.9.6/src/mira'
make[7]: Entering directory '/build/reproducible-path/mira-4.9.6/src/mira'
make[7]: Nothing to be done for 'install-exec-am'.
make[7]: Nothing to be done for 'install-data-am'.
make[7]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/mira'
make[6]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/mira'
make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/mira'
Making install in caf
make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/caf'
make[6]: Entering directory '/build/reproducible-path/mira-4.9.6/src/caf'
make[6]: Nothing to be done for 'install-exec-am'.
make[6]: Nothing to be done for 'install-data-am'.
make[6]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/caf'
make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/caf'
Making install in memorc
make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/memorc'
make[6]: Entering directory '/build/reproducible-path/mira-4.9.6/src/memorc'
make[6]: Nothing to be done for 'install-exec-am'.
make[6]: Nothing to be done for 'install-data-am'.
make[6]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/memorc'
make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/memorc'
Making install in modules
make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/modules'
make[6]: Entering directory '/build/reproducible-path/mira-4.9.6/src/modules'
make[6]: Nothing to be done for 'install-exec-am'.
make[6]: Nothing to be done for 'install-data-am'.
make[6]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/modules'
make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/modules'
Making install in support
make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/support'
make[6]: Entering directory '/build/reproducible-path/mira-4.9.6/src/support'
make[6]: Nothing to be done for 'install-exec-am'.
 /usr/bin/mkdir -p '/build/reproducible-path/mira-4.9.6/debian/mira-assembler/usr/share/mira/support_3rdparty_tools'
 /usr/bin/install -c -m 644 consedrc.13.0 consedtaglib.txt GTAGDB README '/build/reproducible-path/mira-4.9.6/debian/mira-assembler/usr/share/mira/support_3rdparty_tools'
make[6]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/support'
make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/support'
Making install in scripts
make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/scripts'
make[6]: Entering directory '/build/reproducible-path/mira-4.9.6/src/scripts'
make[6]: Nothing to be done for 'install-exec-am'.
make[6]: Nothing to be done for 'install-data-am'.
make[6]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/scripts'
make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/scripts'
Making install in version
make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/version'
make  install-am
make[6]: Entering directory '/build/reproducible-path/mira-4.9.6/src/version'
make[7]: Entering directory '/build/reproducible-path/mira-4.9.6/src/version'
make[7]: Nothing to be done for 'install-exec-am'.
make[7]: Nothing to be done for 'install-data-am'.
make[7]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/version'
make[6]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/version'
make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/version'
Making install in progs
make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/progs'
Making .C out of .xxd compileinfo.itxt
make  install-am
make[6]: Entering directory '/build/reproducible-path/mira-4.9.6/src/progs'
Making .C out of .xxd compileinfo.itxt
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src  -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o compileinfo.itxt.xxd.o compileinfo.itxt.xxd.C
/bin/sh ../../libtool  --tag=CXX   --mode=link g++ -pthread -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -L../version -L../modules -L../debuggersupport -L../memorc -L../io/ -L../util/ -L../errorhandling/ -L../mira -L../caf -L/usr/lib/i386-linux-gnu -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/i386-linux-gnu -L/usr/lib -o mira mira.o quirks.o compileinfo.itxt.xxd.o -lmiraversion -lmiramodules -lmiradebuggersupport  -lmira -lmiraestass -lmiracaf -lmirautil -lmiradptools -lmirafio -lmiraerrorhandling -lmiradebuggersupport -lmirafmttext -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt -lexpat -lm -lz -lbz2
libtool: link: g++ -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -Wl,-z -Wl,relro -Wl,-z -Wl,now -o mira mira.o quirks.o compileinfo.itxt.xxd.o  -L../version -L../modules -L../debuggersupport -L../memorc -L../io/ -L../util/ -L../errorhandling/ -L../mira -L../caf -L/usr/lib/i386-linux-gnu -L/usr/lib -lmiraversion -lmiramodules -lmira -lmiraestass -lmiracaf -lmirautil -lmiradptools -lmirafio -lmiraerrorhandling -lmiradebuggersupport -lmirafmttext -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt -lexpat -lm -lz -lbz2 -fopenmp -pthread
/bin/sh ../../libtool  --tag=CXX   --mode=link g++ -pthread -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security  -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -L../version -L../modules -L../debuggersupport -L../memorc -L../io/ -L../util/ -L../errorhandling/ -L../mira -L../caf -L/usr/lib/i386-linux-gnu -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/i386-linux-gnu -L/usr/lib -o miratest miratest.o compileinfo.itxt.xxd.o -lmiraversion -lmiramodules -lmiradebuggersupport  -lmira -lmiraestass -lmiracaf -lmirautil -lmiradptools -lmirafio -lmiraerrorhandling -lmiradebuggersupport -lmirafmttext -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt -lexpat -lm -lz -lbz2
libtool: link: g++ -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -Wl,-z -Wl,relro -Wl,-z -Wl,now -o miratest miratest.o compileinfo.itxt.xxd.o  -L../version -L../modules -L../debuggersupport -L../memorc -L../io/ -L../util/ -L../errorhandling/ -L../mira -L../caf -L/usr/lib/i386-linux-gnu -L/usr/lib -lmiraversion -lmiramodules -lmira -lmiraestass -lmiracaf -lmirautil -lmiradptools -lmirafio -lmiraerrorhandling -lmiradebuggersupport -lmirafmttext -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt -lexpat -lm -lz -lbz2 -fopenmp -pthread
make[7]: Entering directory '/build/reproducible-path/mira-4.9.6/src/progs'
Making .C out of .xxd compileinfo.itxt
 /usr/bin/mkdir -p '/build/reproducible-path/mira-4.9.6/debian/mira-assembler/usr/bin'
  /bin/sh ../../libtool   --mode=install /usr/bin/install -c mira '/build/reproducible-path/mira-4.9.6/debian/mira-assembler/usr/bin'
libtool: install: /usr/bin/install -c mira /build/reproducible-path/mira-4.9.6/debian/mira-assembler/usr/bin/mira
make  install-exec-hook
make[8]: Entering directory '/build/reproducible-path/mira-4.9.6/src/progs'
cd /build/reproducible-path/mira-4.9.6/debian/mira-assembler/usr/bin && \
rm -f miramem && \
ln -s mira miramem && \
rm -f mirabait && \
ln -s mira mirabait &&\
rm -f miraconvert && \
ln -s mira miraconvert && \
rm -f miramer && \
ln -s mira miramer
make[8]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/progs'
make[7]: Nothing to be done for 'install-data-am'.
make[7]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/progs'
make[6]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/progs'
make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/progs'
Making install in other
make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/other'
Making install in sls
make[6]: Entering directory '/build/reproducible-path/mira-4.9.6/src/other/sls'
Making install in mira-createsls
make[7]: Entering directory '/build/reproducible-path/mira-4.9.6/src/other/sls/mira-createsls'
Making install in bin
make[8]: Entering directory '/build/reproducible-path/mira-4.9.6/src/other/sls/mira-createsls/bin'
make[9]: Entering directory '/build/reproducible-path/mira-4.9.6/src/other/sls/mira-createsls/bin'
make[9]: Nothing to be done for 'install-exec-am'.
make[9]: Nothing to be done for 'install-data-am'.
make[9]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/other/sls/mira-createsls/bin'
make[8]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/other/sls/mira-createsls/bin'
make[8]: Entering directory '/build/reproducible-path/mira-4.9.6/src/other/sls/mira-createsls'
make[9]: Entering directory '/build/reproducible-path/mira-4.9.6/src/other/sls/mira-createsls'
make[9]: Nothing to be done for 'install-exec-am'.
make[9]: Nothing to be done for 'install-data-am'.
make[9]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/other/sls/mira-createsls'
make[8]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/other/sls/mira-createsls'
make[7]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/other/sls/mira-createsls'
make[7]: Entering directory '/build/reproducible-path/mira-4.9.6/src/other/sls'
make[8]: Entering directory '/build/reproducible-path/mira-4.9.6/src/other/sls'
make[8]: Nothing to be done for 'install-exec-am'.
make[8]: Nothing to be done for 'install-data-am'.
make[8]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/other/sls'
make[7]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/other/sls'
make[6]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/other/sls'
make[6]: Entering directory '/build/reproducible-path/mira-4.9.6/src/other'
make[7]: Entering directory '/build/reproducible-path/mira-4.9.6/src/other'
make[7]: Nothing to be done for 'install-exec-am'.
make[7]: Nothing to be done for 'install-data-am'.
make[7]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/other'
make[6]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/other'
make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/other'
make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src'
make[6]: Entering directory '/build/reproducible-path/mira-4.9.6/src'
make[6]: Nothing to be done for 'install-exec-am'.
make[6]: Nothing to be done for 'install-data-am'.
make[6]: Leaving directory '/build/reproducible-path/mira-4.9.6/src'
make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src'
make[4]: Leaving directory '/build/reproducible-path/mira-4.9.6/src'
make[4]: Entering directory '/build/reproducible-path/mira-4.9.6'
make[5]: Entering directory '/build/reproducible-path/mira-4.9.6'
make[5]: Nothing to be done for 'install-exec-am'.
make[5]: Nothing to be done for 'install-data-am'.
make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6'
make[4]: Leaving directory '/build/reproducible-path/mira-4.9.6'
make[3]: Leaving directory '/build/reproducible-path/mira-4.9.6'
make[2]: Leaving directory '/build/reproducible-path/mira-4.9.6'
make[1]: Leaving directory '/build/reproducible-path/mira-4.9.6'
   debian/rules override_dh_auto_install-indep
make[1]: Entering directory '/build/reproducible-path/mira-4.9.6'
#There is no installation target for the docs
mkdir -p /build/reproducible-path/mira-4.9.6/debian/tmp/usr/share/doc/mira-assembler
cp -r -t /build/reproducible-path/mira-4.9.6/debian/tmp/usr/share/doc/mira-assembler doc/docbook/bookfigures doc/docbook/images \
    doc/docbook/doccss doc/docbook/DefinitiveGuideToMIRA.html || true
make[1]: Leaving directory '/build/reproducible-path/mira-4.9.6'
   dh_install
	install -m0755 -d debian/mira-rfam-12s-rrna/usr/share/mira/
	cp --reflink=auto -a ./src/other/sls/mira-install-sls-rrna.sh ./src/other/sls/rfam_rrna-21-12.sls.gz debian/mira-rfam-12s-rrna/usr/share/mira//
	install -m0755 -d debian/mira-doc//usr/share
	cp --reflink=auto -a debian/tmp/usr/share/doc/ debian/mira-doc//usr/share/
   dh_installdocs
	install -m0755 -d debian/mira-assembler/usr/share/doc/mira-assembler
	install -m0755 -d debian/mira-assembler/usr/share/doc/mira-assembler
	cp --reflink=auto -a ./NEWS debian/mira-assembler/usr/share/doc/mira-assembler
	cp --reflink=auto -a ./README debian/mira-assembler/usr/share/doc/mira-assembler
	cp --reflink=auto -a ./THANKS debian/mira-assembler/usr/share/doc/mira-assembler
	cp --reflink=auto -a ./HELP_WANTED debian/mira-assembler/usr/share/doc/mira-assembler
	cp --reflink=auto -a ./debian/README.test debian/mira-assembler/usr/share/doc/mira-assembler
	cp --reflink=auto -a ./debian/tests/run-unit-test debian/mira-assembler/usr/share/doc/mira-assembler
	cp --reflink=auto -a ./debian/tests/est_assembly.conf debian/mira-assembler/usr/share/doc/mira-assembler
	cp --reflink=auto -a ./debian/tests/solexa1.conf debian/mira-assembler/usr/share/doc/mira-assembler
	cp --reflink=auto -a ./debian/tests/solexa2.conf debian/mira-assembler/usr/share/doc/mira-assembler
	cd './debian/tests/test_data//..' && find 'test_data' \( -type f -or -type l \) -and ! -empty -print0 | LC_ALL=C sort -z | xargs -0 -I {} cp --reflink=auto --parents -dp {} /build/reproducible-path/mira-4.9.6/debian/mira-assembler/usr/share/doc/mira-assembler
	chmod -R u\+rw,go=rX debian/mira-assembler/usr/share/doc
	install -p -m0644 debian/copyright debian/mira-assembler/usr/share/doc/mira-assembler/copyright
	install -m0755 -d debian/mira-rfam-12s-rrna/usr/share/doc/mira-rfam-12s-rrna
	install -p -m0644 debian/copyright debian/mira-rfam-12s-rrna/usr/share/doc/mira-rfam-12s-rrna/copyright
	install -m0755 -d debian/mira-doc/usr/share/doc/mira-doc
	install -p -m0644 debian/mira-doc.README.Debian debian/mira-doc/usr/share/doc/mira-doc/README.Debian
	install -p -m0644 debian/copyright debian/mira-doc/usr/share/doc/mira-doc/copyright
	install -m0755 -d debian/mira-doc/usr/share/doc-base/
	install -p -m0644 debian/mira-doc.doc-base debian/mira-doc/usr/share/doc-base/mira-doc.mira-manual
   debian/rules override_dh_installchangelogs
make[1]: Entering directory '/build/reproducible-path/mira-4.9.6'
dh_installchangelogs src/mira/CHANGES.txt
	install -m0755 -d debian/mira-assembler/usr/share/doc/mira-assembler
	install -p -m0644 debian/.debhelper/generated/mira-assembler/dh_installchangelogs.dch.trimmed debian/mira-assembler/usr/share/doc/mira-assembler/changelog.Debian
	install -p -m0644 src/mira/CHANGES.txt debian/mira-assembler/usr/share/doc/mira-assembler/changelog
	install -m0755 -d debian/mira-doc/usr/share/doc/mira-doc
	install -p -m0644 debian/.debhelper/generated/mira-doc/dh_installchangelogs.dch.trimmed debian/mira-doc/usr/share/doc/mira-doc/changelog.Debian
	install -p -m0644 src/mira/CHANGES.txt debian/mira-doc/usr/share/doc/mira-doc/changelog
	install -m0755 -d debian/mira-rfam-12s-rrna/usr/share/doc/mira-rfam-12s-rrna
	install -p -m0644 debian/.debhelper/generated/mira-rfam-12s-rrna/dh_installchangelogs.dch.trimmed debian/mira-rfam-12s-rrna/usr/share/doc/mira-rfam-12s-rrna/changelog.Debian
	install -p -m0644 src/mira/CHANGES.txt debian/mira-rfam-12s-rrna/usr/share/doc/mira-rfam-12s-rrna/changelog
make[1]: Leaving directory '/build/reproducible-path/mira-4.9.6'
   dh_installman
	man-recode --to-code UTF-8 --suffix .dh-new debian/mira-assembler/usr/share/man/man1/mira.1 debian/mira-assembler/usr/share/man/man1/mirabait.1
	man-recode --to-code UTF-8 --suffix .dh-new debian/mira-assembler/usr/share/man/man1/miraconvert.1 debian/mira-assembler/usr/share/man/man1/miradiff.1
	man-recode --to-code UTF-8 --suffix .dh-new debian/mira-assembler/usr/share/man/man1/miramem.1 debian/mira-assembler/usr/share/man/man1/miramer.1
	mv debian/mira-assembler/usr/share/man/man1/mira.1.dh-new debian/mira-assembler/usr/share/man/man1/mira.1
	mv debian/mira-assembler/usr/share/man/man1/mirabait.1.dh-new debian/mira-assembler/usr/share/man/man1/mirabait.1
	chmod 0644 -- debian/mira-assembler/usr/share/man/man1/mira.1 debian/mira-assembler/usr/share/man/man1/mirabait.1
	mv debian/mira-assembler/usr/share/man/man1/miraconvert.1.dh-new debian/mira-assembler/usr/share/man/man1/miraconvert.1
	mv debian/mira-assembler/usr/share/man/man1/miradiff.1.dh-new debian/mira-assembler/usr/share/man/man1/miradiff.1
	chmod 0644 -- debian/mira-assembler/usr/share/man/man1/miraconvert.1 debian/mira-assembler/usr/share/man/man1/miradiff.1
	mv debian/mira-assembler/usr/share/man/man1/miramem.1.dh-new debian/mira-assembler/usr/share/man/man1/miramem.1
	mv debian/mira-assembler/usr/share/man/man1/miramer.1.dh-new debian/mira-assembler/usr/share/man/man1/miramer.1
	chmod 0644 -- debian/mira-assembler/usr/share/man/man1/miramem.1 debian/mira-assembler/usr/share/man/man1/miramer.1
   dh_lintian
	install -m0755 -d debian/mira-assembler/usr/share/lintian/overrides
	install -p -m0644 debian/mira-assembler.lintian-overrides debian/mira-assembler/usr/share/lintian/overrides/mira-assembler
   dh_perl
   dh_link
	rm -f debian/mira-assembler/usr/bin/miraconvert
	ln -s mira debian/mira-assembler/usr/bin/miraconvert
	rm -f debian/mira-assembler/usr/bin/mirabait
	ln -s mira debian/mira-assembler/usr/bin/mirabait
	rm -f debian/mira-assembler/usr/bin/miramem
	ln -s mira debian/mira-assembler/usr/bin/miramem
	rm -f debian/mira-assembler/usr/bin/miramer
	ln -s mira debian/mira-assembler/usr/bin/miramer
   dh_strip_nondeterminism
	Using 1707216070 as canonical time
	Normalizing debian/mira-rfam-12s-rrna/usr/share/mira/rfam_rrna-21-12.sls.gz using File::StripNondeterminism::handlers::gzip
	Using 1707216070 as canonical time
	Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/454sxa_stms_hybdenovo.png using File::StripNondeterminism::handlers::png
	Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/454sxa_hybdenovo.png using File::StripNondeterminism::handlers::png
	Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/haf_danger_join_notok.png using File::StripNondeterminism::handlers::png
	Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/sxa_gcbias_comp20082009.png using File::StripNondeterminism::handlers::png
	Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/gcb99_replocator.png using File::StripNondeterminism::handlers::png
	Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/srmc_in_454sxahyb_1stpass.png using File::StripNondeterminism::handlers::png
	Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/sxa_gcbias_bias2009.png using File::StripNondeterminism::handlers::png
	Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/san_autoedit1.png using File::StripNondeterminism::handlers::png
	Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/pb_elasticdarkinserts03.png using File::StripNondeterminism::handlers::png
	Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/sxa_unsc_ggc4_lenski.png using File::StripNondeterminism::handlers::png
	Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/haf2_haf5_clearshortrepeat.png using File::StripNondeterminism::handlers::png
	Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/454_autoedit1.png using File::StripNondeterminism::handlers::png
	Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/haf2_end_nomoredata.png using File::StripNondeterminism::handlers::png
	Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/sxa_unsc_ggcxg1_lenski.png using File::StripNondeterminism::handlers::png
	Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/sxa_xmastree_lenski1.png using File::StripNondeterminism::handlers::png
	Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/pb_elasticdarkinserts04.png using File::StripNondeterminism::handlers::png
	Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/srmc_in_454sxahyb_lastpass2.png using File::StripNondeterminism::handlers::png
	Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/haf5_haf2_contigcoverage.png using File::StripNondeterminism::handlers::png
	Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/sxa_unsc_ggc1_lenski.png using File::StripNondeterminism::handlers::png
	Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/pb_elasticdarkinserts02.png using File::StripNondeterminism::handlers::png
	Normalizing debian/mira-doc/usr/share/doc/mira-assembler/images/warning.png using File::StripNondeterminism::handlers::png
	Normalizing debian/mira-doc/usr/share/doc/mira-assembler/images/note.png using File::StripNondeterminism::handlers::png
	Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/sxa_sroc_lenski2.png using File::StripNondeterminism::handlers::png
	Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/iontor_indelhpexample.png using File::StripNondeterminism::handlers::png
	Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/ion_dh10bgoodB13.png using File::StripNondeterminism::handlers::png
	Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/sxa_sroc_lenski1.png using File::StripNondeterminism::handlers::png
	Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/sxa_unsc_ggc3_lenski.png using File::StripNondeterminism::handlers::png
	Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/sxa_gcbias_nobias2008.png using File::StripNondeterminism::handlers::png
	Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/454san_stmu_hybdenovo.png using File::StripNondeterminism::handlers::png
	Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/454_autoedit2.png using File::StripNondeterminism::handlers::png
	Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/sxa_wrmcsrmc_hiding_lenski1.png using File::StripNondeterminism::handlers::png
	Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/pb_elasticdarkinserts01.png using File::StripNondeterminism::handlers::png
	Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/sxa_xmastree_lenski2.png using File::StripNondeterminism::handlers::png
	Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/haf5_haf2_contigcoverage_ovals.png using File::StripNondeterminism::handlers::png
	Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/sxa_mcvc_lenski.png using File::StripNondeterminism::handlers::png
	Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/results_miraconvert.png using File::StripNondeterminism::handlers::png
	Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/srmc_in_454sxahyb_lastpass1.png using File::StripNondeterminism::handlers::png
	Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/ion_dh10bdirdepindel.png using File::StripNondeterminism::handlers::png
	Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/pb_c227-11-clcr_res.png using File::StripNondeterminism::handlers::png
	Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/sxa_unsc_ggc2_lenski.png using File::StripNondeterminism::handlers::png
	Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/sxa_cer_reads1.png using File::StripNondeterminism::handlers::png
	Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/san_autoedit2.png using File::StripNondeterminism::handlers::png
	Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/haf5_repend_rrna.png using File::StripNondeterminism::handlers::png
	Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/gcb99_edit.png using File::StripNondeterminism::handlers::png
	Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/sxa_unsc_ggcxg2_lenski.png using File::StripNondeterminism::handlers::png
	Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/results_mira2other.png using File::StripNondeterminism::handlers::png
	Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/haf_danger_join_ok.png using File::StripNondeterminism::handlers::png
	Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/454_stacks_join.png using File::StripNondeterminism::handlers::png
	Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/sxa_cer_reads2.png using File::StripNondeterminism::handlers::png
   dh_compress
	cd debian/mira-assembler
	cd debian/mira-rfam-12s-rrna
	cd debian/mira-doc
	chmod a-x usr/share/doc/mira-rfam-12s-rrna/changelog usr/share/doc/mira-rfam-12s-rrna/changelog.Debian
	chmod a-x usr/share/doc/mira-doc/changelog usr/share/doc/mira-doc/changelog.Debian
	chmod a-x usr/share/doc/mira-assembler/NEWS usr/share/doc/mira-assembler/changelog usr/share/doc/mira-assembler/changelog.Debian usr/share/doc/mira-assembler/test_data/fasta_estset1/tvc_mini.fasta usr/share/doc/mira-assembler/test_data/fasta_estset1/tvc_mini.fasta.qual usr/share/doc/mira-assembler/test_data/solexa_eco_art/ecoli_backbone_in.gbf usr/share/doc/mira-assembler/test_data/solexa_eco_art/ecoli_in.solexa.fasta usr/share/doc/mira-assembler/test_data/solexa_eco_art/ecoli_in.solexa.fasta.qual usr/share/doc/mira-assembler/test_data/solexa_eco_art/ecoli_straindata_in.txt usr/share/man/man1/mira.1 usr/share/man/man1/mirabait.1 usr/share/man/man1/miraconvert.1 usr/share/man/man1/miradiff.1 usr/share/man/man1/miramem.1 usr/share/man/man1/miramer.1
	gzip -9nf usr/share/doc/mira-rfam-12s-rrna/changelog usr/share/doc/mira-rfam-12s-rrna/changelog.Debian
	gzip -9nf usr/share/doc/mira-doc/changelog usr/share/doc/mira-doc/changelog.Debian
	gzip -9nf usr/share/doc/mira-assembler/NEWS usr/share/doc/mira-assembler/changelog usr/share/doc/mira-assembler/changelog.Debian usr/share/doc/mira-assembler/test_data/fasta_estset1/tvc_mini.fasta usr/share/doc/mira-assembler/test_data/fasta_estset1/tvc_mini.fasta.qual usr/share/doc/mira-assembler/test_data/solexa_eco_art/ecoli_backbone_in.gbf usr/share/doc/mira-assembler/test_data/solexa_eco_art/ecoli_in.solexa.fasta usr/share/doc/mira-assembler/test_data/solexa_eco_art/ecoli_in.solexa.fasta.qual usr/share/doc/mira-assembler/test_data/solexa_eco_art/ecoli_straindata_in.txt usr/share/man/man1/mira.1 usr/share/man/man1/mirabait.1 usr/share/man/man1/miraconvert.1 usr/share/man/man1/miradiff.1 usr/share/man/man1/miramem.1 usr/share/man/man1/miramer.1
	cd '/build/reproducible-path/mira-4.9.6'
	cd '/build/reproducible-path/mira-4.9.6'
	cd '/build/reproducible-path/mira-4.9.6'
   dh_fixperms
	find debian/mira-assembler ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
	find debian/mira-rfam-12s-rrna ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
	find debian/mira-doc ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
	find debian/mira-rfam-12s-rrna/usr/share/doc -type f -a -true -a ! -regex 'debian/mira-rfam-12s-rrna/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644
	find debian/mira-doc/usr/share/doc -type f -a -true -a ! -regex 'debian/mira-doc/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644
	find debian/mira-assembler/usr/share/doc -type f -a -true -a ! -regex 'debian/mira-assembler/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644
	find debian/mira-rfam-12s-rrna/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755
	find debian/mira-doc/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755
	find debian/mira-assembler/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755
	find debian/mira-rfam-12s-rrna -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
	find debian/mira-doc -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
	find debian/mira-assembler/usr/share/man debian/mira-assembler/usr/share/lintian/overrides -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
	find debian/mira-assembler -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
	find debian/mira-assembler/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x
   dh_missing
   dh_dwz -a
	dwz -- debian/mira-assembler/usr/bin/mira
   dh_strip -a
	install -m0755 -d debian/.debhelper/mira-assembler/dbgsym-root/usr/lib/debug/.build-id/65
	objcopy --only-keep-debug --compress-debug-sections debian/mira-assembler/usr/bin/mira debian/.debhelper/mira-assembler/dbgsym-root/usr/lib/debug/.build-id/65/81f44c1e1631dba43a2112976a75ec2063bb3d.debug
	chmod 0644 -- debian/.debhelper/mira-assembler/dbgsym-root/usr/lib/debug/.build-id/65/81f44c1e1631dba43a2112976a75ec2063bb3d.debug
	strip --remove-section=.comment --remove-section=.note debian/mira-assembler/usr/bin/mira
	objcopy --add-gnu-debuglink debian/.debhelper/mira-assembler/dbgsym-root/usr/lib/debug/.build-id/65/81f44c1e1631dba43a2112976a75ec2063bb3d.debug debian/mira-assembler/usr/bin/mira
	install -m0755 -d debian/.debhelper/mira-assembler/dbgsym-root/usr/share/doc
	ln -s mira-assembler debian/.debhelper/mira-assembler/dbgsym-root/usr/share/doc/mira-assembler-dbgsym
	install -m0755 -d debian/.debhelper/mira-assembler
   dh_makeshlibs -a
	rm -f debian/mira-assembler/DEBIAN/shlibs
   dh_shlibdeps -a
	install -m0755 -d debian/mira-assembler/DEBIAN
	dpkg-shlibdeps -Tdebian/mira-assembler.substvars debian/mira-assembler/usr/bin/mira
   dh_installdeb
	install -m0755 -d debian/mira-assembler/DEBIAN
	install -m0755 -d debian/mira-rfam-12s-rrna/DEBIAN
	cp -f debian/mira-rfam-12s-rrna.postinst debian/mira-rfam-12s-rrna/DEBIAN/postinst
	[META] Replace #TOKEN#s in "debian/mira-rfam-12s-rrna/DEBIAN/postinst"
	chmod 0755 -- debian/mira-rfam-12s-rrna/DEBIAN/postinst
	cp -f debian/mira-rfam-12s-rrna.postrm debian/mira-rfam-12s-rrna/DEBIAN/postrm
	[META] Replace #TOKEN#s in "debian/mira-rfam-12s-rrna/DEBIAN/postrm"
	chmod 0755 -- debian/mira-rfam-12s-rrna/DEBIAN/postrm
	install -m0755 -d debian/mira-doc/DEBIAN
   dh_gencontrol
	install -m0755 -d debian/mira-rfam-12s-rrna/DEBIAN
	echo misc:Depends= >> debian/mira-rfam-12s-rrna.substvars
	echo misc:Pre-Depends= >> debian/mira-rfam-12s-rrna.substvars
	dpkg-gencontrol -pmira-rfam-12s-rrna -ldebian/changelog -Tdebian/mira-rfam-12s-rrna.substvars -cdebian/control -Pdebian/mira-rfam-12s-rrna
	install -m0755 -d debian/mira-doc/DEBIAN
	echo misc:Depends= >> debian/mira-doc.substvars
	echo misc:Pre-Depends= >> debian/mira-doc.substvars
	dpkg-gencontrol -pmira-doc -ldebian/changelog -Tdebian/mira-doc.substvars -cdebian/control -Pdebian/mira-doc
	install -m0755 -d debian/mira-assembler/DEBIAN
	echo misc:Depends= >> debian/mira-assembler.substvars
	echo misc:Pre-Depends= >> debian/mira-assembler.substvars
	install -m0755 -d debian/.debhelper/mira-assembler/dbgsym-root/DEBIAN
	dpkg-gencontrol -pmira-assembler -ldebian/changelog -Tdebian/mira-assembler.substvars -cdebian/control -Pdebian/.debhelper/mira-assembler/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -UProtected -UBuilt-Using -UStatic-Built-Using -DPackage=mira-assembler-dbgsym "-DDepends=mira-assembler (= \${binary:Version})" "-DDescription=debug symbols for mira-assembler" -DBuild-Ids=6581f44c1e1631dba43a2112976a75ec2063bb3d -DSection=debug -UMulti-Arch -UReplaces -UBreaks
	chmod 0644 -- debian/mira-rfam-12s-rrna/DEBIAN/control
	chmod 0644 -- debian/mira-doc/DEBIAN/control
	chmod 0644 -- debian/.debhelper/mira-assembler/dbgsym-root/DEBIAN/control
	dpkg-gencontrol -pmira-assembler -ldebian/changelog -Tdebian/mira-assembler.substvars -cdebian/control -Pdebian/mira-assembler
	chmod 0644 -- debian/mira-assembler/DEBIAN/control
   dh_md5sums
	install -m0755 -d debian/mira-assembler/DEBIAN
	install -m0755 -d debian/mira-doc/DEBIAN
	install -m0755 -d debian/mira-rfam-12s-rrna/DEBIAN
	cd debian/mira-assembler >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
	cd debian/mira-doc >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
	cd debian/mira-rfam-12s-rrna >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
	chmod 0644 -- debian/mira-doc/DEBIAN/md5sums
	chmod 0644 -- debian/mira-assembler/DEBIAN/md5sums
	install -m0755 -d debian/.debhelper/mira-assembler/dbgsym-root/DEBIAN
	cd debian/.debhelper/mira-assembler/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
	chmod 0644 -- debian/mira-rfam-12s-rrna/DEBIAN/md5sums
	chmod 0644 -- debian/.debhelper/mira-assembler/dbgsym-root/DEBIAN/md5sums
   dh_builddeb
	dpkg-deb --root-owner-group --build debian/mira-assembler ..
	dpkg-deb --root-owner-group --build debian/.debhelper/mira-assembler/dbgsym-root ..
	dpkg-deb --root-owner-group --build debian/mira-rfam-12s-rrna ..
	dpkg-deb --root-owner-group --build debian/mira-doc ..
dpkg-deb: building package 'mira-assembler-dbgsym' in '../mira-assembler-dbgsym_4.9.6-11_i386.deb'.
dpkg-deb: building package 'mira-assembler' in '../mira-assembler_4.9.6-11_i386.deb'.
dpkg-deb: building package 'mira-doc' in '../mira-doc_4.9.6-11_all.deb'.
dpkg-deb: building package 'mira-rfam-12s-rrna' in '../mira-rfam-12s-rrna_4.9.6-11_all.deb'.
 dpkg-genbuildinfo --build=binary -O../mira_4.9.6-11_i386.buildinfo
 dpkg-genchanges --build=binary -O../mira_4.9.6-11_i386.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/2805/tmp/hooks/B01_cleanup starting
I: user script /srv/workspace/pbuilder/2805/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/2805 and its subdirectories
I: Current time: Wed Jan 21 01:56:44 +14 2026
I: pbuilder-time-stamp: 1768910204