I: pbuilder: network access will be disabled during build
I: Current time: Thu Mar 5 16:34:42 +14 2026
I: pbuilder-time-stamp: 1772678082
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz]
I: copying local configuration
W: --override-config is not set; not updating apt.conf Read the manpage for details.
I: mounting /proc filesystem
I: mounting /sys filesystem
I: creating /{dev,run}/shm
I: mounting /dev/pts filesystem
I: redirecting /dev/ptmx to /dev/pts/ptmx
I: policy-rc.d already exists
I: Copying source file
I: copying [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
dpkg-source: warning: cannot verify inline signature for ./mira_4.9.6-11.dsc: unsupported subcommand
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/738978/tmp/hooks/D01_modify_environment starting
debug: Running on codethink03-arm64.
I: Changing host+domainname to test build reproducibility
I: Adding a custom variable just for the fun of it...
I: Changing /bin/sh to bash
'/bin/sh' -> '/bin/bash'
lrwxrwxrwx 1 root root 9 Mar 5 02:34 /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/738978/tmp/hooks/D01_modify_environment finished
I: user script /srv/workspace/pbuilder/738978/tmp/hooks/D02_print_environment starting
I: set
BASH=/bin/sh
BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath
BASH_ALIASES=()
BASH_ARGC=()
BASH_ARGV=()
BASH_CMDS=()
BASH_LINENO=([0]="12" [1]="0")
BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:.
BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment")
BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu")
BASH_VERSION='5.2.37(1)-release'
BUILDDIR=/build/reproducible-path
BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other'
BUILDUSERNAME=pbuilder2
BUILD_ARCH=arm64
DEBIAN_FRONTEND=noninteractive
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 '
DIRSTACK=()
DISTRIBUTION=unstable
EUID=0
FUNCNAME=([0]="Echo" [1]="main")
GROUPS=()
HOME=/root
HOSTNAME=i-capture-the-hostname
HOSTTYPE=aarch64
HOST_ARCH=arm64
IFS='
'
INVOCATION_ID=98f1834ecc2843b39da51d9a3888c5b1
LANG=C
LANGUAGE=nl_BE:nl
LC_ALL=C
MACHTYPE=aarch64-unknown-linux-gnu
MAIL=/var/mail/root
OPTERR=1
OPTIND=1
OSTYPE=linux-gnu
PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path
PBCURRENTCOMMANDLINEOPERATION=build
PBUILDER_OPERATION=build
PBUILDER_PKGDATADIR=/usr/share/pbuilder
PBUILDER_PKGLIBDIR=/usr/lib/pbuilder
PBUILDER_SYSCONFDIR=/etc
PIPESTATUS=([0]="0")
POSIXLY_CORRECT=y
PPID=738978
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.5BtnJ430/pbuilderrc_ggta --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.5BtnJ430/b2 --logfile b2/build.log mira_4.9.6-11.dsc'
SUDO_GID=109
SUDO_UID=104
SUDO_USER=jenkins
TERM=unknown
TZ=/usr/share/zoneinfo/Etc/GMT-14
UID=0
USER=root
_='I: set'
http_proxy=http://192.168.101.4:3128
I: uname -a
Linux i-capture-the-hostname 6.1.0-30-cloud-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux
I: ls -l /bin
lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/738978/tmp/hooks/D02_print_environment finished
-> Attempting to satisfy build-dependencies
-> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: arm64
Maintainer: Debian Pbuilder Team <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, 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 ... 19956 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 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} libcommons-logging-java{a} libcommons-parent-java{a} libdatrie1{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libffi8{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} libgcrypt20{a} libglib2.0-0t64{a} libgpg-error0{a} libgraphite2-3{a} libharfbuzz0b{a} libice6{a} libicu-dev{a} libicu72{a} libio-string-perl{a} libjs-jquery{a} libkpathsea6{a} liblatex-tounicode-perl{a} libmagic-mgc{a} libmagic1t64{a} libmime-charset-perl{a} libmpfi0{a} libpaper-utils{a} libpaper2{a} libpdfbox-java{a} libpipeline1{a} libpixman-1-0{a} libpng16-16t64{a} libpotrace0{a} libproc2-0{a} libptexenc1{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} libsm6{a} libsombok3{a} libsynctex2{a} libteckit0{a} libtexlua53-5{a} libtext-charwidth-perl{a} libtext-wrapi18n-perl{a} libthai-data{a} libthai0{a} libtool{a} libuchardet0{a} libunicode-linebreak-perl{a} libunistring5{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} python3.13{a} python3.13-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 libarchive-cpio-perl libfile-mimeinfo-perl libglib2.0-data libgpg-error-l10n 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, 177 newly installed, 0 to remove and 0 not upgraded.
Need to get 464 MB of archives. After unpacking 1287 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian unstable/main arm64 autoconf-archive all 20220903-3 [775 kB]
Get: 2 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-5 [284 kB]
Get: 3 http://deb.debian.org/debian unstable/main arm64 flex arm64 2.6.4-8.2+b4 [412 kB]
Get: 4 http://deb.debian.org/debian unstable/main arm64 libpython3.13-minimal arm64 3.13.1-3 [852 kB]
Get: 5 http://deb.debian.org/debian unstable/main arm64 libexpat1 arm64 2.6.4-1 [90.7 kB]
Get: 6 http://deb.debian.org/debian unstable/main arm64 python3.13-minimal arm64 3.13.1-3 [1990 kB]
Get: 7 http://deb.debian.org/debian unstable/main arm64 python3-minimal arm64 3.13.1-2 [27.0 kB]
Get: 8 http://deb.debian.org/debian unstable/main arm64 media-types all 10.1.0 [26.9 kB]
Get: 9 http://deb.debian.org/debian unstable/main arm64 netbase all 6.4 [12.8 kB]
Get: 10 http://deb.debian.org/debian unstable/main arm64 tzdata all 2025a-1 [259 kB]
Get: 11 http://deb.debian.org/debian unstable/main arm64 libffi8 arm64 3.4.6-1 [20.9 kB]
Get: 12 http://deb.debian.org/debian unstable/main arm64 readline-common all 8.2-6 [69.4 kB]
Get: 13 http://deb.debian.org/debian unstable/main arm64 libreadline8t64 arm64 8.2-6 [159 kB]
Get: 14 http://deb.debian.org/debian unstable/main arm64 libpython3.13-stdlib arm64 3.13.1-3 [1912 kB]
Get: 15 http://deb.debian.org/debian unstable/main arm64 python3.13 arm64 3.13.1-3 [740 kB]
Get: 16 http://deb.debian.org/debian unstable/main arm64 libpython3-stdlib arm64 3.13.1-2 [9952 B]
Get: 17 http://deb.debian.org/debian unstable/main arm64 python3 arm64 3.13.1-2 [28.0 kB]
Get: 18 http://deb.debian.org/debian unstable/main arm64 sgml-base all 1.31 [15.4 kB]
Get: 19 http://deb.debian.org/debian unstable/main arm64 libproc2-0 arm64 2:4.0.4-7 [62.4 kB]
Get: 20 http://deb.debian.org/debian unstable/main arm64 procps arm64 2:4.0.4-7 [868 kB]
Get: 21 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.24 [24.8 kB]
Get: 22 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB]
Get: 23 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB]
Get: 24 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3+b1 [43.4 kB]
Get: 25 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.23.1-1 [241 kB]
Get: 26 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB]
Get: 27 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-7 [1129 kB]
Get: 28 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.4-2 [91.5 kB]
Get: 29 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB]
Get: 30 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB]
Get: 31 http://deb.debian.org/debian unstable/main arm64 libtext-charwidth-perl arm64 0.04-11+b4 [9652 B]
Get: 32 http://deb.debian.org/debian unstable/main arm64 libtext-wrapi18n-perl all 0.06-10 [8808 B]
Get: 33 http://deb.debian.org/debian unstable/main arm64 ucf all 3.0049 [42.5 kB]
Get: 34 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3 [493 kB]
Get: 35 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB]
Get: 36 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.17-2 [861 kB]
Get: 37 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.23.1-1 [770 kB]
Get: 38 http://deb.debian.org/debian unstable/main arm64 xml-core all 0.19 [20.1 kB]
Get: 39 http://deb.debian.org/debian unstable/main arm64 sgml-data all 2.0.11+nmu1 [179 kB]
Get: 40 http://deb.debian.org/debian unstable/main arm64 docbook-xml all 4.5-13 [77.4 kB]
Get: 41 http://deb.debian.org/debian unstable/main arm64 python-apt-common all 2.9.8 [68.1 kB]
Get: 42 http://deb.debian.org/debian unstable/main arm64 distro-info-data all 0.63 [6408 B]
Get: 43 http://deb.debian.org/debian unstable/main arm64 python3-apt arm64 2.9.8 [177 kB]
Get: 44 http://deb.debian.org/debian unstable/main arm64 tex-common all 6.18 [32.5 kB]
Get: 45 http://deb.debian.org/debian unstable/main arm64 libpaper2 arm64 2.2.5-0.3 [16.3 kB]
Get: 46 http://deb.debian.org/debian unstable/main arm64 libpaper-utils arm64 2.2.5-0.3 [16.1 kB]
Get: 47 http://deb.debian.org/debian unstable/main arm64 libkpathsea6 arm64 2024.20240313.70630+ds-5+b1 [154 kB]
Get: 48 http://deb.debian.org/debian unstable/main arm64 libptexenc1 arm64 2024.20240313.70630+ds-5+b1 [48.2 kB]
Get: 49 http://deb.debian.org/debian unstable/main arm64 libsynctex2 arm64 2024.20240313.70630+ds-5+b1 [60.6 kB]
Get: 50 http://deb.debian.org/debian unstable/main arm64 libtexlua53-5 arm64 2024.20240313.70630+ds-5+b1 [106 kB]
Get: 51 http://deb.debian.org/debian unstable/main arm64 t1utils arm64 1.41-4+b1 [57.6 kB]
Get: 52 http://deb.debian.org/debian unstable/main arm64 libbrotli1 arm64 1.1.0-2+b6 [297 kB]
Get: 53 http://deb.debian.org/debian unstable/main arm64 libpng16-16t64 arm64 1.6.46-1 [275 kB]
Get: 54 http://deb.debian.org/debian unstable/main arm64 libfreetype6 arm64 2.13.3+dfsg-1 [422 kB]
Get: 55 http://deb.debian.org/debian unstable/main arm64 fonts-dejavu-mono all 2.37-8 [489 kB]
Get: 56 http://deb.debian.org/debian unstable/main arm64 fonts-dejavu-core all 2.37-8 [840 kB]
Get: 57 http://deb.debian.org/debian unstable/main arm64 fontconfig-config arm64 2.15.0-2 [317 kB]
Get: 58 http://deb.debian.org/debian unstable/main arm64 libfontconfig1 arm64 2.15.0-2 [386 kB]
Get: 59 http://deb.debian.org/debian unstable/main arm64 libpixman-1-0 arm64 0.44.0-3 [168 kB]
Get: 60 http://deb.debian.org/debian unstable/main arm64 libxau6 arm64 1:1.0.11-1 [20.6 kB]
Get: 61 http://deb.debian.org/debian unstable/main arm64 libxdmcp6 arm64 1:1.1.5-1 [27.8 kB]
Get: 62 http://deb.debian.org/debian unstable/main arm64 libxcb1 arm64 1.17.0-2+b1 [143 kB]
Get: 63 http://deb.debian.org/debian unstable/main arm64 libx11-data all 2:1.8.10-2 [337 kB]
Get: 64 http://deb.debian.org/debian unstable/main arm64 libx11-6 arm64 2:1.8.10-2 [789 kB]
Get: 65 http://deb.debian.org/debian unstable/main arm64 libxcb-render0 arm64 1.17.0-2+b1 [115 kB]
Get: 66 http://deb.debian.org/debian unstable/main arm64 libxcb-shm0 arm64 1.17.0-2+b1 [105 kB]
Get: 67 http://deb.debian.org/debian unstable/main arm64 libxext6 arm64 2:1.3.4-1+b3 [49.2 kB]
Get: 68 http://deb.debian.org/debian unstable/main arm64 libxrender1 arm64 1:0.9.10-1.1+b4 [27.2 kB]
Get: 69 http://deb.debian.org/debian unstable/main arm64 libcairo2 arm64 1.18.2-2 [483 kB]
Get: 70 http://deb.debian.org/debian unstable/main arm64 libgraphite2-3 arm64 1.3.14-2+b1 [70.4 kB]
Get: 71 http://deb.debian.org/debian unstable/main arm64 libglib2.0-0t64 arm64 2.82.4-2 [1413 kB]
Get: 72 http://deb.debian.org/debian unstable/main arm64 libharfbuzz0b arm64 10.2.0-1 [443 kB]
Get: 73 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-6 [9239 kB]
Get: 74 http://deb.debian.org/debian unstable/main arm64 libmpfi0 arm64 1.5.4+ds-4 [34.5 kB]
Get: 75 http://deb.debian.org/debian unstable/main arm64 libpotrace0 arm64 1.16-2+b2 [23.4 kB]
Get: 76 http://deb.debian.org/debian unstable/main arm64 libteckit0 arm64 2.5.12+ds1-1+b1 [303 kB]
Get: 77 http://deb.debian.org/debian unstable/main arm64 x11-common all 1:7.7+24 [217 kB]
Get: 78 http://deb.debian.org/debian unstable/main arm64 libice6 arm64 2:1.1.1-1 [62.1 kB]
Get: 79 http://deb.debian.org/debian unstable/main arm64 libsm6 arm64 2:1.2.4-1 [34.2 kB]
Get: 80 http://deb.debian.org/debian unstable/main arm64 libxt6t64 arm64 1:1.2.1-1.2+b2 [173 kB]
Get: 81 http://deb.debian.org/debian unstable/main arm64 libxmu6 arm64 2:1.1.3-3+b4 [55.7 kB]
Get: 82 http://deb.debian.org/debian unstable/main arm64 libxpm4 arm64 1:3.5.17-1+b3 [53.4 kB]
Get: 83 http://deb.debian.org/debian unstable/main arm64 libxaw7 arm64 2:1.0.16-1 [195 kB]
Get: 84 http://deb.debian.org/debian unstable/main arm64 libxi6 arm64 2:1.8.2-1 [77.8 kB]
Get: 85 http://deb.debian.org/debian unstable/main arm64 libzzip-0-13t64 arm64 0.13.72+dfsg.1-1.3 [56.6 kB]
Get: 86 http://deb.debian.org/debian unstable/main arm64 texlive-binaries arm64 2024.20240313.70630+ds-5+b1 [7357 kB]
Get: 87 http://deb.debian.org/debian unstable/main arm64 xdg-utils all 1.2.1-2 [75.8 kB]
Get: 88 http://deb.debian.org/debian unstable/main arm64 texlive-base all 2024.20250114-1 [22.8 MB]
Get: 89 http://deb.debian.org/debian unstable/main arm64 texlive-fonts-recommended all 2024.20250114-1 [4991 kB]
Get: 90 http://deb.debian.org/debian unstable/main arm64 fonts-lmodern all 2.005-1 [4540 kB]
Get: 91 http://deb.debian.org/debian unstable/main arm64 texlive-latex-base all 2024.20250114-1 [1282 kB]
Get: 92 http://deb.debian.org/debian unstable/main arm64 texlive-latex-recommended all 2024.20250114-1 [8760 kB]
Get: 93 http://deb.debian.org/debian unstable/main arm64 texlive all 2024.20250114-1 [18.6 kB]
Get: 94 http://deb.debian.org/debian unstable/main arm64 libio-string-perl all 1.08-4 [12.1 kB]
Get: 95 http://deb.debian.org/debian unstable/main arm64 liblatex-tounicode-perl all 0.55-1 [28.8 kB]
Get: 96 http://deb.debian.org/debian unstable/main arm64 libbibtex-parser-perl all 1.05+dfsg-1 [17.4 kB]
Get: 97 http://deb.debian.org/debian unstable/main arm64 texlive-bibtex-extra all 2024.20250114-1 [79.5 MB]
Get: 98 http://deb.debian.org/debian unstable/main arm64 libfile-which-perl all 1.27-2 [15.1 kB]
Get: 99 http://deb.debian.org/debian unstable/main arm64 libfile-homedir-perl all 1.006-2 [42.4 kB]
Get: 100 http://deb.debian.org/debian unstable/main arm64 libthai-data all 0.1.29-2 [168 kB]
Get: 101 http://deb.debian.org/debian unstable/main arm64 libdatrie1 arm64 0.2.13-3+b1 [37.6 kB]
Get: 102 http://deb.debian.org/debian unstable/main arm64 libthai0 arm64 0.1.29-2+b1 [48.4 kB]
Get: 103 http://deb.debian.org/debian unstable/main arm64 libsombok3 arm64 2.4.0-2+b2 [29.9 kB]
Get: 104 http://deb.debian.org/debian unstable/main arm64 libmime-charset-perl all 1.013.1-2 [34.0 kB]
Get: 105 http://deb.debian.org/debian unstable/main arm64 libunicode-linebreak-perl arm64 0.0.20190101-1+b7 [93.5 kB]
Get: 106 http://deb.debian.org/debian unstable/main arm64 libyaml-tiny-perl all 1.76-1 [29.8 kB]
Get: 107 http://deb.debian.org/debian unstable/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB]
Get: 108 http://deb.debian.org/debian unstable/main arm64 libfontenc1 arm64 1:1.1.8-1+b2 [22.5 kB]
Get: 109 http://deb.debian.org/debian unstable/main arm64 xfonts-encodings all 1:1.0.4-2.2 [577 kB]
Get: 110 http://deb.debian.org/debian unstable/main arm64 xfonts-utils arm64 1:7.7+7 [89.3 kB]
Get: 111 http://deb.debian.org/debian unstable/main arm64 lmodern all 2.005-1 [9480 kB]
Get: 112 http://deb.debian.org/debian unstable/main arm64 texlive-luatex all 2024.20250114-1 [28.0 MB]
Get: 113 http://deb.debian.org/debian unstable/main arm64 texlive-plain-generic all 2024.20250114-1 [28.9 MB]
Get: 114 http://deb.debian.org/debian unstable/main arm64 texlive-extra-utils all 2024.20250114-1 [67.6 MB]
Get: 115 http://deb.debian.org/debian unstable/main arm64 libapache-pom-java all 33-2 [5852 B]
Get: 116 http://deb.debian.org/debian unstable/main arm64 libcommons-parent-java all 56-1 [10.8 kB]
Get: 117 http://deb.debian.org/debian unstable/main arm64 libcommons-logging-java all 1.3.0-1 [68.6 kB]
Get: 118 http://deb.debian.org/debian unstable/main arm64 libfontbox-java all 1:1.8.16-5 [211 kB]
Get: 119 http://deb.debian.org/debian unstable/main arm64 libpdfbox-java all 1:1.8.16-5 [5527 kB]
Get: 120 http://deb.debian.org/debian unstable/main arm64 preview-latex-style all 13.2-1 [350 kB]
Get: 121 http://deb.debian.org/debian unstable/main arm64 texlive-pictures all 2024.20250114-1 [17.1 MB]
Get: 122 http://deb.debian.org/debian unstable/main arm64 texlive-latex-extra all 2024.20250114-1 [24.7 MB]
Get: 123 http://deb.debian.org/debian unstable/main arm64 fonts-gfs-baskerville all 1.1-6 [43.7 kB]
Get: 124 http://deb.debian.org/debian unstable/main arm64 fonts-gfs-porson all 1.1-7 [33.8 kB]
Get: 125 http://deb.debian.org/debian unstable/main arm64 texlive-lang-greek all 2024.20250114-1 [79.2 MB]
Get: 126 http://deb.debian.org/debian unstable/main arm64 texlive-science all 2024.20250114-1 [3887 kB]
Get: 127 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB]
Get: 128 http://deb.debian.org/debian unstable/main arm64 libgpg-error0 arm64 1.51-3 [78.5 kB]
Get: 129 http://deb.debian.org/debian unstable/main arm64 libgcrypt20 arm64 1.11.0-7 [742 kB]
Get: 130 http://deb.debian.org/debian unstable/main arm64 libxslt1.1 arm64 1.1.35-1.1+b1 [222 kB]
Get: 131 http://deb.debian.org/debian unstable/main arm64 xsltproc arm64 1.1.35-1.1+b1 [115 kB]
Get: 132 http://deb.debian.org/debian unstable/main arm64 dblatex all 0.3.12py3-5 [359 kB]
Get: 133 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.24.1 [90.9 kB]
Get: 134 http://deb.debian.org/debian unstable/main arm64 libtool all 2.5.4-2.1 [539 kB]
Get: 135 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB]
Get: 136 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 137 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.1-1 [19.6 kB]
Get: 138 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.1-1 [8584 B]
Get: 139 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB]
Get: 140 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB]
Get: 141 http://deb.debian.org/debian unstable/main arm64 libunistring5 arm64 1.3-1 [449 kB]
Get: 142 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.23.1-1 [1610 kB]
Get: 143 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 144 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 145 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.24.1 [920 kB]
Get: 146 http://deb.debian.org/debian unstable/main arm64 docbook-xsl all 1.79.2+dfsg-7 [1221 kB]
Get: 147 http://deb.debian.org/debian unstable/main arm64 icu-devtools arm64 72.1-6 [196 kB]
Get: 148 http://deb.debian.org/debian unstable/main arm64 libboost1.83-dev arm64 1.83.0-4 [10.6 MB]
Get: 149 http://deb.debian.org/debian unstable/main arm64 libboost-atomic1.83.0 arm64 1.83.0-4 [233 kB]
Get: 150 http://deb.debian.org/debian unstable/main arm64 libboost-atomic1.83-dev arm64 1.83.0-4 [234 kB]
Get: 151 http://deb.debian.org/debian unstable/main arm64 libboost-chrono1.83.0t64 arm64 1.83.0-4 [239 kB]
Get: 152 http://deb.debian.org/debian unstable/main arm64 libboost-chrono1.83-dev arm64 1.83.0-4 [245 kB]
Get: 153 http://deb.debian.org/debian unstable/main arm64 libboost-date-time1.83.0 arm64 1.83.0-4 [231 kB]
Get: 154 http://deb.debian.org/debian unstable/main arm64 libboost-serialization1.83.0 arm64 1.83.0-4 [325 kB]
Get: 155 http://deb.debian.org/debian unstable/main arm64 libboost-serialization1.83-dev arm64 1.83.0-4 [375 kB]
Get: 156 http://deb.debian.org/debian unstable/main arm64 libboost-date-time1.83-dev arm64 1.83.0-4 [239 kB]
Get: 157 http://deb.debian.org/debian unstable/main arm64 libboost-filesystem1.83.0 arm64 1.83.0-4 [273 kB]
Get: 158 http://deb.debian.org/debian unstable/main arm64 libboost-system1.83.0 arm64 1.83.0-4 [231 kB]
Get: 159 http://deb.debian.org/debian unstable/main arm64 libboost-system1.83-dev arm64 1.83.0-4 [231 kB]
Get: 160 http://deb.debian.org/debian unstable/main arm64 libboost-filesystem1.83-dev arm64 1.83.0-4 [293 kB]
Get: 161 http://deb.debian.org/debian unstable/main arm64 libboost-filesystem-dev arm64 1.83.0.2+b2 [3616 B]
Get: 162 http://deb.debian.org/debian unstable/main arm64 libboost-regex1.83.0 arm64 1.83.0-4 [314 kB]
Get: 163 http://deb.debian.org/debian unstable/main arm64 libicu-dev arm64 72.1-6 [10.3 MB]
Get: 164 http://deb.debian.org/debian unstable/main arm64 libboost-regex1.83-dev arm64 1.83.0-4 [338 kB]
Get: 165 http://deb.debian.org/debian unstable/main arm64 libboost-iostreams1.83-dev arm64 1.83.0-4 [261 kB]
Get: 166 http://deb.debian.org/debian unstable/main arm64 libboost-iostreams-dev arm64 1.83.0.2+b2 [3568 B]
Get: 167 http://deb.debian.org/debian unstable/main arm64 libboost-regex-dev arm64 1.83.0.2+b2 [3852 B]
Get: 168 http://deb.debian.org/debian unstable/main arm64 libboost-system-dev arm64 1.83.0.2+b2 [3720 B]
Get: 169 http://deb.debian.org/debian unstable/main arm64 libboost-thread1.83.0 arm64 1.83.0-4 [265 kB]
Get: 170 http://deb.debian.org/debian unstable/main arm64 libboost-thread1.83-dev arm64 1.83.0-4 [277 kB]
Get: 171 http://deb.debian.org/debian unstable/main arm64 libboost-thread-dev arm64 1.83.0.2+b2 [3616 B]
Get: 172 http://deb.debian.org/debian unstable/main arm64 libbz2-dev arm64 1.0.8-6 [31.9 kB]
Get: 173 http://deb.debian.org/debian unstable/main arm64 libexpat1-dev arm64 2.6.4-1 [143 kB]
Get: 174 http://deb.debian.org/debian unstable/main arm64 libfl2 arm64 2.6.4-8.2+b4 [84.4 kB]
Get: 175 http://deb.debian.org/debian unstable/main arm64 libfl-dev arm64 2.6.4-8.2+b4 [85.6 kB]
Get: 176 http://deb.debian.org/debian unstable/main arm64 xxd arm64 2:9.1.0967-2+b1 [98.3 kB]
Get: 177 http://deb.debian.org/debian unstable/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB]
Fetched 464 MB in 1s (323 MB/s)
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Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64'
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Setting up python3-minimal (3.13.1-2) ...
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Unpacking gettext-base (0.23.1-1) ...
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Selecting previously unselected package libtexlua53-5:arm64.
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Unpacking t1utils (1.41-4+b1) ...
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Preparing to unpack .../155-libbz2-dev_1.0.8-6_arm64.deb ...
Unpacking libbz2-dev:arm64 (1.0.8-6) ...
Selecting previously unselected package libexpat1-dev:arm64.
Preparing to unpack .../156-libexpat1-dev_2.6.4-1_arm64.deb ...
Unpacking libexpat1-dev:arm64 (2.6.4-1) ...
Selecting previously unselected package libfl2:arm64.
Preparing to unpack .../157-libfl2_2.6.4-8.2+b4_arm64.deb ...
Unpacking libfl2:arm64 (2.6.4-8.2+b4) ...
Selecting previously unselected package libfl-dev:arm64.
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Unpacking libfl-dev:arm64 (2.6.4-8.2+b4) ...
Selecting previously unselected package xxd.
Preparing to unpack .../159-xxd_2%3a9.1.0967-2+b1_arm64.deb ...
Unpacking xxd (2:9.1.0967-2+b1) ...
Selecting previously unselected package zlib1g-dev:arm64.
Preparing to unpack .../160-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1+b1_arm64.deb ...
Unpacking zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1+b1) ...
Setting up media-types (10.1.0) ...
Setting up libpipeline1:arm64 (1.5.8-1) ...
Setting up libgraphite2-3:arm64 (1.3.14-2+b1) ...
Setting up libpixman-1-0:arm64 (0.44.0-3) ...
Setting up libtext-charwidth-perl:arm64 (0.04-11+b4) ...
Setting up libfile-which-perl (1.27-2) ...
Setting up libxau6:arm64 (1:1.0.11-1) ...
Setting up libxdmcp6:arm64 (1:1.1.5-1) ...
Setting up libboost1.83-dev:arm64 (1.83.0-4) ...
Setting up libxcb1:arm64 (1.17.0-2+b1) ...
Setting up libicu72:arm64 (72.1-6) ...
Setting up bsdextrautils (2.40.4-2) ...
Setting up fonts-gfs-porson (1.1-7) ...
Setting up libboost-date-time1.83.0:arm64 (1.83.0-4) ...
Setting up libgpg-error0:arm64 (1.51-3) ...
Setting up libdatrie1:arm64 (0.2.13-3+b1) ...
Setting up libmagic-mgc (1:5.45-3+b1) ...
Setting up libxcb-render0:arm64 (1.17.0-2+b1) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up distro-info-data (0.63) ...
Setting up libboost-regex1.83.0:arm64 (1.83.0-4) ...
Setting up libdebhelper-perl (13.24.1) ...
Setting up libbrotli1:arm64 (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:arm64 (1.83.0-4) ...
Setting up libmagic1t64:arm64 (1:5.45-3+b1) ...
Setting up x11-common (1:7.7+24) ...
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:arm64 (1.83.0-4) ...
Setting up gettext-base (0.23.1-1) ...
Setting up m4 (1.4.19-5) ...
Setting up libgcrypt20:arm64 (1.11.0-7) ...
Setting up autoconf-archive (20220903-3) ...
Setting up libxcb-shm0:arm64 (1.17.0-2+b1) ...
Setting up file (1:5.45-3+b1) ...
Setting up libboost-filesystem1.83.0:arm64 (1.83.0-4) ...
Setting up libyaml-tiny-perl (1.76-1) ...
Setting up libtext-wrapi18n-perl (0.06-10) ...
Setting up xxd (2:9.1.0967-2+b1) ...
Setting up libelf1t64:arm64 (0.192-4) ...
Setting up tzdata (2025a-1) ...
Current default time zone: 'Etc/UTC'
Local time is now: Thu Mar 5 02:35:25 UTC 2026.
Universal Time is now: Thu Mar 5 02:35:25 UTC 2026.
Run 'dpkg-reconfigure tzdata' if you wish to change it.
Setting up libboost-atomic1.83.0:arm64 (1.83.0-4) ...
Setting up libboost-serialization1.83.0:arm64 (1.83.0-4) ...
Setting up libio-string-perl (1.08-4) ...
Setting up libfontenc1:arm64 (1:1.1.8-1+b2) ...
Setting up autotools-dev (20220109.1) ...
Setting up libexpat1-dev:arm64 (2.6.4-1) ...
Setting up libzzip-0-13t64:arm64 (0.13.72+dfsg.1-1.3) ...
Setting up libx11-data (2:1.8.10-2) ...
Setting up libboost-chrono1.83.0t64:arm64 (1.83.0-4) ...
Setting up libteckit0:arm64 (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+b1) ...
Setting up libtexlua53-5:arm64 (2024.20240313.70630+ds-5+b1) ...
Setting up libproc2-0:arm64 (2:4.0.4-7) ...
Setting up libunistring5:arm64 (1.3-1) ...
Setting up fonts-dejavu-mono (2.37-8) ...
Setting up libpng16-16t64:arm64 (1.6.46-1) ...
Setting up autopoint (0.23.1-1) ...
Setting up libmpfi0:arm64 (1.5.4+ds-4) ...
Setting up icu-devtools (72.1-6) ...
Setting up fonts-dejavu-core (2.37-8) ...
Setting up libfl2:arm64 (2.6.4-8.2+b4) ...
Setting up libkpathsea6:arm64 (2024.20240313.70630+ds-5+b1) ...
Setting up libboost-atomic1.83-dev:arm64 (1.83.0-4) ...
Setting up autoconf (2.72-3) ...
Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1+b1) ...
Setting up libffi8:arm64 (3.4.6-1) ...
Setting up dwz (0.15-1+b1) ...
Setting up python-apt-common (2.9.8) ...
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:arm64 (0.0.8-1+b2) ...
Setting up procps (2:4.0.4-7) ...
Setting up fonts-lmodern (2.005-1) ...
Setting up libx11-6:arm64 (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 libboost-system1.83-dev:arm64 (1.83.0-4) ...
Setting up libpaper2:arm64 (2.2.5-0.3) ...
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:arm64 (72.1-6) ...
Setting up libxml2:arm64 (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:arm64 (2024.20240313.70630+ds-5+b1) ...
Setting up libbz2-dev:arm64 (1.0.8-6) ...
Setting up libpotrace0:arm64 (1.16-2+b2) ...
Setting up automake (1:1.17-2) ...
update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode
Setting up libfile-stripnondeterminism-perl (1.14.1-1) ...
Setting up libice6:arm64 (2:1.1.1-1) ...
Setting up flex (2.6.4-8.2+b4) ...
Setting up gettext (0.23.1-1) ...
Setting up libpdfbox-java (1:1.8.16-5) ...
Setting up libboost-chrono1.83-dev:arm64 (1.83.0-4) ...
Setting up libxpm4:arm64 (1:3.5.17-1+b3) ...
Setting up libxrender1:arm64 (1:0.9.10-1.1+b4) ...
Setting up libtool (2.5.4-2.1) ...
Setting up fontconfig-config (2.15.0-2) ...
Setting up libboost-system-dev:arm64 (1.83.0.2+b2) ...
Setting up libcommons-parent-java (56-1) ...
Setting up libboost-serialization1.83-dev:arm64 (1.83.0-4) ...
Setting up libcommons-logging-java (1.3.0-1) ...
Setting up libxext6:arm64 (2:1.3.4-1+b3) ...
Setting up libboost-filesystem1.83-dev:arm64 (1.83.0-4) ...
Setting up libpaper-utils (2.2.5-0.3) ...
Setting up libbibtex-parser-perl (1.05+dfsg-1) ...
Setting up libfl-dev:arm64 (2.6.4-8.2+b4) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up dh-autoreconf (20) ...
Setting up libthai0:arm64 (0.1.29-2+b1) ...
Setting up libglib2.0-0t64:arm64 (2.82.4-2) ...
No schema files found: doing nothing.
Setting up libptexenc1:arm64 (2024.20240313.70630+ds-5+b1) ...
Setting up libfreetype6:arm64 (2.13.3+dfsg-1) ...
Setting up libboost-date-time1.83-dev:arm64 (1.83.0-4) ...
Setting up libboost-regex1.83-dev:arm64 (1.83.0-4) ...
Setting up ucf (3.0049) ...
Setting up libreadline8t64:arm64 (8.2-6) ...
Setting up dh-strip-nondeterminism (1.14.1-1) ...
Setting up groff-base (1.23.0-7) ...
Setting up xml-core (0.19) ...
Setting up libxslt1.1:arm64 (1.1.35-1.1+b1) ...
Setting up libharfbuzz0b:arm64 (10.2.0-1) ...
Setting up libfontconfig1:arm64 (2.15.0-2) ...
Setting up libboost-regex-dev:arm64 (1.83.0.2+b2) ...
Setting up libsm6:arm64 (2:1.2.4-1) ...
Setting up libpython3.13-stdlib:arm64 (3.13.1-3) ...
Setting up libboost-filesystem-dev:arm64 (1.83.0.2+b2) ...
Setting up libpython3-stdlib:arm64 (3.13.1-2) ...
Setting up libboost-thread1.83-dev:arm64 (1.83.0-4) ...
Setting up libxi6:arm64 (2:1.8.2-1) ...
Setting up python3.13 (3.13.1-3) ...
Setting up libsombok3:arm64 (2.4.0-2+b2) ...
Setting up libboost-iostreams1.83-dev:arm64 (1.83.0-4) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up xsltproc (1.1.35-1.1+b1) ...
Setting up python3 (3.13.1-2) ...
Setting up libboost-iostreams-dev:arm64 (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:arm64 (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:arm64 (1:1.2.1-1.2+b2) ...
Setting up lmodern (2.005-1) ...
Setting up libboost-thread-dev:arm64 (1.83.0.2+b2) ...
Setting up libxmu6:arm64 (2:1.1.3-3+b4) ...
Setting up python3-apt (2.9.8) ...
Setting up preview-latex-style (13.2-1) ...
Setting up debhelper (13.24.1) ...
Setting up libxaw7:arm64 (2:1.0.16-1) ...
Setting up texlive-binaries (2024.20240313.70630+ds-5+b1) ...
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 (2024.20250114-1) ...
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 texlive-luatex (2024.20250114-1) ...
Setting up texlive-plain-generic (2024.20250114-1) ...
Setting up texlive-lang-greek (2024.20250114-1) ...
Setting up texlive-latex-base (2024.20250114-1) ...
Setting up texlive-extra-utils (2024.20250114-1) ...
Setting up texlive-latex-recommended (2024.20250114-1) ...
Setting up texlive-pictures (2024.20250114-1) ...
Setting up texlive-fonts-recommended (2024.20250114-1) ...
Setting up texlive (2024.20250114-1) ...
Setting up texlive-science (2024.20250114-1) ...
Setting up texlive-latex-extra (2024.20250114-1) ...
Setting up texlive-bibtex-extra (2024.20250114-1) ...
Processing triggers for libc-bin (2.40-6) ...
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 (0.3.12py3-5) ...
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/738978/tmp/hooks/A99_set_merged_usr starting
Not re-configuring usrmerge for unstable
I: user script /srv/workspace/pbuilder/738978/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 arm64
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/aarch64-linux-gnu --with-boost=/usr
./configure --build=aarch64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/aarch64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-boost-libdir=/usr/lib/aarch64-linux-gnu --with-boost=/usr
checking for a BSD-compatible install... /usr/bin/install -c
checking whether sleep supports fractional seconds... yes
checking filesystem timestamp resolution... 0.01
checking whether build environment is sane... yes
checking for a race-free mkdir -p... /usr/bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking xargs -n works... yes
checking whether UID '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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include
CXXFLAGS now: -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include
CXXFLAGS now: -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include
CXXFLAGS now: -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include
LDFLAGS now: -Wl,-z,relro -Wl,-z,now -L/usr/lib
+++++++++++++++++++++++++++++++++++++
checking whether long has 64bit... yes
checking whether enabling 64bit compilation support... yes
checking build system type... aarch64-unknown-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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include -O3 -funroll-loops
LDFLAGS now: -Wl,-z,relro -Wl,-z,now -L/usr/lib
+++++++++++++++++++++++++++++++++++++
checking host system type... aarch64-unknown-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 aarch64-unknown-linux-gnu file names to aarch64-unknown-linux-gnu format... func_convert_file_noop
checking how to convert aarch64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for file... file
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ranlib... ranlib
checking for ar... ar
checking for archiver @FILE support... @
checking for strip... strip
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for a working dd... /usr/bin/dd
checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1
checking for mt... no
checking if : is a manifest tool... no
checking for 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... none needed
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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu
ac_boost_path: /usr
ac_boost_lib_path: /usr/lib/aarch64-linux-gnu
CFLAGS now: -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu
CFLAGS now: -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include -O3 -funroll-loops -Wl,-rpath,/usr/lib/aarch64-linux-gnu
CXXFLAGS now: -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu
ac_boost_path: /usr
ac_boost_lib_path: /usr/lib/aarch64-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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include -O3 -funroll-loops -Wl,-rpath,/usr/lib/aarch64-linux-gnu
CXXFLAGS now: -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu
ac_boost_path: /usr
ac_boost_lib_path: /usr/lib/aarch64-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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include -O3 -funroll-loops -Wl,-rpath,/usr/lib/aarch64-linux-gnu
CXXFLAGS now: -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include -O3 -funroll-loops -pthread -I/usr/include
LDFLAGS now: -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/aarch64-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/aarch64-linux-gnu
ac_boost_path: /usr
ac_boost_lib_path: /usr/lib/aarch64-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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include -O3 -funroll-loops -Wl,-rpath,/usr/lib/aarch64-linux-gnu
CXXFLAGS now: -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu
ac_boost_path: /usr
ac_boost_lib_path: /usr/lib/aarch64-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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include -O3 -funroll-loops -Wl,-rpath,/usr/lib/aarch64-linux-gnu
CXXFLAGS now: -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu
ac_boost_path: /usr
ac_boost_lib_path: /usr/lib/aarch64-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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include -O3 -funroll-loops -Wl,-rpath,/usr/lib/aarch64-linux-gnu
CXXFLAGS now: -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu
ac_boost_path: /usr
ac_boost_lib_path: /usr/lib/aarch64-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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include -O3 -funroll-loops -Wl,-rpath,/usr/lib/aarch64-linux-gnu
CXXFLAGS now: -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include -O3 -funroll-loops -pthread -I/usr/include
LDFLAGS now: -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/aarch64-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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-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_aarch64_dynamic
We are building on ............................... Linux
CPU supports 64 bit? ............................. yes
Compiler family .................................. gcc
Compiler optimisation flags used ................. -O3 -funroll-loops
Do we compile in 64 bit? ......................... yes
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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-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 -j12
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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 cr libmiradebuggersupport.a dbgsupport.o
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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 cr libmirafio.a annotationmappings.o exp.o generalio.o fasta.o fastq-mira.o phd.o scf.o ncbiinfoxml.o exp_flexer.o
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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 cr libmiraerrorhandling.a errorhandling.o
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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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
In file included from /usr/include/c++/14/bits/requires_hosted.h:31,
from /usr/include/c++/14/iostream:38,
from ../../src/util/misc.H:32,
from misc.C:27:
/usr/include/aarch64-linux-gnu/c++/14/bits/c++config.h:670:2: warning: #warning "__STRICT_ANSI__ seems to have been undefined; this is not supported" [-Wcpp]
670 | #warning "__STRICT_ANSI__ seems to have been undefined; this is not supported"
| ^~~~~~~
rm -f libmirafmttext.a
ar cr libmirafmttext.a fmttext.o
ranlib libmirafmttext.a
rm -f libmiradptools.a
ar cr libmiradptools.a dptools.o
ranlib libmiradptools.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 libmirautil.a
ar cr libmirautil.a machineinfo.o fileanddisk.o misc.o
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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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
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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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
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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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
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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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
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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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
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();}
| ^~~~~
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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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
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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 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(
| ^~~~~~~~~~~~~~~~~~~~
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(
| ^~~~~~~~~~~~~~~~~~~~
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(
| ^~~~~~~~~~~~~~~~~~~~
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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/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/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(
| ^~~~~~~~~~~~~~~~~~~~
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/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(
| ^~~~~~~~~~~~~~~~~~~~
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;} }
| ^~~~~
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
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(
| ^~~~~~~~~~~~~~~~~~~~
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/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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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
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(
| ^~~~~~~~~~~~~~~~~~~~
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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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
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_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(
| ^~~~~~~~~~~~~~~~~~~~
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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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
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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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
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/c++/14/string:51,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/ostream:40,
from /usr/include/c++/14/iostream:41,
from ../../src/mira/assembly_info.H:28:
In static member function 'static _Up* std::__copy_move<_IsMove, true, std::random_access_iterator_tag>::__copy_m(_Tp*, _Tp*, _Up*) [with _Tp = long unsigned int; _Up = long unsigned int; bool _IsMove = false]',
inlined from '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = long unsigned int*; _OI = long unsigned int*]' at /usr/include/c++/14/bits/stl_algobase.h:521:30,
inlined from '_OI std::__copy_move_a1(_II, _II, _OI) [with bool _IsMove = false; _II = long unsigned int*; _OI = long unsigned int*]' at /usr/include/c++/14/bits/stl_algobase.h:548:42,
inlined from '_OI std::__copy_move_a(_II, _II, _OI) [with bool _IsMove = false; _II = long unsigned int*; _OI = long unsigned int*]' at /usr/include/c++/14/bits/stl_algobase.h:555:31,
inlined from '_OI std::copy(_II, _II, _OI) [with _II = long unsigned int*; _OI = long unsigned int*]' at /usr/include/c++/14/bits/stl_algobase.h:651:7,
inlined from 'std::vector<bool, _Alloc>::iterator std::vector<bool, _Alloc>::_M_copy_aligned(const_iterator, const_iterator, iterator) [with _Alloc = std::allocator<bool>]' at /usr/include/c++/14/bits/stl_bvector.h:1342:28,
inlined from 'void std::vector<bool, _Alloc>::_M_fill_insert(iterator, size_type, bool) [with _Alloc = std::allocator<bool>]' at /usr/include/c++/14/bits/vector.tcc:1087:34,
inlined from 'std::vector<bool, _Alloc>::iterator std::vector<bool, _Alloc>::insert(const_iterator, size_type, const bool&) [with _Alloc = std::allocator<bool>]' at /usr/include/c++/14/bits/stl_bvector.h:1242:16,
inlined from 'void std::vector<bool, _Alloc>::resize(size_type, bool) [with _Alloc = std::allocator<bool>]' at /usr/include/c++/14/bits/stl_bvector.h:1288:10,
inlined from 'uint32 Assembly::correctPBMain()' at assembly_pbcorrect.C:91:28:
/usr/include/c++/14/bits/stl_algobase.h:452:30: warning: 'void* __builtin_memmove(void*, const void*, long unsigned int)' writing between 9 and 9223372036854775807 bytes into a region of size 8 overflows the destination [-Wstringop-overflow=]
452 | __builtin_memmove(__result, __first, sizeof(_Tp) * _Num);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/aarch64-linux-gnu/c++/14/bits/c++allocator.h:33,
from /usr/include/c++/14/bits/allocator.h:46,
from /usr/include/c++/14/string:43:
In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = long unsigned int]',
inlined from 'static _Tp* std::allocator_traits<std::allocator<_CharT> >::allocate(allocator_type&, size_type) [with _Tp = long unsigned int]' at /usr/include/c++/14/bits/alloc_traits.h:515:28,
inlined from 'std::_Bvector_base<_Alloc>::_Bit_pointer std::_Bvector_base<_Alloc>::_M_allocate(std::size_t) [with _Alloc = std::allocator<bool>]' at /usr/include/c++/14/bits/stl_bvector.h:679:48,
inlined from 'void std::vector<bool, _Alloc>::_M_fill_insert(iterator, size_type, bool) [with _Alloc = std::allocator<bool>]' at /usr/include/c++/14/bits/vector.tcc:1085:40,
inlined from 'std::vector<bool, _Alloc>::iterator std::vector<bool, _Alloc>::insert(const_iterator, size_type, const bool&) [with _Alloc = std::allocator<bool>]' at /usr/include/c++/14/bits/stl_bvector.h:1242:16,
inlined from 'void std::vector<bool, _Alloc>::resize(size_type, bool) [with _Alloc = std::allocator<bool>]' at /usr/include/c++/14/bits/stl_bvector.h:1288:10,
inlined from 'uint32 Assembly::correctPBMain()' at assembly_pbcorrect.C:91:28:
/usr/include/c++/14/bits/new_allocator.h:151:55: note: destination object of size 8 allocated by 'operator new'
151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp)));
| ^
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(
| ^~~~~~~~~~~~~~~~~~~~
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(
| ^~~~~~~~~~~~~~~~~~~~
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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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
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(
| ^~~~~~~~~~~~~~~~~~~~
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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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
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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 ../../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(
| ^~~~~~~~~~~~~~~~~~~~
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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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
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(
| ^~~~~~~~~~~~~~~~~~~~
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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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
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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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
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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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
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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/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(
| ^~~~~~~~~~~~~~~~~~~~
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 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(
| ^~~~~~~~~~~~~~~~~~~~
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(
| ^~~~~~~~~~~~~~~~~~~~
/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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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
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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 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(
| ^~~~~~~~~~~~~~~~~~~~
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(
| ^~~~~~~~~~~~~~~~~~~~
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(
| ^~~~~~~~~~~~~~~~~~~~
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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 ../../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(
| ^~~~~~~~~~~~~~~~~~~~
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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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
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/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(
| ^~~~~~~~~~~~~~~~~~~~
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(
| ^~~~~~~~~~~~~~~~~~~~
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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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
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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 cr libmiraestass.a estassembly.o
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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 cr 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
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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 cr libmiracaf.a caf.o caf_flexer.o
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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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:153:39: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 2 has type 'uint64' {aka 'long unsigned int'} [-Wformat=]
153 | printf("Current alloc counter : %llu\n", MOC_alloccounter);
| ~~~^ ~~~~~~~~~~~~~~~~
| | |
| | uint64 {aka long unsigned int}
| long long unsigned int
| %lu
memorc.C:154:39: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 2 has type 'uint64' {aka 'long unsigned int'} [-Wformat=]
154 | printf("Total checks performed : %llu\n", MOC_checksperformed);
| ~~~^ ~~~~~~~~~~~~~~~~~~~
| | |
| | uint64 {aka long unsigned int}
| long long unsigned int
| %lu
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 'long 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 long unsigned int}
| %lu
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 'long 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 long unsigned int}
| %lu
memorc.C:157:39: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 2 has type 'std::vector<long unsigned int>::size_type' {aka 'long unsigned int'} [-Wformat=]
157 | printf("Num. pending hot blocks: %llu\n", MOC_hotaidsrequested.size());
| ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~
| | |
| long long unsigned int std::vector<long unsigned int>::size_type {aka long unsigned int}
| %lu
memorc.C:158:39: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 2 has type 'size_t' {aka 'long unsigned int'} [-Wformat=]
158 | printf("Total mem reqested : %llu\n", MOC_reqmemalloc);
| ~~~^ ~~~~~~~~~~~~~~~
| | |
| | size_t {aka long unsigned int}
| long long unsigned int
| %lu
memorc.C:159:39: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 2 has type 'size_t' {aka 'long unsigned int'} [-Wformat=]
159 | printf("Total mem allocated : %llu (including pads and fences)\n", MOC_totalmemalloc);
| ~~~^ ~~~~~~~~~~~~~~~~~
| | |
| long long unsigned int size_t {aka long unsigned int}
| %lu
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 'long 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 long unsigned int}
| %lu
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 unsigned int'} [-Wformat=]
311 | printf("Nearest memblock above (%d):\t",reinterpret_cast<uint64>(mbI->first)-reinterpret_cast<uint64>(usraddr));
| ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| | |
| int uint64 {aka long unsigned int}
| %ld
memorc.C:318:43: warning: format '%d' expects argument of type 'int', but argument 2 has type 'uint64' {aka 'long unsigned int'} [-Wformat=]
318 | printf("Nearest memblock below (-%d):\t",reinterpret_cast<uint64>(usraddr)-reinterpret_cast<uint64>(mbI->first));
| ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| | |
| int uint64 {aka long unsigned int}
| %ld
memorc.C: In static member function 'static bool MemORC::checkMemBlock(std::map<void*, memblockinfo_t>::iterator)':
memorc.C:430:63: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long unsigned int' [-Wformat=]
430 | printf("check: lower fence .0 destroyed at position: %d\tExpected: %x\tGot: %x\n", i*sizeof(int32),MOC_clowfencemagic[0], *fencecptr);
| ~^ ~~~~~~~~~~~~~~~
| | |
| int long unsigned int
| %ld
memorc.C:433:63: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long unsigned int' [-Wformat=]
433 | printf("check: lower fence .1 destroyed at position: %d\tExpected: %x\tGot: %x\n", i*sizeof(int32)+1,MOC_clowfencemagic[1], *fencecptr);
| ~^ ~~~~~~~~~~~~~~~~~
| | |
| int long unsigned int
| %ld
memorc.C:436:63: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long unsigned int' [-Wformat=]
436 | printf("check: lower fence .2 destroyed at position: %d\tExpected: %x\tGot: %x\n", i*sizeof(int32)+2,MOC_clowfencemagic[2], *fencecptr);
| ~^ ~~~~~~~~~~~~~~~~~
| | |
| int long unsigned int
| %ld
memorc.C:439:63: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long unsigned int' [-Wformat=]
439 | printf("check: lower fence .3 destroyed at position: %d\tExpected: %x\tGot: %x\n", i*sizeof(int32)+3,MOC_clowfencemagic[3], *fencecptr);
| ~^ ~~~~~~~~~~~~~~~~~
| | |
| int long unsigned int
| %ld
memorc.C:500:22: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 2 has type 'size_t' {aka 'long unsigned int'} [-Wformat=]
500 | printf("Size: %llu\n", mbI->second.size);
| ~~~^ ~~~~~~~~~~~~~~~~
| | |
| | size_t {aka long unsigned int}
| long long unsigned int
| %lu
memorc.C:501:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 2 has type 'uint64' {aka 'long unsigned int'} [-Wformat=]
501 | printf("AllocID: %llu\n", mbI->second.allocid);
| ~~~^ ~~~~~~~~~~~~~~~~~~~
| | |
| | uint64 {aka long unsigned int}
| long long unsigned int
| %lu
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 'long unsigned int'} [-Wformat=]
558 | printf("%p\t%llu\t",mbI->first,mbI->second.size);
| ~~~^ ~~~~~~~~~~~~~~~~
| | |
| long long unsigned int size_t {aka long unsigned int}
| %lu
memorc.C:564:16: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 2 has type 'uint64' {aka 'long unsigned int'} [-Wformat=]
564 | printf("\t%llu\n",mbI->second.allocid);
| ~~~^ ~~~~~~~~~~~~~~~~~~~
| | |
| | uint64 {aka long unsigned int}
| long long unsigned int
| %lu
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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 cr libmemorc.a memorc.o
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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/aarch64-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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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
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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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
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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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
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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 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_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/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/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(
| ^~~~~~~~~~~~~~~~~~~~
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/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/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(
| ^~~~~~~~~~~~~~~~~~~~
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(
| ^~~~~~~~~~~~~~~~~~~~
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("../..");
| ~~~~~^~~~~~~~~
rm -f libmiramodules.a
ar cr 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
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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 cr libmiraversion.a mversion.o
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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/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(
| ^~~~~~~~~~~~~~~~~~~~
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(
| ^~~~~~~~~~~~~~~~~~~~
/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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/aarch64-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
/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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/aarch64-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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-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
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Making all in mira-createsls
make[7]: Entering directory '/build/reproducible-path/mira-4.9.6/src/other/sls/mira-createsls'
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make[4]: Leaving directory '/build/reproducible-path/mira-4.9.6/src'
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make[1]: Leaving directory '/build/reproducible-path/mira-4.9.6'
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 -j12 "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_mirautils_part.html
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Build the book set list...
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Build the listings...
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===================================================
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Build book_3rdparty.pdf
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'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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debian/rules override_dh_auto_test-arch
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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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/aarch64-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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/aarch64-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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-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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debian/rules override_dh_auto_test-indep
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make[1]: Entering directory '/build/reproducible-path/mira-4.9.6'
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Making install in mira
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make install-am
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Making install in modules
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Making install in support
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/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'
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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 -DENABLE64=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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/aarch64-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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/aarch64-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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-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-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
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-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
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
man-recode --to-code UTF-8 --suffix .dh-new 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/miradiff.1
man-recode --to-code UTF-8 --suffix .dh-new debian/mira-assembler/usr/share/man/man1/miramem.1
man-recode --to-code UTF-8 --suffix .dh-new debian/mira-assembler/usr/share/man/man1/miraconvert.1
man-recode --to-code UTF-8 --suffix .dh-new debian/mira-assembler/usr/share/man/man1/miramer.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/miradiff.1
mv debian/mira-assembler/usr/share/man/man1/mira.1.dh-new debian/mira-assembler/usr/share/man/man1/mira.1
chmod 0644 -- debian/mira-assembler/usr/share/man/man1/mira.1
mv debian/mira-assembler/usr/share/man/man1/miraconvert.1.dh-new debian/mira-assembler/usr/share/man/man1/miraconvert.1
chmod 0644 -- debian/mira-assembler/usr/share/man/man1/miraconvert.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/mirabait.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/miramer.1
mv debian/mira-assembler/usr/share/man/man1/miramem.1.dh-new debian/mira-assembler/usr/share/man/man1/miramem.1
chmod 0644 -- debian/mira-assembler/usr/share/man/man1/miramem.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/miramem
ln -s mira debian/mira-assembler/usr/bin/miramem
rm -f debian/mira-assembler/usr/bin/mirabait
ln -s mira debian/mira-assembler/usr/bin/mirabait
rm -f debian/mira-assembler/usr/bin/miraconvert
ln -s mira debian/mira-assembler/usr/bin/miraconvert
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/images/note.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/bookfigures/pb_elasticdarkinserts01.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_xmastree_lenski2.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/srmc_in_454sxahyb_lastpass1.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/454_stacks_join.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/haf5_haf2_contigcoverage.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/ion_dh10bgoodB13.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/pb_elasticdarkinserts02.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/454_autoedit2.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_wrmcsrmc_hiding_lenski1.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/sxa_gcbias_nobias2008.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/sxa_cer_reads2.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/sxa_cer_reads1.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/sxa_unsc_ggc3_lenski.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/haf5_repend_rrna.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/sxa_sroc_lenski2.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/gcb99_edit.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/iontor_indelhpexample.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/pb_elasticdarkinserts03.png using File::StripNondeterminism::handlers::png
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/pb_c227-11-clcr_res.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/454san_stmu_hybdenovo.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/sxa_gcbias_comp20082009.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_ggc4_lenski.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/454_autoedit1.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/ion_dh10bdirdepindel.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-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
chmod a-x usr/share/doc/mira-rfam-12s-rrna/changelog usr/share/doc/mira-rfam-12s-rrna/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
gzip -9nf usr/share/doc/mira-doc/changelog usr/share/doc/mira-doc/changelog.Debian
gzip -9nf usr/share/doc/mira-rfam-12s-rrna/changelog usr/share/doc/mira-rfam-12s-rrna/changelog.Debian
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-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-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-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-assembler/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-rfam-12s-rrna/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755
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-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-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/83
objcopy --only-keep-debug --compress-debug-sections debian/mira-assembler/usr/bin/mira debian/.debhelper/mira-assembler/dbgsym-root/usr/lib/debug/.build-id/83/2708e087a1c970b2f4a0dd461581403ad931d6.debug
chmod 0644 -- debian/.debhelper/mira-assembler/dbgsym-root/usr/lib/debug/.build-id/83/2708e087a1c970b2f4a0dd461581403ad931d6.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/83/2708e087a1c970b2f4a0dd461581403ad931d6.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
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
diversion by libc6 from: /lib/ld-linux-aarch64.so.1
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged
dh_installdeb
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-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-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-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=832708e087a1c970b2f4a0dd461581403ad931d6 -DSection=debug -UMulti-Arch -UReplaces -UBreaks
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-doc/DEBIAN/control
chmod 0644 -- debian/mira-rfam-12s-rrna/DEBIAN/control
chmod 0644 -- debian/mira-assembler/DEBIAN/control
dh_md5sums
install -m0755 -d debian/mira-doc/DEBIAN
install -m0755 -d debian/mira-assembler/DEBIAN
install -m0755 -d debian/mira-rfam-12s-rrna/DEBIAN
cd debian/mira-doc >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
cd debian/mira-assembler >/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-rfam-12s-rrna/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/.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' in '../mira-assembler_4.9.6-11_arm64.deb'.
dpkg-deb: building package 'mira-assembler-dbgsym' in '../mira-assembler-dbgsym_4.9.6-11_arm64.deb'.
dpkg-deb: building package 'mira-rfam-12s-rrna' in '../mira-rfam-12s-rrna_4.9.6-11_all.deb'.
dpkg-deb: building package 'mira-doc' in '../mira-doc_4.9.6-11_all.deb'.
dpkg-genbuildinfo --build=binary -O../mira_4.9.6-11_arm64.buildinfo
dpkg-genchanges --build=binary -O../mira_4.9.6-11_arm64.changes
dpkg-genchanges: info: binary-only upload (no source code included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
dpkg-genchanges: info: not including original source code in upload
I: copying local configuration
I: user script /srv/workspace/pbuilder/738978/tmp/hooks/B01_cleanup starting
I: user script /srv/workspace/pbuilder/738978/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/738978 and its subdirectories
I: Current time: Thu Mar 5 16:42:05 +14 2026
I: pbuilder-time-stamp: 1772678525