I: pbuilder: network access will be disabled during build I: Current time: Sat Jan 13 10:03:40 +14 2024 I: pbuilder-time-stamp: 1705089820 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: using eatmydata during job I: Copying source file I: copying [mira_4.9.6-5.dsc] I: copying [./mira_4.9.6.orig.tar.bz2] I: copying [./mira_4.9.6-5.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.DyLTBb9r/trustedkeys.kbx': General error gpgv: Signature made Thu Sep 17 11:46:15 2020 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tillea@rki.de" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./mira_4.9.6-5.dsc 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_4.9.6-5.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 I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/10537/tmp/hooks/D01_modify_environment starting debug: Running on ionos12-i386. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Jan 12 20:07 /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/10537/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/10537/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") BASH_VERSION='5.1.4(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=i386 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=7 ' DIRSTACK=() DISTRIBUTION=bullseye EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=i686 HOST_ARCH=i386 IFS=' ' INVOCATION_ID=4efb409fa4cb41ce89d22e321e351b62 LANG=C LANGUAGE=de_CH:de LC_ALL=C LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so MACHTYPE=i686-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=10537 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.ar8TtoBH/pbuilderrc_6YMD --distribution bullseye --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ar8TtoBH/b2 --logfile b2/build.log mira_4.9.6-5.dsc' SUDO_GID=112 SUDO_UID=107 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://78.137.99.97:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-17-686-pae #1 SMP PREEMPT_DYNAMIC Debian 6.1.69-1 (2023-12-30) i686 GNU/Linux I: ls -l /bin total 5784 -rwxr-xr-x 1 root root 1367848 Mar 27 2022 bash -rwxr-xr-x 3 root root 38280 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 38280 Jul 20 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep -rwxr-xr-x 3 root root 38280 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 17768 Jul 20 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore -rwxr-xr-x 1 root root 38824 Sep 22 2020 cat -rwxr-xr-x 1 root root 71624 Sep 22 2020 chgrp -rwxr-xr-x 1 root root 67528 Sep 22 2020 chmod -rwxr-xr-x 1 root root 75752 Sep 22 2020 chown -rwxr-xr-x 1 root root 157960 Sep 22 2020 cp -rwxr-xr-x 1 root root 128724 Dec 10 2020 dash -rwxr-xr-x 1 root root 124904 Sep 22 2020 date -rwxr-xr-x 1 root root 92172 Sep 22 2020 dd -rwxr-xr-x 1 root root 100752 Sep 22 2020 df -rwxr-xr-x 1 root root 153964 Sep 22 2020 dir -rwxr-xr-x 1 root root 83644 Jan 20 2022 dmesg lrwxrwxrwx 1 root root 8 Nov 7 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 7 2019 domainname -> hostname -rwxr-xr-x 1 root root 34664 Sep 22 2020 echo -rwxr-xr-x 1 root root 28 Jan 25 2023 egrep -rwxr-xr-x 1 root root 34664 Sep 22 2020 false -rwxr-xr-x 1 root root 28 Jan 25 2023 fgrep -rwxr-xr-x 1 root root 71928 Jan 20 2022 findmnt -rwsr-xr-x 1 root root 30112 Feb 26 2021 fusermount -rwxr-xr-x 1 root root 210488 Jan 25 2023 grep -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe -rwxr-xr-x 1 root root 100952 Apr 10 2022 gzip -rwxr-xr-x 1 root root 21916 Nov 7 2019 hostname -rwxr-xr-x 1 root root 83980 Sep 22 2020 ln -rwxr-xr-x 1 root root 55572 Feb 7 2020 login -rwxr-xr-x 1 root root 153964 Sep 22 2020 ls -rwxr-xr-x 1 root root 153124 Jan 20 2022 lsblk -rwxr-xr-x 1 root root 96328 Sep 22 2020 mkdir -rwxr-xr-x 1 root root 79912 Sep 22 2020 mknod -rwxr-xr-x 1 root root 47048 Sep 22 2020 mktemp -rwxr-xr-x 1 root root 58920 Jan 20 2022 more -rwsr-xr-x 1 root root 50720 Jan 20 2022 mount -rwxr-xr-x 1 root root 13856 Jan 20 2022 mountpoint -rwxr-xr-x 1 root root 157996 Sep 22 2020 mv lrwxrwxrwx 1 root root 8 Nov 7 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Dec 16 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 38824 Sep 22 2020 pwd lrwxrwxrwx 1 root root 4 Mar 27 2022 rbash -> bash -rwxr-xr-x 1 root root 46984 Sep 22 2020 readlink -rwxr-xr-x 1 root root 75720 Sep 22 2020 rm -rwxr-xr-x 1 root root 46984 Sep 22 2020 rmdir -rwxr-xr-x 1 root root 22292 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 125036 Dec 22 2018 sed lrwxrwxrwx 1 root root 9 Jan 12 20:07 sh -> /bin/bash -rwxr-xr-x 1 root root 34696 Sep 22 2020 sleep -rwxr-xr-x 1 root root 83880 Sep 22 2020 stty -rwsr-xr-x 1 root root 79396 Jan 20 2022 su -rwxr-xr-x 1 root root 34696 Sep 22 2020 sync -rwxr-xr-x 1 root root 602584 Feb 17 2021 tar -rwxr-xr-x 1 root root 13860 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 108520 Sep 22 2020 touch -rwxr-xr-x 1 root root 34664 Sep 22 2020 true -rwxr-xr-x 1 root root 17768 Feb 26 2021 ulockmgr_server -rwsr-xr-x 1 root root 30236 Jan 20 2022 umount -rwxr-xr-x 1 root root 34664 Sep 22 2020 uname -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 153964 Sep 22 2020 vdir -rwxr-xr-x 1 root root 63024 Jan 20 2022 wdctl lrwxrwxrwx 1 root root 8 Nov 7 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp -rwxr-xr-x 1 root root 5898 Apr 10 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce -rwxr-xr-x 1 root root 8049 Apr 10 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew I: user script /srv/workspace/pbuilder/10537/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: i386 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), autoconf-archive, libbz2-dev, libexpat1-dev, libgoogle-perftools-dev, perl, flex, libfl-dev, vim-common, 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 ... 17763 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on autoconf-archive; however: Package autoconf-archive is not installed. pbuilder-satisfydepends-dummy depends on libbz2-dev; however: Package libbz2-dev is not installed. pbuilder-satisfydepends-dummy depends on libexpat1-dev; however: Package libexpat1-dev is not installed. pbuilder-satisfydepends-dummy depends on libgoogle-perftools-dev; however: Package libgoogle-perftools-dev is not installed. pbuilder-satisfydepends-dummy depends on flex; however: Package flex is not installed. pbuilder-satisfydepends-dummy depends on libfl-dev; however: Package libfl-dev is not installed. pbuilder-satisfydepends-dummy depends on vim-common; however: Package vim-common 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-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} libboost-atomic1.74-dev{a} libboost-atomic1.74.0{a} libboost-chrono1.74-dev{a} libboost-chrono1.74.0{a} libboost-date-time1.74-dev{a} libboost-date-time1.74.0{a} libboost-filesystem-dev{a} libboost-filesystem1.74-dev{a} libboost-filesystem1.74.0{a} libboost-iostreams-dev{a} libboost-iostreams1.74-dev{a} libboost-regex-dev{a} libboost-regex1.74-dev{a} libboost-regex1.74.0{a} libboost-serialization1.74-dev{a} libboost-serialization1.74.0{a} libboost-system-dev{a} libboost-system1.74-dev{a} libboost-system1.74.0{a} libboost-thread-dev{a} libboost-thread1.74-dev{a} libboost-thread1.74.0{a} libboost1.74-dev{a} libbrotli1{a} libbsd0{a} libbz2-dev{a} libcairo2{a} libcommons-logging-java{a} libcommons-parent-java{a} libdatrie1{a} libdebhelper-perl{a} libelf1{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libfl-dev{a} libfl2{a} libfontbox-java{a} libfontconfig1{a} libfontenc1{a} libfreetype6{a} libglib2.0-0{a} libgoogle-perftools-dev{a} libgoogle-perftools4{a} libgraphite2-3{a} libharfbuzz0b{a} libice6{a} libicu-dev{a} libicu67{a} libjs-jquery{a} libkpathsea6{a} libmagic-mgc{a} libmagic1{a} libmd0{a} libmime-charset-perl{a} libmpdec3{a} libpaper-utils{a} libpaper1{a} libpdfbox-java{a} libpipeline1{a} libpixman-1-0{a} libpng16-16{a} libptexenc1{a} libpython3-stdlib{a} libpython3.9-minimal{a} libpython3.9-stdlib{a} libreadline8{a} libsigsegv2{a} libsm6{a} libsombok3{a} libsub-override-perl{a} libsynctex2{a} libtcmalloc-minimal4{a} libteckit0{a} libtexlua53{a} libtexluajit2{a} libthai-data{a} libthai0{a} libtool{a} libuchardet0{a} libunicode-linebreak-perl{a} libx11-6{a} libx11-data{a} libxau6{a} libxaw7{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxi6{a} libxml2{a} libxmu6{a} libxpm4{a} libxrender1{a} libxslt1.1{a} libxt6{a} libzzip-0-13{a} lmodern{a} m4{a} man-db{a} media-types{a} po-debconf{a} preview-latex-style{a} python-apt-common{a} python3{a} python3-apt{a} python3-minimal{a} python3.9{a} python3.9-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} vim-common{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 dvisvgm ghostscript iso-codes javascript-common libarchive-cpio-perl libfile-homedir-perl libfile-mimeinfo-perl libglib2.0-data liblog-log4perl-perl libltdl-dev libmail-sendmail-perl libnet-dbus-perl libx11-protocol-perl libxml2-utils libyaml-tiny-perl lsb-release lynx ruby shared-mime-info tex-gyre tipa tk vim vim-athena vim-gtk3 vim-nox vim-tiny wget x11-utils x11-xserver-utils xdg-user-dirs 0 packages upgraded, 169 newly installed, 0 to remove and 0 not upgraded. Need to get 404 MB of archives. After unpacking 1097 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main i386 bsdextrautils i386 2.36.1-8+deb11u1 [149 kB] Get: 2 http://deb.debian.org/debian bullseye/main i386 libuchardet0 i386 0.0.7-1 [67.9 kB] Get: 3 http://deb.debian.org/debian bullseye/main i386 groff-base i386 1.22.4-6 [952 kB] Get: 4 http://deb.debian.org/debian bullseye/main i386 libpipeline1 i386 1.5.3-1 [36.8 kB] Get: 5 http://deb.debian.org/debian bullseye/main i386 man-db i386 2.9.4-2 [1367 kB] Get: 6 http://deb.debian.org/debian bullseye/main i386 autoconf-archive all 20190106-2.1 [746 kB] Get: 7 http://deb.debian.org/debian bullseye/main i386 libsigsegv2 i386 2.13-1 [35.1 kB] Get: 8 http://deb.debian.org/debian bullseye/main i386 m4 i386 1.4.18-5 [206 kB] Get: 9 http://deb.debian.org/debian bullseye/main i386 flex i386 2.6.4-8 [434 kB] Get: 10 http://deb.debian.org/debian bullseye/main i386 libpython3.9-minimal i386 3.9.2-1 [801 kB] Get: 11 http://deb.debian.org/debian bullseye/main i386 libexpat1 i386 2.2.10-2+deb11u5 [101 kB] Get: 12 http://deb.debian.org/debian bullseye/main i386 python3.9-minimal i386 3.9.2-1 [1956 kB] Get: 13 http://deb.debian.org/debian bullseye/main i386 python3-minimal i386 3.9.2-3 [38.2 kB] Get: 14 http://deb.debian.org/debian bullseye/main i386 media-types all 4.0.0 [30.3 kB] Get: 15 http://deb.debian.org/debian bullseye/main i386 tzdata all 2021a-1+deb11u10 [286 kB] Get: 16 http://deb.debian.org/debian bullseye/main i386 libmpdec3 i386 2.5.1-1 [91.9 kB] Get: 17 http://deb.debian.org/debian bullseye/main i386 readline-common all 8.1-1 [73.7 kB] Get: 18 http://deb.debian.org/debian bullseye/main i386 libreadline8 i386 8.1-1 [173 kB] Get: 19 http://deb.debian.org/debian bullseye/main i386 libpython3.9-stdlib i386 3.9.2-1 [1703 kB] Get: 20 http://deb.debian.org/debian bullseye/main i386 python3.9 i386 3.9.2-1 [466 kB] Get: 21 http://deb.debian.org/debian bullseye/main i386 libpython3-stdlib i386 3.9.2-3 [21.4 kB] Get: 22 http://deb.debian.org/debian bullseye/main i386 python3 i386 3.9.2-3 [37.9 kB] Get: 23 http://deb.debian.org/debian bullseye/main i386 sgml-base all 1.30 [15.1 kB] Get: 24 http://deb.debian.org/debian bullseye/main i386 sensible-utils all 0.0.14 [14.8 kB] Get: 25 http://deb.debian.org/debian bullseye/main i386 ucf all 3.0043 [74.0 kB] Get: 26 http://deb.debian.org/debian bullseye/main i386 tex-common all 6.16 [53.7 kB] Get: 27 http://deb.debian.org/debian bullseye/main i386 xxd i386 2:8.2.2434-3+deb11u1 [192 kB] Get: 28 http://deb.debian.org/debian bullseye/main i386 vim-common all 2:8.2.2434-3+deb11u1 [226 kB] Get: 29 http://deb.debian.org/debian bullseye/main i386 libmagic-mgc i386 1:5.39-3+deb11u1 [273 kB] Get: 30 http://deb.debian.org/debian bullseye/main i386 libmagic1 i386 1:5.39-3+deb11u1 [135 kB] Get: 31 http://deb.debian.org/debian bullseye/main i386 file i386 1:5.39-3+deb11u1 [69.2 kB] Get: 32 http://deb.debian.org/debian bullseye/main i386 gettext-base i386 0.21-4 [176 kB] Get: 33 http://deb.debian.org/debian bullseye/main i386 autoconf all 2.69-14 [313 kB] Get: 34 http://deb.debian.org/debian bullseye/main i386 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 35 http://deb.debian.org/debian bullseye/main i386 automake all 1:1.16.3-2 [814 kB] Get: 36 http://deb.debian.org/debian bullseye/main i386 autopoint all 0.21-4 [510 kB] Get: 37 http://deb.debian.org/debian bullseye/main i386 xml-core all 0.18+nmu1 [23.8 kB] Get: 38 http://deb.debian.org/debian bullseye/main i386 sgml-data all 2.0.11+nmu1 [179 kB] Get: 39 http://deb.debian.org/debian bullseye/main i386 docbook-xml all 4.5-9 [84.4 kB] Get: 40 http://deb.debian.org/debian bullseye/main i386 python-apt-common all 2.2.1 [96.5 kB] Get: 41 http://deb.debian.org/debian bullseye/main i386 distro-info-data all 0.51+deb11u4 [8048 B] Get: 42 http://deb.debian.org/debian bullseye/main i386 python3-apt i386 2.2.1 [194 kB] Get: 43 http://deb.debian.org/debian bullseye/main i386 libpaper1 i386 1.1.28+b1 [21.7 kB] Get: 44 http://deb.debian.org/debian bullseye/main i386 libpaper-utils i386 1.1.28+b1 [18.6 kB] Get: 45 http://deb.debian.org/debian bullseye/main i386 libkpathsea6 i386 2020.20200327.54578-7+deb11u1 [176 kB] Get: 46 http://deb.debian.org/debian bullseye/main i386 libptexenc1 i386 2020.20200327.54578-7+deb11u1 [65.2 kB] Get: 47 http://deb.debian.org/debian bullseye/main i386 libsynctex2 i386 2020.20200327.54578-7+deb11u1 [86.1 kB] Get: 48 http://deb.debian.org/debian bullseye/main i386 libtexlua53 i386 2020.20200327.54578-7+deb11u1 [146 kB] Get: 49 http://deb.debian.org/debian bullseye/main i386 libtexluajit2 i386 2020.20200327.54578-7+deb11u1 [284 kB] Get: 50 http://deb.debian.org/debian bullseye/main i386 t1utils i386 1.41-4 [62.3 kB] Get: 51 http://deb.debian.org/debian bullseye/main i386 libbrotli1 i386 1.0.9-2+b2 [286 kB] Get: 52 http://deb.debian.org/debian bullseye/main i386 libpng16-16 i386 1.6.37-3 [303 kB] Get: 53 http://deb.debian.org/debian bullseye/main i386 libfreetype6 i386 2.10.4+dfsg-1+deb11u1 [430 kB] Get: 54 http://deb.debian.org/debian bullseye/main i386 fonts-dejavu-core all 2.37-2 [1069 kB] Get: 55 http://deb.debian.org/debian bullseye/main i386 fontconfig-config all 2.13.1-4.2 [281 kB] Get: 56 http://deb.debian.org/debian bullseye/main i386 libfontconfig1 i386 2.13.1-4.2 [358 kB] Get: 57 http://deb.debian.org/debian bullseye/main i386 libpixman-1-0 i386 0.40.0-1.1~deb11u1 [545 kB] Get: 58 http://deb.debian.org/debian bullseye/main i386 libxau6 i386 1:1.0.9-1 [20.0 kB] Get: 59 http://deb.debian.org/debian bullseye/main i386 libmd0 i386 1.0.3-3 [28.9 kB] Get: 60 http://deb.debian.org/debian bullseye/main i386 libbsd0 i386 0.11.3-1+deb11u1 [111 kB] Get: 61 http://deb.debian.org/debian bullseye/main i386 libxdmcp6 i386 1:1.1.2-3 [26.7 kB] Get: 62 http://deb.debian.org/debian bullseye/main i386 libxcb1 i386 1.14-3 [144 kB] Get: 63 http://deb.debian.org/debian bullseye/main i386 libx11-data all 2:1.7.2-1+deb11u1 [311 kB] Get: 64 http://deb.debian.org/debian bullseye/main i386 libx11-6 i386 2:1.7.2-1+deb11u1 [796 kB] Get: 65 http://deb.debian.org/debian bullseye/main i386 libxcb-render0 i386 1.14-3 [112 kB] Get: 66 http://deb.debian.org/debian bullseye/main i386 libxcb-shm0 i386 1.14-3 [102 kB] Get: 67 http://deb.debian.org/debian bullseye/main i386 libxext6 i386 2:1.3.3-1.1 [55.2 kB] Get: 68 http://deb.debian.org/debian bullseye/main i386 libxrender1 i386 1:0.9.10-1 [34.1 kB] Get: 69 http://deb.debian.org/debian bullseye/main i386 libcairo2 i386 1.16.0-5 [746 kB] Get: 70 http://deb.debian.org/debian bullseye/main i386 libgraphite2-3 i386 1.3.14-1 [84.0 kB] Get: 71 http://deb.debian.org/debian bullseye/main i386 libglib2.0-0 i386 2.66.8-1 [1437 kB] Get: 72 http://deb.debian.org/debian bullseye/main i386 libharfbuzz0b i386 2.7.4-1 [1490 kB] Get: 73 http://deb.debian.org/debian bullseye/main i386 libicu67 i386 67.1-7 [8775 kB] Get: 74 http://deb.debian.org/debian bullseye/main i386 libteckit0 i386 2.5.10+ds1-3 [277 kB] Get: 75 http://deb.debian.org/debian bullseye/main i386 x11-common all 1:7.7+22 [252 kB] Get: 76 http://deb.debian.org/debian bullseye/main i386 libice6 i386 2:1.0.10-1 [60.8 kB] Get: 77 http://deb.debian.org/debian bullseye/main i386 libsm6 i386 2:1.2.3-1 [35.7 kB] Get: 78 http://deb.debian.org/debian bullseye/main i386 libxt6 i386 1:1.2.0-1 [195 kB] Get: 79 http://deb.debian.org/debian bullseye/main i386 libxmu6 i386 2:1.1.2-2+b3 [62.8 kB] Get: 80 http://deb.debian.org/debian bullseye/main i386 libxpm4 i386 1:3.5.12-1.1~deb11u1 [51.2 kB] Get: 81 http://deb.debian.org/debian bullseye/main i386 libxaw7 i386 2:1.0.13-1.1 [210 kB] Get: 82 http://deb.debian.org/debian bullseye/main i386 libxi6 i386 2:1.7.10-1 [85.1 kB] Get: 83 http://deb.debian.org/debian bullseye/main i386 libzzip-0-13 i386 0.13.62-3.3+deb11u1 [57.7 kB] Get: 84 http://deb.debian.org/debian bullseye/main i386 texlive-binaries i386 2020.20200327.54578-7+deb11u1 [10.1 MB] Get: 85 http://deb.debian.org/debian bullseye/main i386 xdg-utils all 1.1.3-4.1 [75.5 kB] Get: 86 http://deb.debian.org/debian bullseye/main i386 texlive-base all 2020.20210202-3 [20.8 MB] Get: 87 http://deb.debian.org/debian bullseye/main i386 texlive-fonts-recommended all 2020.20210202-3 [5002 kB] Get: 88 http://deb.debian.org/debian bullseye/main i386 fonts-lmodern all 2.004.5-6.1 [4540 kB] Get: 89 http://deb.debian.org/debian bullseye/main i386 texlive-latex-base all 2020.20210202-3 [1120 kB] Get: 90 http://deb.debian.org/debian bullseye/main i386 texlive-latex-recommended all 2020.20210202-3 [14.5 MB] Get: 91 http://deb.debian.org/debian bullseye/main i386 texlive all 2020.20210202-3 [34.2 kB] Get: 92 http://deb.debian.org/debian bullseye/main i386 texlive-bibtex-extra all 2020.20210202-3 [67.2 MB] Get: 93 http://deb.debian.org/debian bullseye/main i386 libthai-data all 0.1.28-3 [170 kB] Get: 94 http://deb.debian.org/debian bullseye/main i386 libdatrie1 i386 0.2.13-1 [44.5 kB] Get: 95 http://deb.debian.org/debian bullseye/main i386 libthai0 i386 0.1.28-3 [55.3 kB] Get: 96 http://deb.debian.org/debian bullseye/main i386 libsombok3 i386 2.4.0-2+b1 [33.2 kB] Get: 97 http://deb.debian.org/debian bullseye/main i386 libmime-charset-perl all 1.012.2-1 [35.4 kB] Get: 98 http://deb.debian.org/debian bullseye/main i386 libunicode-linebreak-perl i386 0.0.20190101-1+b2 [106 kB] Get: 99 http://deb.debian.org/debian bullseye/main i386 libjs-jquery all 3.5.1+dfsg+~3.5.5-7 [315 kB] Get: 100 http://deb.debian.org/debian bullseye/main i386 libfontenc1 i386 1:1.1.4-1 [24.5 kB] Get: 101 http://deb.debian.org/debian bullseye/main i386 xfonts-encodings all 1:1.0.4-2.1 [573 kB] Get: 102 http://deb.debian.org/debian bullseye/main i386 xfonts-utils i386 1:7.7+6 [95.2 kB] Get: 103 http://deb.debian.org/debian bullseye/main i386 lmodern all 2.004.5-6.1 [9489 kB] Get: 104 http://deb.debian.org/debian bullseye/main i386 texlive-luatex all 2020.20210202-3 [14.4 MB] Get: 105 http://deb.debian.org/debian bullseye/main i386 texlive-plain-generic all 2020.20210202-3 [27.0 MB] Get: 106 http://deb.debian.org/debian bullseye/main i386 texlive-extra-utils all 2020.20210202-3 [55.5 MB] Get: 107 http://deb.debian.org/debian bullseye/main i386 libapache-pom-java all 18-1 [4676 B] Get: 108 http://deb.debian.org/debian bullseye/main i386 libcommons-parent-java all 43-1 [10.8 kB] Get: 109 http://deb.debian.org/debian bullseye/main i386 libcommons-logging-java all 1.2-2 [62.2 kB] Get: 110 http://deb.debian.org/debian bullseye/main i386 libfontbox-java all 1:1.8.16-2 [211 kB] Get: 111 http://deb.debian.org/debian bullseye/main i386 libpdfbox-java all 1:1.8.16-2 [5205 kB] Get: 112 http://deb.debian.org/debian bullseye/main i386 preview-latex-style all 12.2-1 [201 kB] Get: 113 http://deb.debian.org/debian bullseye/main i386 texlive-pictures all 2020.20210202-3 [6743 kB] Get: 114 http://deb.debian.org/debian bullseye/main i386 texlive-latex-extra all 2020.20210202-3 [13.7 MB] Get: 115 http://deb.debian.org/debian bullseye/main i386 fonts-gfs-baskerville all 1.1-6 [43.7 kB] Get: 116 http://deb.debian.org/debian bullseye/main i386 fonts-gfs-porson all 1.1-7 [33.8 kB] Get: 117 http://deb.debian.org/debian bullseye/main i386 texlive-lang-greek all 2020.20210202-2 [77.6 MB] Get: 118 http://deb.debian.org/debian bullseye/main i386 texlive-science all 2020.20210202-3 [3367 kB] Get: 119 http://deb.debian.org/debian bullseye/main i386 libxml2 i386 2.9.10+dfsg-6.7+deb11u4 [728 kB] Get: 120 http://deb.debian.org/debian bullseye/main i386 libxslt1.1 i386 1.1.34-4+deb11u1 [251 kB] Get: 121 http://deb.debian.org/debian bullseye/main i386 xsltproc i386 1.1.34-4+deb11u1 [124 kB] Get: 122 http://deb.debian.org/debian bullseye/main i386 dblatex all 0.3.12py3-1 [371 kB] Get: 123 http://deb.debian.org/debian bullseye/main i386 libdebhelper-perl all 13.3.4 [189 kB] Get: 124 http://deb.debian.org/debian bullseye/main i386 libtool all 2.4.6-15 [513 kB] Get: 125 http://deb.debian.org/debian bullseye/main i386 dh-autoreconf all 20 [17.1 kB] Get: 126 http://deb.debian.org/debian bullseye/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 127 http://deb.debian.org/debian bullseye/main i386 libsub-override-perl all 0.09-2 [10.2 kB] Get: 128 http://deb.debian.org/debian bullseye/main i386 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 129 http://deb.debian.org/debian bullseye/main i386 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 130 http://deb.debian.org/debian bullseye/main i386 libelf1 i386 0.183-1 [171 kB] Get: 131 http://deb.debian.org/debian bullseye/main i386 dwz i386 0.13+20210201-1 [179 kB] Get: 132 http://deb.debian.org/debian bullseye/main i386 gettext i386 0.21-4 [1322 kB] Get: 133 http://deb.debian.org/debian bullseye/main i386 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 134 http://deb.debian.org/debian bullseye/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 135 http://deb.debian.org/debian bullseye/main i386 debhelper all 13.3.4 [1049 kB] Get: 136 http://deb.debian.org/debian bullseye/main i386 docbook-xsl all 1.79.2+dfsg-1 [1237 kB] Get: 137 http://deb.debian.org/debian bullseye/main i386 icu-devtools i386 67.1-7 [209 kB] Get: 138 http://deb.debian.org/debian bullseye/main i386 libboost1.74-dev i386 1.74.0-9 [9534 kB] Get: 139 http://deb.debian.org/debian bullseye/main i386 libboost-atomic1.74.0 i386 1.74.0-9 [244 kB] Get: 140 http://deb.debian.org/debian bullseye/main i386 libboost-atomic1.74-dev i386 1.74.0-9 [245 kB] Get: 141 http://deb.debian.org/debian bullseye/main i386 libboost-chrono1.74.0 i386 1.74.0-9 [254 kB] Get: 142 http://deb.debian.org/debian bullseye/main i386 libboost-chrono1.74-dev i386 1.74.0-9 [262 kB] Get: 143 http://deb.debian.org/debian bullseye/main i386 libboost-date-time1.74.0 i386 1.74.0-9 [241 kB] Get: 144 http://deb.debian.org/debian bullseye/main i386 libboost-serialization1.74.0 i386 1.74.0-9 [346 kB] Get: 145 http://deb.debian.org/debian bullseye/main i386 libboost-serialization1.74-dev i386 1.74.0-9 [390 kB] Get: 146 http://deb.debian.org/debian bullseye/main i386 libboost-date-time1.74-dev i386 1.74.0-9 [250 kB] Get: 147 http://deb.debian.org/debian bullseye/main i386 libboost-filesystem1.74.0 i386 1.74.0-9 [288 kB] Get: 148 http://deb.debian.org/debian bullseye/main i386 libboost-system1.74.0 i386 1.74.0-9 [241 kB] Get: 149 http://deb.debian.org/debian bullseye/main i386 libboost-system1.74-dev i386 1.74.0-9 [243 kB] Get: 150 http://deb.debian.org/debian bullseye/main i386 libboost-filesystem1.74-dev i386 1.74.0-9 [311 kB] Get: 151 http://deb.debian.org/debian bullseye/main i386 libboost-filesystem-dev i386 1.74.0.3 [4368 B] Get: 152 http://deb.debian.org/debian bullseye/main i386 libboost-regex1.74.0 i386 1.74.0-9 [542 kB] Get: 153 http://deb.debian.org/debian bullseye/main i386 libicu-dev i386 67.1-7 [9801 kB] Get: 154 http://deb.debian.org/debian bullseye/main i386 libboost-regex1.74-dev i386 1.74.0-9 [618 kB] Get: 155 http://deb.debian.org/debian bullseye/main i386 libboost-iostreams1.74-dev i386 1.74.0-9 [275 kB] Get: 156 http://deb.debian.org/debian bullseye/main i386 libboost-iostreams-dev i386 1.74.0.3 [4320 B] Get: 157 http://deb.debian.org/debian bullseye/main i386 libboost-regex-dev i386 1.74.0.3 [4596 B] Get: 158 http://deb.debian.org/debian bullseye/main i386 libboost-system-dev i386 1.74.0.3 [4472 B] Get: 159 http://deb.debian.org/debian bullseye/main i386 libboost-thread1.74.0 i386 1.74.0-9 [282 kB] Get: 160 http://deb.debian.org/debian bullseye/main i386 libboost-thread1.74-dev i386 1.74.0-9 [294 kB] Get: 161 http://deb.debian.org/debian bullseye/main i386 libboost-thread-dev i386 1.74.0.3 [4356 B] Get: 162 http://deb.debian.org/debian bullseye/main i386 libbz2-dev i386 1.0.8-4 [31.3 kB] Get: 163 http://deb.debian.org/debian bullseye/main i386 libexpat1-dev i386 2.2.10-2+deb11u5 [149 kB] Get: 164 http://deb.debian.org/debian bullseye/main i386 libfl2 i386 2.6.4-8 [103 kB] Get: 165 http://deb.debian.org/debian bullseye/main i386 libfl-dev i386 2.6.4-8 [105 kB] Get: 166 http://deb.debian.org/debian bullseye/main i386 libtcmalloc-minimal4 i386 2.8.1-1 [94.9 kB] Get: 167 http://deb.debian.org/debian bullseye/main i386 libgoogle-perftools4 i386 2.8.1-1 [203 kB] Get: 168 http://deb.debian.org/debian bullseye/main i386 libgoogle-perftools-dev i386 2.8.1-1 [463 kB] Get: 169 http://deb.debian.org/debian bullseye/main i386 zlib1g-dev i386 1:1.2.11.dfsg-2+deb11u2 [194 kB] Fetched 404 MB in 3min 2s (2221 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 17763 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.36.1-8+deb11u1_i386.deb ... Unpacking bsdextrautils (2.36.1-8+deb11u1) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../01-libuchardet0_0.0.7-1_i386.deb ... Unpacking libuchardet0:i386 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-6_i386.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../03-libpipeline1_1.5.3-1_i386.deb ... Unpacking libpipeline1:i386 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.9.4-2_i386.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package autoconf-archive. Preparing to unpack .../05-autoconf-archive_20190106-2.1_all.deb ... Unpacking autoconf-archive (20190106-2.1) ... Selecting previously unselected package libsigsegv2:i386. Preparing to unpack .../06-libsigsegv2_2.13-1_i386.deb ... Unpacking libsigsegv2:i386 (2.13-1) ... Selecting previously unselected package m4. Preparing to unpack .../07-m4_1.4.18-5_i386.deb ... Unpacking m4 (1.4.18-5) ... Selecting previously unselected package flex. Preparing to unpack .../08-flex_2.6.4-8_i386.deb ... Unpacking flex (2.6.4-8) ... Selecting previously unselected package libpython3.9-minimal:i386. Preparing to unpack .../09-libpython3.9-minimal_3.9.2-1_i386.deb ... Unpacking libpython3.9-minimal:i386 (3.9.2-1) ... Selecting previously unselected package libexpat1:i386. Preparing to unpack .../10-libexpat1_2.2.10-2+deb11u5_i386.deb ... Unpacking libexpat1:i386 (2.2.10-2+deb11u5) ... Selecting previously unselected package python3.9-minimal. Preparing to unpack .../11-python3.9-minimal_3.9.2-1_i386.deb ... Unpacking python3.9-minimal (3.9.2-1) ... Setting up libpython3.9-minimal:i386 (3.9.2-1) ... Setting up libexpat1:i386 (2.2.10-2+deb11u5) ... Setting up python3.9-minimal (3.9.2-1) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19959 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.9.2-3_i386.deb ... Unpacking python3-minimal (3.9.2-3) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_4.0.0_all.deb ... Unpacking media-types (4.0.0) ... Selecting previously unselected package tzdata. Preparing to unpack .../2-tzdata_2021a-1+deb11u10_all.deb ... Unpacking tzdata (2021a-1+deb11u10) ... Selecting previously unselected package libmpdec3:i386. Preparing to unpack .../3-libmpdec3_2.5.1-1_i386.deb ... Unpacking libmpdec3:i386 (2.5.1-1) ... Selecting previously unselected package readline-common. Preparing to unpack .../4-readline-common_8.1-1_all.deb ... Unpacking readline-common (8.1-1) ... Selecting previously unselected package libreadline8:i386. Preparing to unpack .../5-libreadline8_8.1-1_i386.deb ... Unpacking libreadline8:i386 (8.1-1) ... Selecting previously unselected package libpython3.9-stdlib:i386. Preparing to unpack .../6-libpython3.9-stdlib_3.9.2-1_i386.deb ... Unpacking libpython3.9-stdlib:i386 (3.9.2-1) ... Selecting previously unselected package python3.9. Preparing to unpack .../7-python3.9_3.9.2-1_i386.deb ... Unpacking python3.9 (3.9.2-1) ... Selecting previously unselected package libpython3-stdlib:i386. Preparing to unpack .../8-libpython3-stdlib_3.9.2-3_i386.deb ... Unpacking libpython3-stdlib:i386 (3.9.2-3) ... Setting up python3-minimal (3.9.2-3) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 22242 files and directories currently installed.) Preparing to unpack .../000-python3_3.9.2-3_i386.deb ... Unpacking python3 (3.9.2-3) ... Selecting previously unselected package sgml-base. Preparing to unpack .../001-sgml-base_1.30_all.deb ... Unpacking sgml-base (1.30) ... Selecting previously unselected package sensible-utils. 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Unpacking libboost-system1.74-dev:i386 (1.74.0-9) ... Selecting previously unselected package libboost-filesystem1.74-dev:i386. Preparing to unpack .../128-libboost-filesystem1.74-dev_1.74.0-9_i386.deb ... Unpacking libboost-filesystem1.74-dev:i386 (1.74.0-9) ... Selecting previously unselected package libboost-filesystem-dev:i386. Preparing to unpack .../129-libboost-filesystem-dev_1.74.0.3_i386.deb ... Unpacking libboost-filesystem-dev:i386 (1.74.0.3) ... Selecting previously unselected package libboost-regex1.74.0:i386. Preparing to unpack .../130-libboost-regex1.74.0_1.74.0-9_i386.deb ... Unpacking libboost-regex1.74.0:i386 (1.74.0-9) ... Selecting previously unselected package libicu-dev:i386. Preparing to unpack .../131-libicu-dev_67.1-7_i386.deb ... Unpacking libicu-dev:i386 (67.1-7) ... Selecting previously unselected package libboost-regex1.74-dev:i386. Preparing to unpack .../132-libboost-regex1.74-dev_1.74.0-9_i386.deb ... Unpacking libboost-regex1.74-dev:i386 (1.74.0-9) ... Selecting previously unselected package libboost-iostreams1.74-dev:i386. Preparing to unpack .../133-libboost-iostreams1.74-dev_1.74.0-9_i386.deb ... Unpacking libboost-iostreams1.74-dev:i386 (1.74.0-9) ... Selecting previously unselected package libboost-iostreams-dev:i386. Preparing to unpack .../134-libboost-iostreams-dev_1.74.0.3_i386.deb ... Unpacking libboost-iostreams-dev:i386 (1.74.0.3) ... Selecting previously unselected package libboost-regex-dev:i386. Preparing to unpack .../135-libboost-regex-dev_1.74.0.3_i386.deb ... Unpacking libboost-regex-dev:i386 (1.74.0.3) ... Selecting previously unselected package libboost-system-dev:i386. Preparing to unpack .../136-libboost-system-dev_1.74.0.3_i386.deb ... Unpacking libboost-system-dev:i386 (1.74.0.3) ... Selecting previously unselected package libboost-thread1.74.0:i386. Preparing to unpack .../137-libboost-thread1.74.0_1.74.0-9_i386.deb ... Unpacking libboost-thread1.74.0:i386 (1.74.0-9) ... Selecting previously unselected package libboost-thread1.74-dev:i386. Preparing to unpack .../138-libboost-thread1.74-dev_1.74.0-9_i386.deb ... Unpacking libboost-thread1.74-dev:i386 (1.74.0-9) ... Selecting previously unselected package libboost-thread-dev:i386. Preparing to unpack .../139-libboost-thread-dev_1.74.0.3_i386.deb ... Unpacking libboost-thread-dev:i386 (1.74.0.3) ... Selecting previously unselected package libbz2-dev:i386. Preparing to unpack .../140-libbz2-dev_1.0.8-4_i386.deb ... Unpacking libbz2-dev:i386 (1.0.8-4) ... Selecting previously unselected package libexpat1-dev:i386. Preparing to unpack .../141-libexpat1-dev_2.2.10-2+deb11u5_i386.deb ... Unpacking libexpat1-dev:i386 (2.2.10-2+deb11u5) ... Selecting previously unselected package libfl2:i386. Preparing to unpack .../142-libfl2_2.6.4-8_i386.deb ... Unpacking libfl2:i386 (2.6.4-8) ... Selecting previously unselected package libfl-dev:i386. Preparing to unpack .../143-libfl-dev_2.6.4-8_i386.deb ... Unpacking libfl-dev:i386 (2.6.4-8) ... Selecting previously unselected package libtcmalloc-minimal4:i386. Preparing to unpack .../144-libtcmalloc-minimal4_2.8.1-1_i386.deb ... Unpacking libtcmalloc-minimal4:i386 (2.8.1-1) ... Selecting previously unselected package libgoogle-perftools4:i386. Preparing to unpack .../145-libgoogle-perftools4_2.8.1-1_i386.deb ... Unpacking libgoogle-perftools4:i386 (2.8.1-1) ... Selecting previously unselected package libgoogle-perftools-dev:i386. Preparing to unpack .../146-libgoogle-perftools-dev_2.8.1-1_i386.deb ... Unpacking libgoogle-perftools-dev:i386 (2.8.1-1) ... Selecting previously unselected package zlib1g-dev:i386. Preparing to unpack .../147-zlib1g-dev_1%3a1.2.11.dfsg-2+deb11u2_i386.deb ... Unpacking zlib1g-dev:i386 (1:1.2.11.dfsg-2+deb11u2) ... Setting up libboost-chrono1.74.0:i386 (1.74.0-9) ... Setting up media-types (4.0.0) ... Setting up libpipeline1:i386 (1.5.3-1) ... Setting up libboost-system1.74.0:i386 (1.74.0-9) ... Setting up libgraphite2-3:i386 (1.3.14-1) ... Setting up libpixman-1-0:i386 (0.40.0-1.1~deb11u1) ... Setting up libxau6:i386 (1:1.0.9-1) ... Setting up libboost1.74-dev:i386 (1.74.0-9) ... Setting up libboost-atomic1.74.0:i386 (1.74.0-9) ... Setting up bsdextrautils (2.36.1-8+deb11u1) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up fonts-gfs-porson (1.1-7) ... Setting up libicu67:i386 (67.1-7) ... Setting up libdatrie1:i386 (0.2.13-1) ... Setting up libmagic-mgc (1:5.39-3+deb11u1) ... Setting up libtexlua53:i386 (2020.20200327.54578-7+deb11u1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libglib2.0-0:i386 (2.66.8-1) ... No schema files found: doing nothing. Setting up distro-info-data (0.51+deb11u4) ... Setting up libtexluajit2:i386 (2020.20200327.54578-7+deb11u1) ... Setting up libdebhelper-perl (13.3.4) ... Setting up libbrotli1:i386 (1.0.9-2+b2) ... Setting up libfontbox-java (1:1.8.16-2) ... Setting up libboost-chrono1.74-dev:i386 (1.74.0-9) ... Setting up x11-common (1:7.7+22) ... invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libtcmalloc-minimal4:i386 (2.8.1-1) ... Setting up libmagic1:i386 (1:5.39-3+deb11u1) ... Setting up gettext-base (0.21-4) ... Setting up libboost-filesystem1.74.0:i386 (1.74.0-9) ... Setting up autoconf-archive (20190106-2.1) ... Setting up libzzip-0-13:i386 (0.13.62-3.3+deb11u1) ... Setting up file (1:5.39-3+deb11u1) ... Setting up xxd (2:8.2.2434-3+deb11u1) ... Setting up tzdata (2021a-1+deb11u10) ... Current default time zone: 'Etc/UTC' Local time is now: Fri Jan 12 20:21:13 UTC 2024. Universal Time is now: Fri Jan 12 20:21:13 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libfontenc1:i386 (1:1.1.4-1) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up vim-common (2:8.2.2434-3+deb11u1) ... Setting up libexpat1-dev:i386 (2.2.10-2+deb11u5) ... Setting up libx11-data (2:1.7.2-1+deb11u1) ... Setting up libteckit0:i386 (2.5.10+ds1-3) ... Setting up libapache-pom-java (18-1) ... Setting up libboost-system1.74-dev:i386 (1.74.0-9) ... Setting up libsigsegv2:i386 (2.13-1) ... Setting up xfonts-encodings (1:1.0.4-2.1) ... Setting up libboost-regex1.74.0:i386 (1.74.0-9) ... Setting up t1utils (1.41-4) ... Setting up libpng16-16:i386 (1.6.37-3) ... Setting up autopoint (0.21-4) ... Setting up icu-devtools (67.1-7) ... Setting up fonts-dejavu-core (2.37-2) ... Setting up libfl2:i386 (2.6.4-8) ... Setting up libkpathsea6:i386 (2020.20200327.54578-7+deb11u1) ... Setting up libboost-atomic1.74-dev:i386 (1.74.0-9) ... Setting up libboost-serialization1.74.0:i386 (1.74.0-9) ... Setting up zlib1g-dev:i386 (1:1.2.11.dfsg-2+deb11u2) ... Setting up libmd0:i386 (1.0.3-3) ... Setting up python-apt-common (2.2.1) ... Setting up fonts-gfs-baskerville (1.1-6) ... Setting up sensible-utils (0.0.14) ... Setting up libmime-charset-perl (1.012.2-1) ... Setting up libuchardet0:i386 (0.0.7-1) ... Setting up libmpdec3:i386 (2.5.1-1) ... Setting up fonts-lmodern (2.004.5-6.1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libthai-data (0.1.28-3) ... Setting up sgml-base (1.30) ... Setting up libboost-filesystem1.74-dev:i386 (1.74.0-9) ... Setting up libjs-jquery (3.5.1+dfsg+~3.5.5-7) ... Setting up libboost-date-time1.74.0:i386 (1.74.0-9) ... Setting up libbsd0:i386 (0.11.3-1+deb11u1) ... Setting up libelf1:i386 (0.183-1) ... Setting up readline-common (8.1-1) ... Setting up libicu-dev:i386 (67.1-7) ... Setting up libxml2:i386 (2.9.10+dfsg-6.7+deb11u4) ... Setting up xdg-utils (1.1.3-4.1) ... update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode Setting up libboost-filesystem-dev:i386 (1.74.0.3) ... Setting up libgoogle-perftools4:i386 (2.8.1-1) ... Setting up libsynctex2:i386 (2020.20200327.54578-7+deb11u1) ... Setting up libboost-thread1.74.0:i386 (1.74.0-9) ... Setting up libbz2-dev:i386 (1.0.8-4) ... Setting up libfile-stripnondeterminism-perl (1.12.0-1) ... Setting up libice6:i386 (2:1.0.10-1) ... Setting up libxdmcp6:i386 (1:1.1.2-3) ... Setting up libxcb1:i386 (1.14-3) ... Setting up gettext (0.21-4) ... Setting up libpdfbox-java (1:1.8.16-2) ... Setting up libtool (2.4.6-15) ... Setting up libxcb-render0:i386 (1.14-3) ... Setting up libgoogle-perftools-dev:i386 (2.8.1-1) ... Setting up libreadline8:i386 (8.1-1) ... Setting up libboost-system-dev:i386 (1.74.0.3) ... Setting up libcommons-parent-java (43-1) ... Setting up libcommons-logging-java (1.2-2) ... Setting up m4 (1.4.18-5) ... Setting up libxcb-shm0:i386 (1.14-3) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libthai0:i386 (0.1.28-3) ... Setting up libptexenc1:i386 (2020.20200327.54578-7+deb11u1) ... Setting up libfreetype6:i386 (2.10.4+dfsg-1+deb11u1) ... Setting up ucf (3.0043) ... Setting up autoconf (2.69-14) ... Setting up libboost-serialization1.74-dev:i386 (1.74.0-9) ... Setting up dh-strip-nondeterminism (1.12.0-1) ... Setting up dwz (0.13+20210201-1) ... Setting up libboost-regex1.74-dev:i386 (1.74.0-9) ... Setting up groff-base (1.22.4-6) ... Setting up xml-core (0.18+nmu1) ... Setting up libxslt1.1:i386 (1.1.34-4+deb11u1) ... Setting up libx11-6:i386 (2:1.7.2-1+deb11u1) ... Setting up libharfbuzz0b:i386 (2.7.4-1) ... Setting up libboost-regex-dev:i386 (1.74.0.3) ... Setting up libsm6:i386 (2:1.2.3-1) ... Setting up libpython3.9-stdlib:i386 (3.9.2-1) ... Setting up libpython3-stdlib:i386 (3.9.2-3) ... Setting up automake (1:1.16.3-2) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libpaper1:i386 (1.1.28+b1) ... Creating config file /etc/papersize with new version Setting up flex (2.6.4-8) ... Setting up libxpm4:i386 (1:3.5.12-1.1~deb11u1) ... Setting up libxrender1:i386 (1:0.9.10-1) ... Setting up libsombok3:i386 (2.4.0-2+b1) ... Setting up fontconfig-config (2.13.1-4.2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up xsltproc (1.1.34-4+deb11u1) ... Setting up libxext6:i386 (2:1.3.3-1.1) ... Setting up libpaper-utils (1.1.28+b1) ... Setting up xfonts-utils (1:7.7+6) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libfl-dev:i386 (2.6.4-8) ... Setting up libboost-iostreams1.74-dev:i386 (1.74.0-9) ... Setting up dh-autoreconf (20) ... Setting up tex-common (6.16) ... update-language: texlive-base not installed and configured, doing nothing! Setting up libboost-date-time1.74-dev:i386 (1.74.0-9) ... Setting up libunicode-linebreak-perl (0.0.20190101-1+b2) ... Setting up libxt6:i386 (1:1.2.0-1) ... Setting up lmodern (2.004.5-6.1) ... Setting up libboost-thread1.74-dev:i386 (1.74.0-9) ... Setting up libfontconfig1:i386 (2.13.1-4.2) ... Setting up python3.9 (3.9.2-1) ... Setting up libboost-thread-dev:i386 (1.74.0.3) ... Setting up libxmu6:i386 (2:1.1.2-2+b3) ... Setting up libxi6:i386 (2:1.7.10-1) ... Setting up preview-latex-style (12.2-1) ... Setting up debhelper (13.3.4) ... Setting up python3 (3.9.2-3) ... Setting up libxaw7:i386 (2:1.0.13-1.1) ... Setting up libboost-iostreams-dev:i386 (1.74.0.3) ... Setting up libcairo2:i386 (1.16.0-5) ... Setting up texlive-binaries (2020.20200327.54578-7+deb11u1) ... 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 (2020.20210202-3) ... 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 (2020.20210202-3) ... Setting up python3-apt (2.2.1) ... Setting up texlive-plain-generic (2020.20210202-3) ... Setting up texlive-lang-greek (2020.20210202-2) ... Setting up texlive-latex-base (2020.20210202-3) ... Setting up texlive-extra-utils (2020.20210202-3) ... Setting up texlive-latex-recommended (2020.20210202-3) ... Setting up texlive-pictures (2020.20210202-3) ... Setting up texlive-fonts-recommended (2020.20210202-3) ... Setting up texlive (2020.20210202-3) ... Setting up texlive-science (2020.20210202-3) ... Setting up texlive-latex-extra (2020.20210202-3) ... Setting up texlive-bibtex-extra (2020.20210202-3) ... Processing triggers for libc-bin (2.31-13+deb11u6) ... Processing triggers for sgml-base (1.30) ... Setting up docbook-xsl (1.79.2+dfsg-1) ... Setting up sgml-data (2.0.11+nmu1) ... Processing triggers for sgml-base (1.30) ... Setting up docbook-xml (4.5-9) ... Processing triggers for sgml-base (1.30) ... Setting up dblatex (0.3.12py3-1) ... Processing triggers for tex-common (6.16) ... 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/10537/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for bullseye I: user script /srv/workspace/pbuilder/10537/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_4.9.6-5_source.changes dpkg-buildpackage: info: source package mira dpkg-buildpackage: info: source version 4.9.6-5 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nilesh Patra dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/mira-4.9.6' ( cd doc ; make clean ) || true make[2]: Entering directory '/build/reproducible-path/mira-4.9.6/doc' cd .. && make am--refresh make[3]: Entering directory '/build/reproducible-path/mira-4.9.6' make[3]: *** No rule to make target 'am--refresh'. Stop. make[3]: Leaving directory '/build/reproducible-path/mira-4.9.6' make[2]: *** [Makefile:263: ../config.status] Error 2 make[2]: Leaving directory '/build/reproducible-path/mira-4.9.6/doc' dh_auto_clean || true install -d /build/reproducible-path/mira-4.9.6/debian/.debhelper/generated/_source/home find * -name Makefile -exec rm '{}' ';' find * -name '*.xxd.H' -exec rm '{}' ';' find * -name '*.par.H' -exec rm '{}' ';' find * -name 'compileinfo.*' -exec rm '{}' ';' 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 \ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \) debian/rules binary dh binary dh_update_autotools_config install -d debian/.debhelper/bucket/files 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: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 dh_auto_configure install -d /build/reproducible-path/mira-4.9.6/debian/.debhelper/generated/_source/home ./configure --build=i686-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/i386-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether UID '2222' is supported by ustar format... yes checking whether GID '2222' is supported by ustar format... yes checking how to create a ustar tar archive... gnutar checking for a sed that does not truncate output... /bin/sed checking whether to add --prefix as include path... yes +++++++++++++++++++++++++++++++++++++ systemuname: Linux CFLAGS now: -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include CXXFLAGS now: -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include LDFLAGS now: -Wl,-z,relro -Wl,-z,now -L/usr/lib +++++++++++++++++++++++++++++++++++++ checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... 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 we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes 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 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include CXXFLAGS now: -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include LDFLAGS now: -Wl,-z,relro -Wl,-z,now -L/usr/lib +++++++++++++++++++++++++++++++++++++ checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for int64_t... yes +++++++++++++++++++++++++++++++++++++ CFLAGS now: -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include CXXFLAGS now: -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include LDFLAGS now: -Wl,-z,relro -Wl,-z,now -L/usr/lib +++++++++++++++++++++++++++++++++++++ checking whether long has 64bit... no checking whether enabling 64bit compilation support... no checking build system type... i686-pc-linux-gnu checking for compiler optimisation settings... -O3 -funroll-loops +++++++++++++++++++++++++++++++++++++ CFLAGS now: -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops CXXFLAGS now: -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops LDFLAGS now: -Wl,-z,relro -Wl,-z,now -L/usr/lib +++++++++++++++++++++++++++++++++++++ checking host system type... i686-pc-linux-gnu checking how to print strings... printf checking for a sed that does not truncate output... (cached) /bin/sed checking for fgrep... /bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert i686-pc-linux-gnu file names to i686-pc-linux-gnu format... func_convert_file_noop checking how to convert i686-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /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 lex output file root... lex.yy checking lex library... -lfl checking whether yytext is a pointer... yes checking for flex++... yes checking for xxd... yes checking for ANSI C header files... (cached) yes checking for stdbool.h that conforms to C99... yes checking for _Bool... 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 stdlib.h... (cached) yes checking for GNU libc compatible malloc... yes checking for stdlib.h... (cached) 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 special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... 64 checking for _LARGEFILE_SOURCE value needed for large files... no checking for isblank... yes +++++++++++++++++++++++++++++++++++++ CFLAGS now: -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops CXXFLAGS now: -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops LDFLAGS now: -Wl,-z,relro -Wl,-z,now -L/usr/lib +++++++++++++++++++++++++++++++++++++ checking for boostlib >= 1.48.0... yes +++++++++++++++++++++++++++++++++++++ BOOST_CPPFLAGS: -I/usr/include BOOST LDFLAGS: -L/usr/lib/i386-linux-gnu ac_boost_path: ac_boost_lib_path: CFLAGS now: -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops CXXFLAGS now: -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops LDFLAGS now: -Wl,-z,relro -Wl,-z,now -L/usr/lib +++++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++++++++++++++ BOOST_CPPFLAGS: -I/usr/include BOOST LDFLAGS: -L/usr/lib/i386-linux-gnu CFLAGS now: -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -Wl,-rpath, CXXFLAGS now: -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops LDFLAGS now: -Wl,-z,relro -Wl,-z,now -L/usr/lib +++++++++++++++++++++++++++++++++++++ checking whether the Boost::Thread library is available... yes checking for exit in -lboost_thread... yes +++++++++++++++++++++++++++++++++++++ BOOST_CPPFLAGS: -pthread -I/usr/include BOOST LDFLAGS: -L/usr/lib/i386-linux-gnu ac_boost_path: ac_boost_lib_path: BOOST_THREAD_LIB: -lboost_thread CFLAGS now: -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -Wl,-rpath, CXXFLAGS now: -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops LDFLAGS now: -Wl,-z,relro -Wl,-z,now -L/usr/lib +++++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++++++++++++++ BOOST_CPPFLAGS: -pthread -I/usr/include BOOST LDFLAGS: -L/usr/lib/i386-linux-gnu ac_boost_path: ac_boost_lib_path: BOOST_THREAD_LIB: -lboost_thread CFLAGS now: -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -Wl,-rpath, CXXFLAGS now: -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include LDFLAGS now: -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/i386-linux-gnu LIBS now: -lboost_thread +++++++++++++++++++++++++++++++++++++ checking whether the Boost::Regex library is available... yes checking for exit in -lboost_regex... yes +++++++++++++++++++++++++++++++++++++ BOOST_CPPFLAGS: -pthread -I/usr/include BOOST LDFLAGS: -L/usr/lib/i386-linux-gnu ac_boost_path: ac_boost_lib_path: BOOST_REGEX_LIB: -lboost_regex CFLAGS now: -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -Wl,-rpath, CXXFLAGS now: -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include LIBS now: -lboost_thread -lboost_regex +++++++++++++++++++++++++++++++++++++ checking whether the Boost::System library is available... yes checking for exit in -lboost_system... yes +++++++++++++++++++++++++++++++++++++ BOOST_CPPFLAGS: -pthread -I/usr/include BOOST LDFLAGS: -L/usr/lib/i386-linux-gnu ac_boost_path: ac_boost_lib_path: BOOST_SYSTEM_LIB: -lboost_system CFLAGS now: -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -Wl,-rpath, CXXFLAGS now: -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include LIBS now: -lboost_thread -lboost_regex -lboost_system +++++++++++++++++++++++++++++++++++++ checking whether the Boost::Filesystem library is available... yes checking for exit in -lboost_filesystem... yes +++++++++++++++++++++++++++++++++++++ BOOST_CPPFLAGS: -pthread -I/usr/include BOOST LDFLAGS: -L/usr/lib/i386-linux-gnu ac_boost_path: ac_boost_lib_path: BOOST_FILESYSTEM_LIB: -lboost_filesystem CFLAGS now: -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -Wl,-rpath, CXXFLAGS now: -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include LIBS now: -lboost_thread -lboost_regex -lboost_system -lboost_filesystem +++++++++++++++++++++++++++++++++++++ checking whether the Boost::IOStreams library is available... yes checking for exit in -lboost_iostreams... yes +++++++++++++++++++++++++++++++++++++ BOOST_CPPFLAGS: -pthread -I/usr/include BOOST LDFLAGS: -L/usr/lib/i386-linux-gnu ac_boost_path: ac_boost_lib_path: BOOST_IOSTREAMS_LIB: -lboost_iostreams CFLAGS now: -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -Wl,-rpath, CXXFLAGS now: -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include LIBS now: -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams +++++++++++++++++++++++++++++++++++++ checking for clock_gettime in -lrt... yes +++++++++++++++++++++++++++++++++++++ Need to specifically use rt library LIBS now: -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt +++++++++++++++++++++++++++++++++++++ BOOST is through, yay. +++++++++++++++++++++++++++++++++++++ CFLAGS now: -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops CXXFLAGS now: -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include LDFLAGS now: -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/i386-linux-gnu LIBS now: -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt +++++++++++++++++++++++++++++++++++++ checking for Expat XML Parser headers in /usr/include... found checking for Expat XML Parser libraries... found checking for Expat XML Parser... yes +++++++++++++++++++++++++++++++++++++ CFLAGS now: -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -I/usr/include CXXFLAGS now: -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include LDFLAGS now: -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/i386-linux-gnu -L/usr/lib LIBS now: -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt -lexpat +++++++++++++++++++++++++++++++++++++ checking if zlib is wanted... yes +++++++++++++++++++++++++++++++++++++ CFLAGS now: -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -I/usr/include CXXFLAGS now: -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include LDFLAGS now: -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/i386-linux-gnu -L/usr/lib LIBS now: -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt -lexpat -lm -lz +++++++++++++++++++++++++++++++++++++ checking for gzoffset in -lz... yes checking for BZ2_bzRead in -lbz2... yes checking for flex version compatible with MIRA... yes checking for profiling settings... no checking for purify... no checking whether mira should compile in public quiet mode... yes checking whether mira should compile with bound tracking... yes checking whether mira should compile with bug tracking... yes checking whether mira should compile with extended bug tracking... no checking whether mira should compile with function trace... no checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating src/other/Makefile config.status: creating src/other/sls/Makefile config.status: creating src/other/sls/mira-createsls/Makefile config.status: creating src/other/sls/mira-createsls/bin/Makefile config.status: creating src/stdinc/Makefile config.status: creating src/debuggersupport/Makefile config.status: creating src/memorc/Makefile config.status: creating src/errorhandling/Makefile config.status: creating src/util/Makefile config.status: creating src/io/Makefile config.status: creating src/mira/Makefile config.status: creating src/caf/Makefile config.status: creating src/support/Makefile config.status: creating src/scripts/Makefile config.status: creating src/modules/Makefile config.status: creating src/version/Makefile config.status: creating src/progs/Makefile config.status: creating man/Makefile config.status: creating doc/Makefile config.status: creating doc/docbook/Makefile config.status: creating distribution/Makefile config.status: executing depfiles commands config.status: executing libtool commands -------------------------------------------------------------------------------- Summary of MIRA configuration -------------------------------------------------------------------------------- Building version ................................. 4.9.6_linux-gnu_i686_32_dynamic We are building on ............................... Linux CPU supports 64 bit? ............................. no Compiler family .................................. gcc Compiler optimisation flags used ................. -O3 -funroll-loops Building completely static? ...................... no BOOST expected to compile and link? .............. yes Have OpenMP? ..................................... yes Have complete zlib support? ...................... yes Can MIRA be built on this system? ................ yes Using CFLAGS : -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -I/usr/include -Werror=uninitialized -Werror=return-type -fopenmp Using CXXFLAGS : -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp Using LDFLAGS : -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/i386-linux-gnu -L/usr/lib Using LIBS : -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt -lexpat -lm -lz -lbz2 Looks good, we do not expect compilation problems. -------------------------------------------------------------------------------- Type 'make' to make the binaries and then 'make install' to install binaries and man pages. Type 'make docinstall' to install extensive documentation as HTML and PDF. 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 dh_auto_build make -j7 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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o dbgsupport.o dbgsupport.C rm -f libmiradebuggersupport.a ar cru libmiradebuggersupport.a dbgsupport.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libmiradebuggersupport.a make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/debuggersupport' Making all in io make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/io' Making .H out of .xxd mira_ft_set.xxd.H Making .H out of .xxd gap4_ft_so_map.xxd.H Reducing so.obo for smaller so.obo.xxd Making .H out of .xxd so2xgap4map.xxd.H Making .H out of .xxd oldso2so.xxd.H Making .H out of .xxd so.obo.xxd.H make all-am make[6]: Entering directory '/build/reproducible-path/mira-4.9.6/src/io' g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o annotationmappings.o annotationmappings.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o exp.o exp.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o generalio.o generalio.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o fasta.o fasta.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o fastq-mira.o fastq-mira.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o phd.o phd.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o scf.o scf.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o ncbiinfoxml.o ncbiinfoxml.C /bin/sh ../../ylwrap exp_flexer.ll lex.yy.c exp_flexer.cc -- flex g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o exp_flexer.o exp_flexer.cc rm -f libmirafio.a ar cru libmirafio.a annotationmappings.o exp.o generalio.o fasta.o fastq-mira.o phd.o scf.o ncbiinfoxml.o exp_flexer.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libmirafio.a make[6]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/io' make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/io' Making all in stdinc make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/stdinc' make[5]: Nothing to be done for 'all'. make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/stdinc' Making all in errorhandling make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/errorhandling' g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o errorhandling.o errorhandling.C rm -f libmiraerrorhandling.a ar cru libmiraerrorhandling.a errorhandling.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libmiraerrorhandling.a make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/errorhandling' Making all in util make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/util' g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o machineinfo.o machineinfo.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o fileanddisk.o fileanddisk.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o misc.o misc.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o dptools.o dptools.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o fmttext.o fmttext.C rm -f libmirafmttext.a ar cru libmirafmttext.a fmttext.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libmirafmttext.a fileanddisk.C: In function 'int64 myGZRead(gzFile_s*&, void*, uint64)': fileanddisk.C:173:12: warning: ignoring return value of 'char* strerror_r(int, char*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 173 | strerror_r(errno,buf,1024); | ~~~~~~~~~~^~~~~~~~~~~~~~~~ rm -f libmiradptools.a ar cru libmiradptools.a dptools.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libmiradptools.a rm -f libmirautil.a ar cru libmirautil.a machineinfo.o fileanddisk.o misc.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libmirautil.a make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/util' Making all in mira make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/mira' Making .H out of .xxd adaptorsforclip.454.xxd.H Making .H out of .xxd adaptorsforclip.solexa.xxd.H Making .H out of .xxd adaptorsforclip.iontor.xxd.H Making .H out of .xxd adaptorsregex.solexa.xxd.H Making .H out of .xxd adaptorsregex.iontor.xxd.H Making .H out of .xxd seqforfilter_phix174.solexa.xxd.H make all-am make[6]: Entering directory '/build/reproducible-path/mira-4.9.6/src/mira' g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o estassembly.o estassembly.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o hashstats_sdbg.o hashstats_sdbg.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o hashstats.o hashstats.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o skim.o skim.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o assembly.o assembly.C 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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o contig.o contig.C 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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o read.o read.C hashstats.C:1088: warning: "CEBUG" redefined 1088 | #define CEBUG(bla) {cout << bla; cout.flush();} | hashstats.C:83: note: this is the location of the previous definition 83 | #define CEBUG(bla) | hashstats.C:1197: warning: "CEBUG" redefined 1197 | #define CEBUG(bla) | hashstats.C:1088: note: this is the location of the previous definition 1088 | #define CEBUG(bla) {cout << bla; cout.flush();} | In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/date_time/time_clock.hpp:17, from /usr/include/boost/thread/thread_time.hpp:9, from /usr/include/boost/thread/lock_types.hpp:18, from /usr/include/boost/thread/pthread/thread_data.hpp:12, 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 + 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/bind.hpp:30, from ../../src/mira/stringcontainer.H:38, from ../../src/mira/multitag.H:40, 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 + 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/bind.hpp:30, from ../../src/mira/stringcontainer.H:38, from ../../src/mira/multitag.H:40, 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 + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/date_time/time_clock.hpp:17, from /usr/include/boost/thread/thread_time.hpp:9, from /usr/include/boost/thread/lock_types.hpp:18, from /usr/include/boost/thread/pthread/mutex.hpp:16, 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 + 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/bind.hpp:30, from ../../src/mira/stringcontainer.H:38, from ../../src/mira/multitag.H:40, 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 + 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/bind.hpp:30, from ../../src/mira/stringcontainer.H:38, from ../../src/mira/multitag.H:40, 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 + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/date_time/time_clock.hpp:17, from /usr/include/boost/thread/thread_time.hpp:9, from /usr/include/boost/thread/lock_types.hpp:18, from /usr/include/boost/thread/pthread/mutex.hpp:16, from /usr/include/boost/thread/mutex.hpp:16, from ../../src/mira/skim.H:26, 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 + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ read.C: In member function 'void Read::dumpAsReadname(std::ostream&)': read.C:1242:25: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'Read*' [-Wformat=] 1242 | sprintf(buffer, "%x", this) ; | ~^ ~~~~ | | | | | Read* | unsigned int read.C: In member function 'void Read::dumpAsFASTA(std::ostream&, bool, bool, bool)': read.C:1273:25: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'Read*' [-Wformat=] 1273 | sprintf(buffer, "%x", this) ; | ~^ ~~~~ | | | | | Read* | unsigned int read.C: In member function 'void Read::dumpAsFASTQ(std::ostream&, bool, bool, bool)': read.C:1357:25: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'Read*' [-Wformat=] 1357 | sprintf(buffer, "%x", this) ; | ~^ ~~~~ | | | | | Read* | unsigned int read.C: In member function 'void Read::dumpAsFASTAQual(std::ostream&, bool, bool, bool)': read.C:1458:25: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'Read*' [-Wformat=] 1458 | sprintf(buffer, "%x", this) ; | ~^ ~~~~ | | | | | Read* | unsigned int read.C: In member function 'void Read::dumpAsCAF(std::ostream&)': read.C:1530:25: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'Read*' [-Wformat=] 1530 | sprintf(buffer, "%x", this) ; | ~^ ~~~~ | | | | | Read* | unsigned int read.C: In member function 'void Read::dumpAsMAF(std::ostream&)': read.C:1945:25: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'Read*' [-Wformat=] 1945 | sprintf(buffer, "%x", this) ; | ~^ ~~~~ | | | | | Read* | unsigned int g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o contig_analysis.o contig_analysis.C In file included from /usr/include/boost/bind.hpp:30, from ../../src/mira/stringcontainer.H:38, from ../../src/mira/multitag.H:40, 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 + 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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o ads.o ads.C 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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o adsfacts.o adsfacts.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o align.o align.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o assembly_info.o assembly_info.C 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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o assembly_buildcontigs.o assembly_buildcontigs.C 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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o assembly_io.o assembly_io.C 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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o assembly_misc.o assembly_misc.C assembly_buildcontigs.C:80: warning: "CEBUG" redefined 80 | #define CEBUG(bla) {cout << bla; cout.flush(); } | assembly_buildcontigs.C:55: note: this is the location of the previous definition 55 | #define CEBUG(bla) | assembly_buildcontigs.C:1251: warning: "CEBUG" redefined 1251 | #define CEBUG(bla) | assembly_buildcontigs.C:80: note: this is the location of the previous definition 80 | #define CEBUG(bla) {cout << bla; cout.flush(); } | assembly_buildcontigs.C:1332: warning: "CEBUG" redefined 1332 | #define CEBUG(bla) {cout << bla; cout.flush(); } | assembly_buildcontigs.C:1251: note: this is the location of the previous definition 1251 | #define CEBUG(bla) | assembly_buildcontigs.C:1485: warning: "CEBUG" redefined 1485 | #define CEBUG(bla) | assembly_buildcontigs.C:1332: note: this is the location of the previous definition 1332 | #define CEBUG(bla) {cout << bla; cout.flush(); } | assembly_buildcontigs.C:1496: warning: "CEBUG" redefined 1496 | #define CEBUG(bla) {cout << bla; cout.flush(); } | assembly_buildcontigs.C:1485: note: this is the location of the previous definition 1485 | #define CEBUG(bla) | assembly_buildcontigs.C:1621: warning: "CEBUG" redefined 1621 | #define CEBUG(bla) | assembly_buildcontigs.C:1496: note: this is the location of the previous definition 1496 | #define CEBUG(bla) {cout << bla; cout.flush(); } | assembly_buildcontigs.C:2304: warning: "VCOUT" redefined 2304 | #define VCOUT(bla) | assembly_buildcontigs.C:2043: note: this is the location of the previous definition 2043 | #define VCOUT(bla) {if(verbose) {cout << bla;} } | In file included from /usr/include/boost/bind.hpp:30, from ../../src/mira/stringcontainer.H:38, from ../../src/mira/multitag.H:40, 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 + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ assembly_misc.C:1871: warning: "CEBUG" redefined 1871 | #define CEBUG(bla) {cout << bla; cout.flush();} | assembly_misc.C:55: note: this is the location of the previous definition 55 | #define CEBUG(bla) | assembly_misc.C:1905: warning: "CEBUG" redefined 1905 | #define CEBUG(bla) | assembly_misc.C:1871: note: this is the location of the previous definition 1871 | #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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o assembly_output.o assembly_output.C In file included from /usr/include/boost/bind.hpp:30, from ../../src/mira/stringcontainer.H:38, from ../../src/mira/multitag.H:40, 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 + 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/bind.hpp:30, from ../../src/mira/stringcontainer.H:38, from ../../src/mira/multitag.H:40, 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_io.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 + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/regex/v4/regex_workaround.hpp:44, from /usr/include/boost/regex/v4/regex.hpp:32, from /usr/include/boost/regex.hpp:31, from assembly_misc.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 + 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/bind.hpp:30, from ../../src/mira/stringcontainer.H:38, from ../../src/mira/multitag.H:40, 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 + 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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o assembly_pbcorrect.o assembly_pbcorrect.C assembly_misc.C: In member function 'void Assembly::priv_phahelper(const string&, const string&, uint32, bool, int32, std::string, std::string, std::string)': assembly_misc.C:376:3: warning: use of an operand of type 'bool' in 'operator++' is deprecated [-Wdeprecated] 376 | countedthisseq++; | ^~~~~~~~~~~~~~ assembly_misc.C: In instantiation of 'void Assembly::priv_phahelper(const string&, const string&, uint32, bool, int32, std::string, std::string, std::string) [with TVHASH_T = long long unsigned int; std::string = std::__cxx11::basic_string; uint32 = unsigned int; int32 = int]': assembly_misc.C:471:118: required from here assembly_misc.C:376:3: warning: use of an operand of type 'bool' in 'operator++' is deprecated [-Wdeprecated] assembly_misc.C: In instantiation of 'void Assembly::priv_phahelper(const string&, const string&, uint32, bool, int32, std::string, std::string, std::string) [with TVHASH_T = VLuint<128>; std::string = std::__cxx11::basic_string; uint32 = unsigned int; int32 = int]': assembly_misc.C:473:119: required from here assembly_misc.C:376:3: warning: use of an operand of type 'bool' in 'operator++' is deprecated [-Wdeprecated] assembly_misc.C: In instantiation of 'void Assembly::priv_phahelper(const string&, const string&, uint32, bool, int32, std::string, std::string, std::string) [with TVHASH_T = VLuint<256>; std::string = std::__cxx11::basic_string; uint32 = unsigned int; int32 = int]': assembly_misc.C:475:119: required from here assembly_misc.C:376:3: warning: use of an operand of type 'bool' in 'operator++' is deprecated [-Wdeprecated] assembly_misc.C: In instantiation of 'void Assembly::priv_phahelper(const string&, const string&, uint32, bool, int32, std::string, std::string, std::string) [with TVHASH_T = VLuint<512>; std::string = std::__cxx11::basic_string; uint32 = unsigned int; int32 = int]': assembly_misc.C:477:119: required from here assembly_misc.C:376:3: warning: use of an operand of type 'bool' in 'operator++' is deprecated [-Wdeprecated] assembly_pbcorrect.C:59: warning: "CEBUG" redefined 59 | #define CEBUG(bla) { if(docebug) {cout << bla; cout.flush();}} | assembly_pbcorrect.C:45: note: this is the location of the previous definition 45 | #define CEBUG(bla) | In file included from /usr/include/boost/bind.hpp:30, from ../../src/mira/stringcontainer.H:38, from ../../src/mira/multitag.H:40, 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 + 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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o assembly_reduceskimhits.o assembly_reduceskimhits.C assembly_reduceskimhits.C:1111: warning: "CEBUG" redefined 1111 | #define CEBUG(bla) {cout << bla; cout.flush();} | assembly_reduceskimhits.C:878: note: this is the location of the previous definition 878 | #define CEBUG(bla) | assembly_reduceskimhits.C:1151: warning: "CEBUG" redefined 1151 | #define CEBUG(bla) | assembly_reduceskimhits.C:1111: note: this is the location of the previous definition 1111 | #define CEBUG(bla) {cout << bla; cout.flush();} | assembly_reduceskimhits.C:2742: warning: "CEBUG" redefined 2742 | #define CEBUG(bla) {cout << bla; cout.flush();} | assembly_reduceskimhits.C:1151: note: this is the location of the previous definition 1151 | #define CEBUG(bla) | assembly_reduceskimhits.C:2760: warning: "CEBUG" redefined 2760 | #define CEBUG(bla) | assembly_reduceskimhits.C:2742: note: this is the location of the previous definition 2742 | #define CEBUG(bla) {cout << bla; cout.flush();} | assembly_reduceskimhits.C:2764: warning: "CEBUG" redefined 2764 | #define CEBUG(bla) {cout << bla; cout.flush();} | assembly_reduceskimhits.C:2760: note: this is the location of the previous definition 2760 | #define CEBUG(bla) | assembly_reduceskimhits.C:2803: warning: "CEBUG" redefined 2803 | #define CEBUG(bla) | assembly_reduceskimhits.C:2764: note: this is the location of the previous definition 2764 | #define CEBUG(bla) {cout << bla; cout.flush();} | assembly_reduceskimhits.C:2808: warning: "CEBUG" redefined 2808 | #define CEBUG(bla) {cout << bla; cout.flush();} | assembly_reduceskimhits.C:2803: note: this is the location of the previous definition 2803 | #define CEBUG(bla) | assembly_reduceskimhits.C:2887: warning: "CEBUG" redefined 2887 | #define CEBUG(bla) | assembly_reduceskimhits.C:2808: note: this is the location of the previous definition 2808 | #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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o assembly_swalign.o assembly_swalign.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o contig_consensus.o contig_consensus.C In file included from /usr/include/boost/bind.hpp:30, from ../../src/mira/stringcontainer.H:38, from ../../src/mira/multitag.H:40, 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 + 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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o contig_covanalysis.o contig_covanalysis.C In file included from /usr/include/boost/bind.hpp:30, from ../../src/mira/stringcontainer.H:38, from ../../src/mira/multitag.H:40, 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 + 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/bind.hpp:30, from ../../src/mira/stringcontainer.H:38, from ../../src/mira/multitag.H:40, 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 + 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/bind.hpp:30, from ../../src/mira/stringcontainer.H:38, from ../../src/mira/multitag.H:40, 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 + 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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o contig_edit.o contig_edit.C 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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o contig_featureinfo.o contig_featureinfo.C 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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o contig_output.o contig_output.C contig_featureinfo.C:512: warning: "CEBUGF2" redefined 512 | #define CEBUGF2 | contig_featureinfo.C:473: note: this is the location of the previous definition 473 | #define CEBUGF2(bla) | In file included from /usr/include/boost/bind.hpp:30, from ../../src/mira/stringcontainer.H:38, from ../../src/mira/multitag.H:40, 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 + 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/bind.hpp:30, from ../../src/mira/stringcontainer.H:38, from ../../src/mira/multitag.H:40, 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 + 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/bind.hpp:30, from ../../src/mira/stringcontainer.H:38, from ../../src/mira/multitag.H:40, 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 + 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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o contig_pairconsistency.o contig_pairconsistency.C contig_pairconsistency.C:313: warning: "CEBUG" redefined 313 | #define CEBUG(bla) | contig_pairconsistency.C:34: note: this is the location of the previous definition 34 | #define CEBUG(bla) {cout << bla; cout.flush();} | contig_pairconsistency.C:315: warning: "CEBUG" redefined 315 | #define CEBUG(bla) {cout << bla; cout.flush();} | contig_pairconsistency.C:313: note: this is the location of the previous definition 313 | #define CEBUG(bla) | contig_pairconsistency.C:399: warning: "CEBUG" redefined 399 | #define CEBUG(bla) | contig_pairconsistency.C:315: note: this is the location of the previous definition 315 | #define CEBUG(bla) {cout << bla; cout.flush();} | In file included from /usr/include/boost/bind.hpp:30, from ../../src/mira/stringcontainer.H:38, from ../../src/mira/multitag.H:40, 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 + 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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o dataprocessing.o dataprocessing.C 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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o dynamic.o dynamic.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o gbf_parse.o gbf_parse.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o gff_parse.o gff_parse.C 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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o gff_save.o gff_save.C In file included from /usr/include/boost/bind.hpp:30, from ../../src/mira/stringcontainer.H:38, from ../../src/mira/multitag.H:40, from gbf_parse.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 + 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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o maf_parse.o maf_parse.C In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/date_time/time_clock.hpp:17, from /usr/include/boost/thread/thread_time.hpp:9, from /usr/include/boost/thread/lock_types.hpp:18, from /usr/include/boost/thread/pthread/mutex.hpp:16, 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 + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/regex/v4/regex_workaround.hpp:44, from /usr/include/boost/regex/v4/regex.hpp:32, from /usr/include/boost/regex.hpp:31, from ../../src/mira/gff_parse.H:33, from gff_parse.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 + 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/bind.hpp:30, from ../../src/mira/stringcontainer.H:38, from ../../src/mira/multitag.H:40, 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 + 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/bind.hpp:30, from ../../src/mira/stringcontainer.H:38, from ../../src/mira/multitag.H:40, 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 + 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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o manifest.o manifest.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o multitag.o multitag.C /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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o parameters.o parameters.C In file included from /usr/include/boost/bind.hpp:30, from ../../src/mira/stringcontainer.H:38, from ../../src/mira/multitag.H:40, from multitag.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 + 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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o pcrcontainer.o pcrcontainer.C In file included from /usr/include/boost/bind.hpp:30, from ../../src/mira/stringcontainer.H:38, from ../../src/mira/multitag.H:40, from ../../src/mira/read.H:38, from parameters.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 + 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/bind.hpp:30, from ../../src/mira/stringcontainer.H:38, from ../../src/mira/multitag.H:40, 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 + 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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o ppathfinder.o ppathfinder.C In file included from /usr/include/boost/bind.hpp:30, from ../../src/mira/stringcontainer.H:38, from ../../src/mira/multitag.H:40, 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 + 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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o preventinitfiasco.o preventinitfiasco.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o readgrouplib.o readgrouplib.C In file included from /usr/include/boost/bind.hpp:30, from ../../src/mira/stringcontainer.H:38, from ../../src/mira/multitag.H:40, from preventinitfiasco.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 + 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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o readlotstat.o readlotstat.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o readpool.o readpool.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o readpool_io.o readpool_io.C In file included from /usr/include/boost/bind.hpp:30, from ../../src/mira/stringcontainer.H:38, from ../../src/mira/multitag.H:40, 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 + 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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o sam_collect.o sam_collect.C In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/regex/v4/regex_workaround.hpp:44, from /usr/include/boost/regex/v4/regex.hpp:32, from /usr/include/boost/regex.hpp:31, from ../../src/mira/gff_parse.H:33, from ../../src/mira/readpool_io.H:37, from readpool_io.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 + 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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o scaffolder.o scaffolder.C scaffolder.C:203: warning: "CEBUG" redefined 203 | #define CEBUG(bla) | scaffolder.C:84: note: this is the location of the previous definition 84 | #define CEBUG(bla) {cout << bla; cout.flush(); } | In file included from /usr/include/boost/bind.hpp:30, from ../../src/mira/stringcontainer.H:38, from ../../src/mira/multitag.H:40, 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 + 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/bind.hpp:30, from ../../src/mira/stringcontainer.H:38, from ../../src/mira/multitag.H:40, 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 + 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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o seqtohash.o seqtohash.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o simplebloomfilter.o simplebloomfilter.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o skim_lowbph.o skim_lowbph.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o warnings.o warnings.C rm -f libmiraestass.a ar cru libmiraestass.a estassembly.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libmiraestass.a g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o parameters_flexer.o parameters_flexer.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/date_time/time_clock.hpp:17, from /usr/include/boost/thread/thread_time.hpp:9, from /usr/include/boost/thread/lock_types.hpp:18, from /usr/include/boost/thread/pthread/mutex.hpp:16, from /usr/include/boost/thread/mutex.hpp:16, from skim.H:26, 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 + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ rm -f libmira.a ar cru libmira.a hashstats_sdbg.o hashstats.o skim.o assembly.o contig.o read.o contig_analysis.o ads.o adsfacts.o align.o assembly_info.o assembly_buildcontigs.o assembly_io.o assembly_misc.o assembly_output.o assembly_pbcorrect.o assembly_reduceskimhits.o assembly_swalign.o contig_consensus.o contig_covanalysis.o contig_edit.o contig_featureinfo.o contig_output.o contig_pairconsistency.o dataprocessing.o dynamic.o gbf_parse.o gff_parse.o gff_save.o maf_parse.o manifest.o multitag.o parameters_flexer.o parameters.o pcrcontainer.o ppathfinder.o preventinitfiasco.o readgrouplib.o readlotstat.o readpool.o readpool_io.o sam_collect.o scaffolder.o seqtohash.o simplebloomfilter.o skim_lowbph.o warnings.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libmira.a make[6]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/mira' make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/mira' Making all in caf make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/caf' g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o caf.o caf.C /bin/sh ../../ylwrap caf_flexer.ll lex.yy.c caf_flexer.cc -- flex g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o caf_flexer.o caf_flexer.cc In file included from /usr/include/boost/bind.hpp:30, from ../../src/mira/stringcontainer.H:38, from ../../src/mira/multitag.H:40, from ../../src/mira/read.H:38, from ../../src/caf/caf.H:45, 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 + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ rm -f libmiracaf.a ar cru libmiracaf.a caf.o caf_flexer.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libmiracaf.a make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/caf' Making all in memorc make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/memorc' g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o memorc.o memorc.C memorc.C: In static member function 'static void MemORC::statistics()': memorc.C:155:39: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 2 has type 'std::map::size_type' {aka 'unsigned int'} [-Wformat=] 155 | printf("Num. memory blocks : %llu\n", MOC_memblocks.size()); | ~~~^ ~~~~~~~~~~~~~~~~~~~~ | | | | long long unsigned int std::map::size_type {aka unsigned int} | %u memorc.C:156:39: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 2 has type 'std::map::size_type' {aka 'unsigned int'} [-Wformat=] 156 | printf("Num. active hot blocks : %llu\n", MOC_hotblocks.size()); | ~~~^ ~~~~~~~~~~~~~~~~~~~~ | | | | long long unsigned int std::map::size_type {aka unsigned int} | %u memorc.C:157:39: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] 157 | printf("Num. pending hot blocks: %llu\n", MOC_hotaidsrequested.size()); | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long long unsigned int std::vector::size_type {aka unsigned int} | %u memorc.C:158:39: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 2 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 158 | printf("Total mem reqested : %llu\n", MOC_reqmemalloc); | ~~~^ ~~~~~~~~~~~~~~~ | | | | | size_t {aka unsigned int} | long long unsigned int | %u memorc.C:159:39: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 2 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 159 | printf("Total mem allocated : %llu (including pads and fences)\n", MOC_totalmemalloc); | ~~~^ ~~~~~~~~~~~~~~~~~ | | | | long long unsigned int size_t {aka unsigned int} | %u memorc.C: In static member function 'static void* MemORC::newMemBlock(size_t)': memorc.C:225:51: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 2 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 225 | printf("Used malloc()\nTried to allocate %llu byte.\nSorry, memory allocation failed. Bailing out.\n", totaln); | ~~~^ ~~~~~~ | | | | long long unsigned int size_t {aka unsigned int} | %u memorc.C: In static member function 'static void MemORC::deleteMemBlock(void*)': memorc.C:311:35: warning: format '%d' expects argument of type 'int', but argument 2 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 311 | printf("Nearest memblock above (%d):\t",reinterpret_cast(mbI->first)-reinterpret_cast(usraddr)); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int uint64 {aka long long unsigned int} | %lld memorc.C:318:36: warning: format '%d' expects argument of type 'int', but argument 2 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 318 | printf("Nearest memblock below (-%d):\t",reinterpret_cast(usraddr)-reinterpret_cast(mbI->first)); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int uint64 {aka long long unsigned int} | %lld memorc.C: In static member function 'static bool MemORC::checkMemBlock(std::map::iterator)': memorc.C:500:22: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 2 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 500 | printf("Size: %llu\n", mbI->second.size); | ~~~^ ~~~~~~~~~~~~~~~~ | | | | | size_t {aka unsigned int} | long long unsigned int | %u memorc.C: In static member function 'static void MemORC::printMemBlockInfo(std::map::iterator)': memorc.C:558:18: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 558 | printf("%p\t%llu\t",mbI->first,mbI->second.size); | ~~~^ ~~~~~~~~~~~~~~~~ | | | | long long unsigned int size_t {aka unsigned int} | %u g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o main.o main.C rm -f libmemorc.a ar cru libmemorc.a memorc.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libmemorc.a /bin/sh ../../libtool --tag=CXX --mode=link g++ -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -L../io/ -L../util/ -L../errorhandling/ -L../mira -L../caf/ -L/usr/lib/i386-linux-gnu -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/i386-linux-gnu -L/usr/lib -o main main.o -lmiraerrorhandling -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt -lexpat -lm -lz -lbz2 libtool: link: g++ -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -Wl,-z -Wl,relro -Wl,-z -Wl,now -o main main.o -L../io/ -L../util/ -L../errorhandling/ -L../mira -L../caf/ -L/usr/lib/i386-linux-gnu -L/usr/lib -lmiraerrorhandling -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt -lexpat -lm -lz -lbz2 -fopenmp -pthread make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/memorc' Making all in modules make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/modules' g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o mod_sigconex.o mod_sigconex.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o mod_scaffold.o mod_scaffold.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o mod_bait.o mod_bait.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o mod_dbgreplay.o mod_dbgreplay.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o mod_diff.o mod_diff.C 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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o mod_mer.o mod_mer.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o mod_mira.o mod_mira.C In file included from /usr/include/boost/bind.hpp:30, from ../../src/mira/stringcontainer.H:38, from ../../src/mira/multitag.H:40, 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 + 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/bind.hpp:30, from ../../src/mira/stringcontainer.H:38, from ../../src/mira/multitag.H:40, 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 + 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/bind.hpp:30, from ../../src/mira/stringcontainer.H:38, from ../../src/mira/multitag.H:40, 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 + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/regex/v4/regex_workaround.hpp:44, from /usr/include/boost/regex/v4/regex.hpp:32, from /usr/include/boost/regex.hpp:31, from ../../src/mira/gff_parse.H:33, from ../../src/mira/readpool_io.H:37, 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 + 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/bind.hpp:30, from ../../src/mira/stringcontainer.H:38, from ../../src/mira/multitag.H:40, 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_mira.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 + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/date_time/time_clock.hpp:17, from /usr/include/boost/thread/thread_time.hpp:9, from /usr/include/boost/thread/lock_types.hpp:18, from /usr/include/boost/thread/pthread/mutex.hpp:16, 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 + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/regex/v4/regex_workaround.hpp:44, from /usr/include/boost/regex/v4/regex.hpp:32, from /usr/include/boost/regex.hpp:31, from ../../src/mira/gff_parse.H:33, from ../../src/mira/readpool_io.H:37, 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 + 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("../.."); | ~~~~~^~~~~~~~~ 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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o mod_convert.o mod_convert.C In file included from /usr/include/boost/bind.hpp:30, from ../../src/mira/stringcontainer.H:38, from ../../src/mira/multitag.H:40, 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 + 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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o mod_memestim.o mod_memestim.C In file included from /usr/include/boost/bind.hpp:30, from ../../src/mira/stringcontainer.H:38, from ../../src/mira/multitag.H:40, 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 + 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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o mod_tagsnp.o mod_tagsnp.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o misc.o misc.C In file included from /usr/include/boost/bind.hpp:30, from ../../src/mira/stringcontainer.H:38, from ../../src/mira/multitag.H:40, from ../../src/mira/read.H:38, from ../../src/caf/caf.H:45, 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 + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ rm -f libmiramodules.a ar cru libmiramodules.a mod_sigconex.o mod_scaffold.o mod_bait.o mod_dbgreplay.o mod_diff.o mod_mer.o mod_mira.o mod_convert.o mod_memestim.o mod_tagsnp.o misc.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libmiramodules.a make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/modules' Making all in support make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/support' make[5]: Nothing to be done for 'all'. make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/support' Making all in scripts make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/scripts' make[5]: Nothing to be done for 'all'. make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/scripts' Making all in version make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/version' make all-am make[6]: Entering directory '/build/reproducible-path/mira-4.9.6/src/version' g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o mversion.o mversion.C rm -f libmiraversion.a ar cru libmiraversion.a mversion.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libmiraversion.a make[6]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/version' make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/version' Making all in progs make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/progs' Making .C out of .xxd compileinfo.itxt make all-am make[6]: Entering directory '/build/reproducible-path/mira-4.9.6/src/progs' g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o mira.o mira.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o quirks.o quirks.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o miratest.o miratest.C Making .C out of .xxd compileinfo.itxt g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o compileinfo.itxt.xxd.o compileinfo.itxt.xxd.C In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, 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 + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/regex/v4/regex_workaround.hpp:44, from /usr/include/boost/regex/v4/regex.hpp:32, from /usr/include/boost/regex.hpp:31, from ../../src/mira/gff_parse.H:33, from ../../src/mira/readpool_io.H:37, from ../../src/modules/mod_bait.H:37, from mira.C:42: /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 + 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 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -L../version -L../modules -L../debuggersupport -L../memorc -L../io/ -L../util/ -L../errorhandling/ -L../mira -L../caf -L/usr/lib/i386-linux-gnu -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/i386-linux-gnu -L/usr/lib -o mira mira.o quirks.o compileinfo.itxt.xxd.o -lmiraversion -lmiramodules -lmiradebuggersupport -lmira -lmiraestass -lmiracaf -lmirautil -lmiradptools -lmirafio -lmiraerrorhandling -lmiradebuggersupport -lmirafmttext -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt -lexpat -lm -lz -lbz2 /bin/sh ../../libtool --tag=CXX --mode=link g++ -pthread -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -L../version -L../modules -L../debuggersupport -L../memorc -L../io/ -L../util/ -L../errorhandling/ -L../mira -L../caf -L/usr/lib/i386-linux-gnu -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/i386-linux-gnu -L/usr/lib -o miratest miratest.o compileinfo.itxt.xxd.o -lmiraversion -lmiramodules -lmiradebuggersupport -lmira -lmiraestass -lmiracaf -lmirautil -lmiradptools -lmirafio -lmiraerrorhandling -lmiradebuggersupport -lmirafmttext -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt -lexpat -lm -lz -lbz2 libtool: link: g++ -pthread -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -Wl,-z -Wl,relro -Wl,-z -Wl,now -o mira mira.o quirks.o compileinfo.itxt.xxd.o -L../version -L../modules -L../debuggersupport -L../memorc -L../io/ -L../util/ -L../errorhandling/ -L../mira -L../caf -L/usr/lib/i386-linux-gnu -L/usr/lib -lmiraversion -lmiramodules -lmira -lmiraestass -lmiracaf -lmirautil -lmiradptools -lmirafio -lmiraerrorhandling -lmiradebuggersupport -lmirafmttext -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt -lexpat -lm -lz -lbz2 -fopenmp -pthread libtool: link: g++ -pthread -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -Wl,-z -Wl,relro -Wl,-z -Wl,now -o miratest miratest.o compileinfo.itxt.xxd.o -L../version -L../modules -L../debuggersupport -L../memorc -L../io/ -L../util/ -L../errorhandling/ -L../mira -L../caf -L/usr/lib/i386-linux-gnu -L/usr/lib -lmiraversion -lmiramodules -lmira -lmiraestass -lmiracaf -lmirautil -lmiradptools -lmirafio -lmiraerrorhandling -lmiradebuggersupport -lmirafmttext -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt -lexpat -lm -lz -lbz2 -fopenmp -pthread make[6]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/progs' make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/progs' Making all in other make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/other' Making all in sls make[6]: Entering directory '/build/reproducible-path/mira-4.9.6/src/other/sls' Making all in mira-createsls make[7]: Entering directory '/build/reproducible-path/mira-4.9.6/src/other/sls/mira-createsls' Making all in bin make[8]: Entering directory '/build/reproducible-path/mira-4.9.6/src/other/sls/mira-createsls/bin' make[8]: Nothing to be done for 'all'. make[8]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/other/sls/mira-createsls/bin' make[8]: Entering directory '/build/reproducible-path/mira-4.9.6/src/other/sls/mira-createsls' make[8]: Nothing to be done for 'all-am'. make[8]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/other/sls/mira-createsls' make[7]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/other/sls/mira-createsls' make[7]: Entering directory '/build/reproducible-path/mira-4.9.6/src/other/sls' make[7]: Nothing to be done for 'all-am'. make[7]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/other/sls' make[6]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/other/sls' make[6]: Entering directory '/build/reproducible-path/mira-4.9.6/src/other' make[6]: Nothing to be done for 'all-am'. 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[5]: Nothing to be done for 'all-am'. make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src' make[4]: Leaving directory '/build/reproducible-path/mira-4.9.6/src' make[4]: Entering directory '/build/reproducible-path/mira-4.9.6' make[4]: Nothing to be done for 'all-am'. make[4]: Leaving directory '/build/reproducible-path/mira-4.9.6' make[3]: Leaving directory '/build/reproducible-path/mira-4.9.6' make[2]: Leaving directory '/build/reproducible-path/mira-4.9.6' make[1]: Leaving directory '/build/reproducible-path/mira-4.9.6' 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 -j7 "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 Making .html out of _part.xml chap_bitsandpieces_part.html Making .html out of _part.xml chap_est_part.html ERROR: xref linking to chap_dataprep has no generated link text. Error: no ID for constraint linkend: "chap_dataprep". ERROR: xref linking to chap_denovo has no generated link text. Error: no ID for constraint linkend: "chap_denovo". ERROR: xref linking to chap_results has no generated link text. Error: no ID for constraint linkend: "chap_results". ERROR: xref linking to sect_res_looking_at_results has no generated link text. Error: no ID for constraint linkend: "sect_res_looking_at_results". ERROR: xref linking to sect_res_first_look:the_assembly_info has no generated link text. Error: no ID for constraint linkend: "sect_res_first_look:the_assembly_info". ERROR: xref linking to sect_res_converting_results has no generated link text. Error: no ID for constraint linkend: "sect_res_converting_results". ERROR: xref linking to sect_res_filtering_of_results has no generated link text. Error: no ID for constraint linkend: "sect_res_filtering_of_results". ERROR: xref linking to sect_res_places_of_importance_in_a_de_novo_assembly has no generated link text. Error: no ID for constraint linkend: "sect_res_places_of_importance_in_a_de_novo_assembly". ERROR: xref linking to chap_reference has no generated link text. Error: no ID for constraint linkend: "chap_reference". ERROR: xref linking to sect_ref_manifest_basics has no generated link text. Error: no ID for constraint linkend: "sect_ref_manifest_basics". ERROR: xref linking to sect_ref_manifest_readgroups has no generated link text. Error: no ID for constraint linkend: "sect_ref_manifest_readgroups". ERROR: xref linking to sect_ref_manifest_parameters has no generated link text. Error: no ID for constraint linkend: "sect_ref_manifest_parameters". Making .html out of _part.xml chap_faq_part.html Build the book set list... Build the book set list... Making .html out of _part.xml chap_hard_part.html Making .html out of _part.xml chap_logfiles_part.html Making .html out of _part.xml chap_maf_part.html Making .html out of _part.xml chap_reference_part.html Build the listings... Making .html out of _part.xml chap_installation_part.html Making .html out of _part.xml chap_intro_part.html Making .html out of _part.xml chap_results_part.html XSLT stylesheets DocBook - LaTeX 2e (0.3.12) =================================================== No template matches copyright in chapterinfo. No template matches year in copyright. No template matches holder in copyright. Making .html out of _part.xml chap_sra_part.html Element emph in namespace '' encountered in note, but no template matches. Making .html out of _part.xml chap_seqadvice_part.html Making .html out of _part.xml chap_bonus_part.html Build book_3rdparty.pdf Making .html out of _part.xml chap_preface_part.html Element emph in namespace '' encountered in note, but no template matches. Build the listings... '3rdparty_MIRA.pdf' successfully built XSLT stylesheets DocBook - LaTeX 2e (0.3.12) =================================================== No template matches copyright in chapterinfo. No template matches year in copyright. No template matches holder in copyright. No template matches copyright in chapterinfo. No template matches year in copyright. No template matches holder in copyright. prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen No template matches emph in note. No template matches copyright in chapterinfo. No template matches year in copyright. No template matches holder in copyright. prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen No template matches copyright in chapterinfo. No template matches year in copyright. No template matches holder in copyright. prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen No template matches copyright in chapterinfo. No template matches year in copyright. No template matches holder in copyright. prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen No template matches copyright in chapterinfo. No template matches year in copyright. No template matches holder in copyright. prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen No template matches copyright in chapterinfo. No template matches year in copyright. No template matches holder in copyright. prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen No template matches copyright in chapterinfo. No template matches year in copyright. No template matches holder in copyright. No template matches copyright in chapterinfo. No template matches year in copyright. No template matches holder in copyright. prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen No template matches copyright in chapterinfo. No template matches year in copyright. No template matches holder in copyright. prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen No template matches copyright in chapterinfo. No template matches year in copyright. No template matches holder in copyright. prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen No template matches copyright in chapterinfo. No template matches year in copyright. No template matches holder in copyright. No template matches copyright in chapterinfo. No template matches year in copyright. No template matches holder in copyright. No template matches copyright in chapterinfo. No template matches year in copyright. No template matches holder in copyright. prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen prompt: default template used in programlisting or screen No template matches copyright in chapterinfo. No template matches year in copyright. No template matches holder in copyright. No template matches copyright in chapterinfo. No template matches year in copyright. No template matches holder in copyright. No template matches copyright in chapterinfo. No template matches year in copyright. No template matches holder in copyright. Build book_definitiveguide.pdf 'DefinitiveGuideToMIRA.pdf' successfully built make[3]: Leaving directory '/build/reproducible-path/mira-4.9.6/doc/docbook' make[3]: Entering directory '/build/reproducible-path/mira-4.9.6/doc' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/build/reproducible-path/mira-4.9.6/doc' make[2]: Leaving directory '/build/reproducible-path/mira-4.9.6/doc' make[1]: Leaving directory '/build/reproducible-path/mira-4.9.6' rm -f debian/mira-doc.debhelper.log debian/mira-rfam-12s-rrna.debhelper.log debian/rules override_dh_auto_test-arch make[1]: Entering directory '/build/reproducible-path/mira-4.9.6' make check make[2]: Entering directory '/build/reproducible-path/mira-4.9.6' make check-recursive make[3]: Entering directory '/build/reproducible-path/mira-4.9.6' Making check in man make[4]: Entering directory '/build/reproducible-path/mira-4.9.6/man' make[4]: Nothing to be done for 'check'. make[4]: Leaving directory '/build/reproducible-path/mira-4.9.6/man' Making check in src make[4]: Entering directory '/build/reproducible-path/mira-4.9.6/src' Making check in debuggersupport make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/debuggersupport' make[5]: Nothing to be done for 'check'. make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/debuggersupport' Making check in io make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/io' make check-am make[6]: Entering directory '/build/reproducible-path/mira-4.9.6/src/io' make[6]: Nothing to be done for 'check-am'. 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 check in stdinc make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/stdinc' make[5]: Nothing to be done for 'check'. make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/stdinc' Making check in errorhandling make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/errorhandling' make[5]: Nothing to be done for 'check'. make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/errorhandling' Making check in util make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/util' make[5]: Nothing to be done for 'check'. make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/util' Making check in mira make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/mira' make check-am make[6]: Entering directory '/build/reproducible-path/mira-4.9.6/src/mira' make[6]: Nothing to be done for 'check-am'. 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 check in caf make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/caf' make[5]: Nothing to be done for 'check'. make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/caf' Making check in memorc make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/memorc' make[5]: Nothing to be done for 'check'. make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/memorc' Making check in modules make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/modules' make[5]: Nothing to be done for 'check'. make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/modules' Making check in support make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/support' make[5]: Nothing to be done for 'check'. make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/support' Making check in scripts make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/scripts' make[5]: Nothing to be done for 'check'. make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/scripts' Making check in version make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/version' make check-am make[6]: Entering 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 check in progs make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/progs' Making .C out of .xxd compileinfo.itxt make check-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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o compileinfo.itxt.xxd.o compileinfo.itxt.xxd.C /bin/sh ../../libtool --tag=CXX --mode=link g++ -pthread -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -L../version -L../modules -L../debuggersupport -L../memorc -L../io/ -L../util/ -L../errorhandling/ -L../mira -L../caf -L/usr/lib/i386-linux-gnu -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/i386-linux-gnu -L/usr/lib -o mira mira.o quirks.o compileinfo.itxt.xxd.o -lmiraversion -lmiramodules -lmiradebuggersupport -lmira -lmiraestass -lmiracaf -lmirautil -lmiradptools -lmirafio -lmiraerrorhandling -lmiradebuggersupport -lmirafmttext -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt -lexpat -lm -lz -lbz2 libtool: link: g++ -pthread -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -Wl,-z -Wl,relro -Wl,-z -Wl,now -o mira mira.o quirks.o compileinfo.itxt.xxd.o -L../version -L../modules -L../debuggersupport -L../memorc -L../io/ -L../util/ -L../errorhandling/ -L../mira -L../caf -L/usr/lib/i386-linux-gnu -L/usr/lib -lmiraversion -lmiramodules -lmira -lmiraestass -lmiracaf -lmirautil -lmiradptools -lmirafio -lmiraerrorhandling -lmiradebuggersupport -lmirafmttext -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt -lexpat -lm -lz -lbz2 -fopenmp -pthread /bin/sh ../../libtool --tag=CXX --mode=link g++ -pthread -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -L../version -L../modules -L../debuggersupport -L../memorc -L../io/ -L../util/ -L../errorhandling/ -L../mira -L../caf -L/usr/lib/i386-linux-gnu -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/i386-linux-gnu -L/usr/lib -o miratest miratest.o compileinfo.itxt.xxd.o -lmiraversion -lmiramodules -lmiradebuggersupport -lmira -lmiraestass -lmiracaf -lmirautil -lmiradptools -lmirafio -lmiraerrorhandling -lmiradebuggersupport -lmirafmttext -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt -lexpat -lm -lz -lbz2 libtool: link: g++ -pthread -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -Wl,-z -Wl,relro -Wl,-z -Wl,now -o miratest miratest.o compileinfo.itxt.xxd.o -L../version -L../modules -L../debuggersupport -L../memorc -L../io/ -L../util/ -L../errorhandling/ -L../mira -L../caf -L/usr/lib/i386-linux-gnu -L/usr/lib -lmiraversion -lmiramodules -lmira -lmiraestass -lmiracaf -lmirautil -lmiradptools -lmirafio -lmiraerrorhandling -lmiradebuggersupport -lmirafmttext -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt -lexpat -lm -lz -lbz2 -fopenmp -pthread make[6]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/progs' make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/progs' Making check in other make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/other' Making check in sls make[6]: Entering directory '/build/reproducible-path/mira-4.9.6/src/other/sls' Making check in mira-createsls make[7]: Entering directory '/build/reproducible-path/mira-4.9.6/src/other/sls/mira-createsls' Making check in bin make[8]: Entering directory '/build/reproducible-path/mira-4.9.6/src/other/sls/mira-createsls/bin' make[8]: Nothing to be done for 'check'. make[8]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/other/sls/mira-createsls/bin' make[8]: Entering directory '/build/reproducible-path/mira-4.9.6/src/other/sls/mira-createsls' make[8]: Nothing to be done for 'check-am'. make[8]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/other/sls/mira-createsls' make[7]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/other/sls/mira-createsls' make[7]: Entering directory '/build/reproducible-path/mira-4.9.6/src/other/sls' make[7]: Nothing to be done for 'check-am'. make[7]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/other/sls' make[6]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/other/sls' make[6]: Entering directory '/build/reproducible-path/mira-4.9.6/src/other' make[6]: Nothing to be done for 'check-am'. 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[5]: Nothing to be done for 'check-am'. make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src' make[4]: Leaving directory '/build/reproducible-path/mira-4.9.6/src' make[4]: Entering directory '/build/reproducible-path/mira-4.9.6' make[4]: Nothing to be done for 'check-am'. make[4]: Leaving directory '/build/reproducible-path/mira-4.9.6' make[3]: Leaving directory '/build/reproducible-path/mira-4.9.6' make[2]: Leaving directory '/build/reproducible-path/mira-4.9.6' make[1]: Leaving directory '/build/reproducible-path/mira-4.9.6' debian/rules override_dh_auto_test-indep make[1]: Entering directory '/build/reproducible-path/mira-4.9.6' echo no tests for -indep no tests for -indep make[1]: Leaving directory '/build/reproducible-path/mira-4.9.6' create-stamp debian/debhelper-build-stamp dh_prep rm -f -- debian/mira-assembler.substvars debian/mira-rfam-12s-rrna.substvars debian/mira-doc.substvars rm -fr -- debian/.debhelper/generated/mira-assembler/ debian/mira-assembler/ debian/tmp/ debian/.debhelper/generated/mira-rfam-12s-rrna/ debian/mira-rfam-12s-rrna/ debian/.debhelper/generated/mira-doc/ debian/mira-doc/ debian/rules override_dh_auto_install-arch make[1]: Entering directory '/build/reproducible-path/mira-4.9.6' make install DESTDIR=/build/reproducible-path/mira-4.9.6/debian/mira-assembler make[2]: Entering directory '/build/reproducible-path/mira-4.9.6' make install-recursive make[3]: Entering directory '/build/reproducible-path/mira-4.9.6' Making install in man make[4]: Entering directory '/build/reproducible-path/mira-4.9.6/man' make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/man' make[5]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/build/reproducible-path/mira-4.9.6/debian/mira-assembler/usr/share/man/man1' /usr/bin/install -c -m 644 mirabait.1 miradiff.1 miramer.1 mira.1 miraconvert.1 miramem.1 '/build/reproducible-path/mira-4.9.6/debian/mira-assembler/usr/share/man/man1' make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/man' make[4]: Leaving directory '/build/reproducible-path/mira-4.9.6/man' Making install in src make[4]: Entering directory '/build/reproducible-path/mira-4.9.6/src' Making install in debuggersupport make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/debuggersupport' make[6]: Entering directory '/build/reproducible-path/mira-4.9.6/src/debuggersupport' make[6]: Nothing to be done for 'install-exec-am'. make[6]: Nothing to be done for 'install-data-am'. make[6]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/debuggersupport' make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/debuggersupport' Making install in io make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/io' make install-am make[6]: Entering directory '/build/reproducible-path/mira-4.9.6/src/io' make[7]: Entering directory '/build/reproducible-path/mira-4.9.6/src/io' make[7]: Nothing to be done for 'install-exec-am'. make[7]: Nothing to be done for 'install-data-am'. make[7]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/io' make[6]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/io' make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/io' Making install in stdinc make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/stdinc' make[6]: Entering directory '/build/reproducible-path/mira-4.9.6/src/stdinc' make[6]: Nothing to be done for 'install-exec-am'. make[6]: Nothing to be done for 'install-data-am'. make[6]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/stdinc' make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/stdinc' Making install in errorhandling make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/errorhandling' make[6]: Entering directory '/build/reproducible-path/mira-4.9.6/src/errorhandling' make[6]: Nothing to be done for 'install-exec-am'. make[6]: Nothing to be done for 'install-data-am'. make[6]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/errorhandling' make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/errorhandling' Making install in util make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/util' make[6]: Entering directory '/build/reproducible-path/mira-4.9.6/src/util' make[6]: Nothing to be done for 'install-exec-am'. make[6]: Nothing to be done for 'install-data-am'. make[6]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/util' make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/util' Making install in mira make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/mira' make install-am make[6]: Entering directory '/build/reproducible-path/mira-4.9.6/src/mira' make[7]: Entering directory '/build/reproducible-path/mira-4.9.6/src/mira' make[7]: Nothing to be done for 'install-exec-am'. make[7]: Nothing to be done for 'install-data-am'. make[7]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/mira' make[6]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/mira' make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/mira' Making install in caf make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/caf' make[6]: Entering directory '/build/reproducible-path/mira-4.9.6/src/caf' make[6]: Nothing to be done for 'install-exec-am'. make[6]: Nothing to be done for 'install-data-am'. make[6]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/caf' make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/caf' Making install in memorc make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/memorc' make[6]: Entering directory '/build/reproducible-path/mira-4.9.6/src/memorc' make[6]: Nothing to be done for 'install-exec-am'. make[6]: Nothing to be done for 'install-data-am'. make[6]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/memorc' make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/memorc' Making install in modules make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/modules' make[6]: Entering directory '/build/reproducible-path/mira-4.9.6/src/modules' make[6]: Nothing to be done for 'install-exec-am'. make[6]: Nothing to be done for 'install-data-am'. make[6]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/modules' make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/modules' Making install in support make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/support' make[6]: Entering directory '/build/reproducible-path/mira-4.9.6/src/support' make[6]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/build/reproducible-path/mira-4.9.6/debian/mira-assembler/usr/share/mira/support_3rdparty_tools' /usr/bin/install -c -m 644 consedrc.13.0 consedtaglib.txt GTAGDB README '/build/reproducible-path/mira-4.9.6/debian/mira-assembler/usr/share/mira/support_3rdparty_tools' make[6]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/support' make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/support' Making install in scripts make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/scripts' make[6]: Entering directory '/build/reproducible-path/mira-4.9.6/src/scripts' make[6]: Nothing to be done for 'install-exec-am'. make[6]: Nothing to be done for 'install-data-am'. make[6]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/scripts' make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/scripts' Making install in version make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/version' make install-am make[6]: Entering directory '/build/reproducible-path/mira-4.9.6/src/version' make[7]: Entering directory '/build/reproducible-path/mira-4.9.6/src/version' make[7]: Nothing to be done for 'install-exec-am'. make[7]: Nothing to be done for 'install-data-am'. make[7]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/version' make[6]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/version' make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/version' Making install in progs make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/progs' Making .C out of .xxd compileinfo.itxt make install-am make[6]: Entering directory '/build/reproducible-path/mira-4.9.6/src/progs' Making .C out of .xxd compileinfo.itxt g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o compileinfo.itxt.xxd.o compileinfo.itxt.xxd.C /bin/sh ../../libtool --tag=CXX --mode=link g++ -pthread -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -L../version -L../modules -L../debuggersupport -L../memorc -L../io/ -L../util/ -L../errorhandling/ -L../mira -L../caf -L/usr/lib/i386-linux-gnu -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/i386-linux-gnu -L/usr/lib -o mira mira.o quirks.o compileinfo.itxt.xxd.o -lmiraversion -lmiramodules -lmiradebuggersupport -lmira -lmiraestass -lmiracaf -lmirautil -lmiradptools -lmirafio -lmiraerrorhandling -lmiradebuggersupport -lmirafmttext -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt -lexpat -lm -lz -lbz2 libtool: link: g++ -pthread -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -Wl,-z -Wl,relro -Wl,-z -Wl,now -o mira mira.o quirks.o compileinfo.itxt.xxd.o -L../version -L../modules -L../debuggersupport -L../memorc -L../io/ -L../util/ -L../errorhandling/ -L../mira -L../caf -L/usr/lib/i386-linux-gnu -L/usr/lib -lmiraversion -lmiramodules -lmira -lmiraestass -lmiracaf -lmirautil -lmiradptools -lmirafio -lmiraerrorhandling -lmiradebuggersupport -lmirafmttext -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt -lexpat -lm -lz -lbz2 -fopenmp -pthread /bin/sh ../../libtool --tag=CXX --mode=link g++ -pthread -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -L../version -L../modules -L../debuggersupport -L../memorc -L../io/ -L../util/ -L../errorhandling/ -L../mira -L../caf -L/usr/lib/i386-linux-gnu -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/i386-linux-gnu -L/usr/lib -o miratest miratest.o compileinfo.itxt.xxd.o -lmiraversion -lmiramodules -lmiradebuggersupport -lmira -lmiraestass -lmiracaf -lmirautil -lmiradptools -lmirafio -lmiraerrorhandling -lmiradebuggersupport -lmirafmttext -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt -lexpat -lm -lz -lbz2 libtool: link: g++ -pthread -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -Wl,-z -Wl,relro -Wl,-z -Wl,now -o miratest miratest.o compileinfo.itxt.xxd.o -L../version -L../modules -L../debuggersupport -L../memorc -L../io/ -L../util/ -L../errorhandling/ -L../mira -L../caf -L/usr/lib/i386-linux-gnu -L/usr/lib -lmiraversion -lmiramodules -lmira -lmiraestass -lmiracaf -lmirautil -lmiradptools -lmirafio -lmiraerrorhandling -lmiradebuggersupport -lmirafmttext -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt -lexpat -lm -lz -lbz2 -fopenmp -pthread make[7]: Entering directory '/build/reproducible-path/mira-4.9.6/src/progs' Making .C out of .xxd compileinfo.itxt /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 -d debian/.debhelper/generated/mira-assembler install -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 -d debian/.debhelper/generated/mira-rfam-12s-rrna install -d debian/mira-doc//usr/share cp --reflink=auto -a debian/tmp/usr/share/doc/ debian/mira-doc//usr/share/ install -d debian/.debhelper/generated/mira-doc dh_installdocs install -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 -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 -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 -d debian/mira-doc/usr/share/doc-base/ install -p -m0644 debian/mira-doc.doc-base debian/mira-doc/usr/share/doc-base/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 -p -m0644 debian/changelog 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 -p -m0644 debian/changelog debian/mira-assembler/usr/share/doc/mira-assembler/changelog.Debian install -p -m0644 src/mira/CHANGES.txt debian/mira-assembler/usr/share/doc/mira-assembler/changelog install -p -m0644 debian/changelog debian/mira-rfam-12s-rrna/usr/share/doc/mira-rfam-12s-rrna/changelog.Debian install -p -m0644 src/mira/CHANGES.txt debian/mira-rfam-12s-rrna/usr/share/doc/mira-rfam-12s-rrna/changelog make[1]: Leaving directory '/build/reproducible-path/mira-4.9.6' dh_installman man-recode --to-code UTF-8 --suffix .dh-new debian/mira-assembler/usr/share/man/man1/mira.1 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/miraconvert.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/miramer.1 man-recode --to-code UTF-8 --suffix .dh-new debian/mira-assembler/usr/share/man/man1/miramem.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/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/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/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/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/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 -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/mirabait ln -s mira debian/mira-assembler/usr/bin/mirabait rm -f debian/mira-assembler/usr/bin/miramem ln -s mira debian/mira-assembler/usr/bin/miramem rm -f debian/mira-assembler/usr/bin/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 1600340667 as canonical time Normalizing debian/mira-rfam-12s-rrna/usr/share/mira/rfam_rrna-21-12.sls.gz using File::StripNondeterminism::handlers::gzip Using 1600340667 as canonical time 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/haf_danger_join_notok.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/sxa_gcbias_nobias2008.png using File::StripNondeterminism::handlers::png Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/sxa_unsc_ggc1_lenski.png using File::StripNondeterminism::handlers::png Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/pb_elasticdarkinserts03.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/srmc_in_454sxahyb_1stpass.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/haf2_end_nomoredata.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/san_autoedit1.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/sxa_gcbias_bias2009.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_xmastree_lenski2.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_elasticdarkinserts04.png using File::StripNondeterminism::handlers::png Normalizing debian/mira-doc/usr/share/doc/mira-assembler/images/note.png using File::StripNondeterminism::handlers::png Normalizing debian/mira-doc/usr/share/doc/mira-assembler/images/warning.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_lastpass2.png using File::StripNondeterminism::handlers::png Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/pb_elasticdarkinserts01.png using File::StripNondeterminism::handlers::png Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/sxa_wrmcsrmc_hiding_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_cer_reads2.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/haf2_haf5_clearshortrepeat.png using File::StripNondeterminism::handlers::png Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/ion_dh10bdirdepindel.png using File::StripNondeterminism::handlers::png Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/454san_stmu_hybdenovo.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_mcvc_lenski.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_repend_rrna.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_unsc_ggc2_lenski.png using File::StripNondeterminism::handlers::png Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/sxa_cer_reads1.png using File::StripNondeterminism::handlers::png Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/454sxa_stms_hybdenovo.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/srmc_in_454sxahyb_lastpass1.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/pb_elasticdarkinserts02.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/gcb99_edit.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/results_mira2other.png using File::StripNondeterminism::handlers::png Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/sxa_unsc_ggcxg1_lenski.png using File::StripNondeterminism::handlers::png Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/sxa_xmastree_lenski1.png using File::StripNondeterminism::handlers::png dh_compress cd debian/mira-assembler cd debian/mira-rfam-12s-rrna cd debian/mira-doc chmod a-x usr/share/doc/mira-rfam-12s-rrna/changelog usr/share/doc/mira-rfam-12s-rrna/changelog.Debian chmod a-x usr/share/doc/mira-assembler/NEWS usr/share/doc/mira-assembler/changelog usr/share/doc/mira-assembler/changelog.Debian usr/share/doc/mira-assembler/test_data/fasta_estset1/tvc_mini.fasta usr/share/doc/mira-assembler/test_data/fasta_estset1/tvc_mini.fasta.qual usr/share/doc/mira-assembler/test_data/solexa_eco_art/ecoli_backbone_in.gbf usr/share/doc/mira-assembler/test_data/solexa_eco_art/ecoli_in.solexa.fasta usr/share/doc/mira-assembler/test_data/solexa_eco_art/ecoli_in.solexa.fasta.qual usr/share/doc/mira-assembler/test_data/solexa_eco_art/ecoli_straindata_in.txt usr/share/man/man1/mira.1 usr/share/man/man1/mirabait.1 usr/share/man/man1/miraconvert.1 usr/share/man/man1/miradiff.1 usr/share/man/man1/miramem.1 usr/share/man/man1/miramer.1 gzip -9nf usr/share/doc/mira-rfam-12s-rrna/changelog usr/share/doc/mira-rfam-12s-rrna/changelog.Debian gzip -9nf usr/share/doc/mira-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-doc/changelog usr/share/doc/mira-doc/changelog.Debian cd '/build/reproducible-path/mira-4.9.6' gzip -9nf usr/share/doc/mira-doc/changelog usr/share/doc/mira-doc/changelog.Debian cd '/build/reproducible-path/mira-4.9.6' cd '/build/reproducible-path/mira-4.9.6' dh_fixperms find debian/mira-assembler ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/mira-rfam-12s-rrna ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/mira-doc ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/mira-rfam-12s-rrna/usr/share/doc -type f -a -true -a ! -regex 'debian/mira-rfam-12s-rrna/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/mira-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 d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/mira-assembler/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/mira-rfam-12s-rrna -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/mira-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-doc/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 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-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/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 -d debian/.debhelper/mira-assembler/dbgsym-root/usr/lib/debug/.build-id/41 objcopy --only-keep-debug --compress-debug-sections debian/mira-assembler/usr/bin/mira debian/.debhelper/mira-assembler/dbgsym-root/usr/lib/debug/.build-id/41/80eb5c15b21c94f0435d08d595e88fb73c8383.debug chmod 0644 -- debian/.debhelper/mira-assembler/dbgsym-root/usr/lib/debug/.build-id/41/80eb5c15b21c94f0435d08d595e88fb73c8383.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/41/80eb5c15b21c94f0435d08d595e88fb73c8383.debug debian/mira-assembler/usr/bin/mira install -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 dh_makeshlibs -a rm -f debian/mira-assembler/DEBIAN/shlibs dh_shlibdeps -a install -d debian/mira-assembler/DEBIAN dpkg-shlibdeps -Tdebian/mira-assembler.substvars debian/mira-assembler/usr/bin/mira dh_installdeb install -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 -d debian/mira-doc/DEBIAN dh_gencontrol 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 -Pdebian/mira-rfam-12s-rrna 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 -Pdebian/mira-doc echo misc:Depends= >> debian/mira-assembler.substvars echo misc:Pre-Depends= >> debian/mira-assembler.substvars install -d debian/.debhelper/mira-assembler/dbgsym-root/DEBIAN dpkg-gencontrol -pmira-assembler -ldebian/changelog -Tdebian/mira-assembler.substvars -Pdebian/.debhelper/mira-assembler/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -UBuilt-Using -DAuto-Built-Package=debug-symbols -UProtected -DPackage=mira-assembler-dbgsym "-DDepends=mira-assembler (= \${binary:Version})" "-DDescription=debug symbols for mira-assembler" -DBuild-Ids=4180eb5c15b21c94f0435d08d595e88fb73c8383 -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 -Pdebian/mira-assembler chmod 0644 -- debian/mira-rfam-12s-rrna/DEBIAN/control chmod 0644 -- debian/mira-doc/DEBIAN/control chmod 0644 -- debian/mira-assembler/DEBIAN/control dh_md5sums cd debian/mira-rfam-12s-rrna >/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-doc >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/mira-doc/DEBIAN/md5sums chmod 0644 -- debian/mira-assembler/DEBIAN/md5sums cd debian/.debhelper/mira-assembler/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/mira-rfam-12s-rrna/DEBIAN/md5sums chmod 0644 -- debian/.debhelper/mira-assembler/dbgsym-root/DEBIAN/md5sums dh_builddeb dpkg-deb --root-owner-group --build debian/mira-assembler .. dpkg-deb --root-owner-group --build debian/.debhelper/mira-assembler/dbgsym-root .. dpkg-deb --root-owner-group --build debian/mira-rfam-12s-rrna .. dpkg-deb --root-owner-group --build debian/mira-doc .. dpkg-deb: building package 'mira-assembler-dbgsym' in '../mira-assembler-dbgsym_4.9.6-5_i386.deb'. dpkg-deb: building package 'mira-assembler' in '../mira-assembler_4.9.6-5_i386.deb'. dpkg-deb: building package 'mira-rfam-12s-rrna' in '../mira-rfam-12s-rrna_4.9.6-5_all.deb'. dpkg-deb: building package 'mira-doc' in '../mira-doc_4.9.6-5_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../mira_4.9.6-5_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/10537/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/10537/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/10537 and its subdirectories I: Current time: Sat Jan 13 10:39:01 +14 2024 I: pbuilder-time-stamp: 1705091941