Thu Jan 18 13:45:20 UTC 2024 I: starting to build mira/bookworm/i386 on jenkins on '2024-01-18 13:45' Thu Jan 18 13:45:20 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_5/7450/console.log Thu Jan 18 13:45:20 UTC 2024 I: Downloading source for bookworm/mira=4.9.6-7 --2024-01-18 13:45:20-- http://cdn-fastly.deb.debian.org/debian/pool/main/m/mira/mira_4.9.6-7.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2444 (2.4K) [text/prs.lines.tag] Saving to: ‘mira_4.9.6-7.dsc’ 0K .. 100% 10.7M=0s 2024-01-18 13:45:20 (10.7 MB/s) - ‘mira_4.9.6-7.dsc’ saved [2444/2444] Thu Jan 18 13:45:20 UTC 2024 I: mira_4.9.6-7.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: mira Binary: mira-assembler, mira-rfam-12s-rrna, mira-doc Architecture: any all Version: 4.9.6-7 Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Andreas Tille , Michael R. Crusoe Homepage: https://sourceforge.net/p/mira-assembler/wiki/Home/ Standards-Version: 4.6.0 Vcs-Browser: https://salsa.debian.org/med-team/mira Vcs-Git: https://salsa.debian.org/med-team/mira.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), autoconf-archive, libbz2-dev, libexpat1-dev, libgoogle-perftools-dev [i386 amd64], perl, flex, libfl-dev, xxd, zlib1g-dev, libboost-thread-dev, libboost-regex-dev, libboost-filesystem-dev, libboost-system-dev, libboost-iostreams-dev Build-Depends-Indep: docbook-xsl, dblatex Package-List: mira-assembler deb science optional arch=any mira-doc deb doc optional arch=all mira-rfam-12s-rrna deb science optional arch=all Checksums-Sha1: d8c2b4322a7b51409055c5e48ab30dc3c8a45fb0 15006355 mira_4.9.6.orig.tar.bz2 5b8971694074d2d4c288e488eb1346fb0561f17b 34276 mira_4.9.6-7.debian.tar.xz Checksums-Sha256: e910479bc5f3f205913ac81cd2a24449cc175a6d1ae1fe3ae33ea0e100435b16 15006355 mira_4.9.6.orig.tar.bz2 be3f8131ffe087724c6f07c4ae7708b6793570009e9194d5d01a36123f47b96e 34276 mira_4.9.6-7.debian.tar.xz Files: b0391f9900156aece2dd9bc2ad863e1e 15006355 mira_4.9.6.orig.tar.bz2 c3476b50956ce51ad344981f413b3912 34276 mira_4.9.6-7.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJGBAEBCgAwFiEEPpmlJvXcwMu/HO6mALrnSzQzafEFAmK2HrgSHG5pbGVzaEBk ZWJpYW4ub3JnAAoJEAC650s0M2nxjEIP/0ZgbWPJrNlzk6PUsJ6WpMtorM41hdwG nDSPD5gc0fSeaw2CvSyOaZX9FvDBdzPBLW15i2YTIDBS1+eHaCrD3b19KOUaSL2S ES4cfFAusk73qfrA4SPXJz2JEEX2UBtsnLJ9RwkLQn18xZtE8T2UnZc31Dg3KHgB 6NJN5SCzHjSeQn8mmIjRTHrO92u9HI6lAKO3SSDXcbOgJgIoEwZgrSLOswc0Byf/ v59AzTrw5AxC/1Yhno+jWXyNeKi6h3Azu+Yk2n3jHtWPXIZogeHtPQom5HovtTyG US11EYucNovbAuuatLr5adxpfoG+8mPzWNxLaVqZQdggY/NI6eJrIqxxeuKC8R5Q 3WQZE1RwOsuDhkbxdCU2ExmuJu8NihvsqnnNAQey8jORsWTsztVMhdUurv6J7VLk yFNecZbLYTdP+4Nz8pYFHOtEkZjNzSJtqvolWElNVqzRFzRjZafW4zPt76D0qYDB ezkDMqOQqIUE5zLKc6gG5vikaPo/d36VYF1EiFqCoeO0Q3RMhoElEViE1j92SH5z NSFS+SA5R5CFIJfOL0nrPoimHnbJ/JK2+Z1j4sLCLvMZgprcsGzwfvBANaPNVf/G WsapyWU5TXRlhELW14csdkn7QXhEbSkgTffHpemJVj65UScYTGcanx4rLDdh7m2t KJpGQpcoKi8m =3xU8 -----END PGP SIGNATURE----- Thu Jan 18 13:45:20 UTC 2024 I: Checking whether the package is not for us Thu Jan 18 13:45:20 UTC 2024 I: Starting 1st build on remote node ionos12-i386.debian.net. Thu Jan 18 13:45:20 UTC 2024 I: Preparing to do remote build '1' on ionos12-i386.debian.net. Thu Jan 18 13:56:32 UTC 2024 I: Deleting $TMPDIR on ionos12-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu Jan 18 01:45:23 -12 2024 I: pbuilder-time-stamp: 1705585523 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-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_4.9.6-7.dsc] I: copying [./mira_4.9.6.orig.tar.bz2] I: copying [./mira_4.9.6-7.debian.tar.xz] I: Extracting source gpgv: Signature made Fri Jun 24 20:29:44 2022 gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 gpgv: issuer "nilesh@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./mira_4.9.6-7.dsc: no acceptable signature found dpkg-source: info: extracting mira in mira-4.9.6 dpkg-source: info: unpacking mira_4.9.6.orig.tar.bz2 dpkg-source: info: unpacking mira_4.9.6-7.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying spelling.patch dpkg-source: info: applying sls-rrna-fix dpkg-source: info: applying man-directory dpkg-source: info: applying fix_buildorder.patch dpkg-source: info: applying gcc-12.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/15184/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='i386' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8 ' DISTRIBUTION='bookworm' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='7208cf5f303f40e9aa778fcc43490051' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' LD_LIBRARY_PATH='/usr/lib/libeatmydata' LD_PRELOAD='libeatmydata.so' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='15184' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.ylEm2WXX/pbuilderrc_Nwy6 --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ylEm2WXX/b1 --logfile b1/build.log mira_4.9.6-7.dsc' SUDO_GID='112' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://78.137.99.97:3128' I: uname -a Linux ionos12-i386 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 6036 -rwxr-xr-x 1 root root 1408088 Apr 23 2023 bash -rwxr-xr-x 3 root root 38404 Sep 19 2022 bunzip2 -rwxr-xr-x 3 root root 38404 Sep 19 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep -rwxr-xr-x 3 root root 38404 Sep 19 2022 bzip2 -rwxr-xr-x 1 root root 17892 Sep 19 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore -rwxr-xr-x 1 root root 42920 Sep 20 2022 cat -rwxr-xr-x 1 root root 79816 Sep 20 2022 chgrp -rwxr-xr-x 1 root root 67496 Sep 20 2022 chmod -rwxr-xr-x 1 root root 79816 Sep 20 2022 chown -rwxr-xr-x 1 root root 162024 Sep 20 2022 cp -rwxr-xr-x 1 root root 136916 Jan 5 2023 dash -rwxr-xr-x 1 root root 137160 Sep 20 2022 date -rwxr-xr-x 1 root root 100364 Sep 20 2022 dd -rwxr-xr-x 1 root root 108940 Sep 20 2022 df -rwxr-xr-x 1 root root 162152 Sep 20 2022 dir -rwxr-xr-x 1 root root 87760 Mar 23 2023 dmesg lrwxrwxrwx 1 root root 8 Dec 19 2022 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 19 2022 domainname -> hostname -rwxr-xr-x 1 root root 38760 Sep 20 2022 echo -rwxr-xr-x 1 root root 41 Jan 24 2023 egrep -rwxr-xr-x 1 root root 34664 Sep 20 2022 false -rwxr-xr-x 1 root root 41 Jan 24 2023 fgrep -rwxr-xr-x 1 root root 84272 Mar 23 2023 findmnt -rwsr-xr-x 1 root root 30240 Mar 23 2023 fusermount -rwxr-xr-x 1 root root 218680 Jan 24 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 Dec 19 2022 hostname -rwxr-xr-x 1 root root 75756 Sep 20 2022 ln -rwxr-xr-x 1 root root 55600 Mar 23 2023 login -rwxr-xr-x 1 root root 162152 Sep 20 2022 ls -rwxr-xr-x 1 root root 214568 Mar 23 2023 lsblk -rwxr-xr-x 1 root root 96328 Sep 20 2022 mkdir -rwxr-xr-x 1 root root 84008 Sep 20 2022 mknod -rwxr-xr-x 1 root root 38792 Sep 20 2022 mktemp -rwxr-xr-x 1 root root 63016 Mar 23 2023 more -rwsr-xr-x 1 root root 58912 Mar 23 2023 mount -rwxr-xr-x 1 root root 13856 Mar 23 2023 mountpoint -rwxr-xr-x 1 root root 157932 Sep 20 2022 mv lrwxrwxrwx 1 root root 8 Dec 19 2022 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 3 2023 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 38792 Sep 20 2022 pwd lrwxrwxrwx 1 root root 4 Apr 23 2023 rbash -> bash -rwxr-xr-x 1 root root 51080 Sep 20 2022 readlink -rwxr-xr-x 1 root root 75720 Sep 20 2022 rm -rwxr-xr-x 1 root root 51080 Sep 20 2022 rmdir -rwxr-xr-x 1 root root 22308 Jul 28 23:46 run-parts -rwxr-xr-x 1 root root 133224 Jan 5 2023 sed lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash -rwxr-xr-x 1 root root 38760 Sep 20 2022 sleep -rwxr-xr-x 1 root root 87976 Sep 20 2022 stty -rwsr-xr-x 1 root root 83492 Mar 23 2023 su -rwxr-xr-x 1 root root 38792 Sep 20 2022 sync -rwxr-xr-x 1 root root 598456 Apr 6 2023 tar -rwxr-xr-x 1 root root 13860 Jul 28 23:46 tempfile -rwxr-xr-x 1 root root 120776 Sep 20 2022 touch -rwxr-xr-x 1 root root 34664 Sep 20 2022 true -rwxr-xr-x 1 root root 17892 Mar 23 2023 ulockmgr_server -rwsr-xr-x 1 root root 30236 Mar 23 2023 umount -rwxr-xr-x 1 root root 38760 Sep 20 2022 uname -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 162152 Sep 20 2022 vdir -rwxr-xr-x 1 root root 71216 Mar 23 2023 wdctl lrwxrwxrwx 1 root root 8 Dec 19 2022 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 6460 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 8103 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/15184/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, xxd, zlib1g-dev, libboost-thread-dev, libboost-regex-dev, libboost-filesystem-dev, libboost-system-dev, libboost-iostreams-dev, docbook-xsl, dblatex dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 18156 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on autoconf-archive; however: Package autoconf-archive is not installed. pbuilder-satisfydepends-dummy depends on libbz2-dev; however: Package libbz2-dev is not installed. pbuilder-satisfydepends-dummy depends on libexpat1-dev; however: Package libexpat1-dev is not installed. pbuilder-satisfydepends-dummy depends on libgoogle-perftools-dev; however: Package libgoogle-perftools-dev is not installed. pbuilder-satisfydepends-dummy depends on flex; however: Package flex is not installed. pbuilder-satisfydepends-dummy depends on libfl-dev; however: Package libfl-dev is not installed. pbuilder-satisfydepends-dummy depends on xxd; however: Package xxd is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-thread-dev; however: Package libboost-thread-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-regex-dev; however: Package libboost-regex-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-filesystem-dev; however: Package libboost-filesystem-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-system-dev; however: Package libboost-system-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-iostreams-dev; however: Package libboost-iostreams-dev is not installed. pbuilder-satisfydepends-dummy depends on docbook-xsl; however: Package docbook-xsl is not installed. pbuilder-satisfydepends-dummy depends on dblatex; however: Package dblatex is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} autoconf-archive{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} dblatex{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} distro-info-data{a} docbook-xml{a} docbook-xsl{a} dwz{a} file{a} flex{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-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} libicu72{a} libjs-jquery{a} libkpathsea6{a} libmagic-mgc{a} libmagic1{a} libmime-charset-perl{a} libpaper-utils{a} libpaper1{a} libpdfbox-java{a} libpipeline1{a} libpixman-1-0{a} libpng16-16{a} libptexenc1{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8{a} libsm6{a} libsombok3{a} libsub-override-perl{a} libsynctex2{a} libtcmalloc-minimal4{a} libteckit0{a} libtexlua53-5{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} python3.11{a} python3.11-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} ucf{a} x11-common{a} xdg-utils{a} xfonts-encodings{a} xfonts-utils{a} xml-core{a} xsltproc{a} xxd{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc ca-certificates curl dblatex-doc default-jre dvisvgm ghostscript iso-codes javascript-common libarchive-cpio-perl libfile-homedir-perl libfile-mimeinfo-perl libglib2.0-data liblog-log4perl-perl libltdl-dev libmail-sendmail-perl libnet-dbus-perl libspreadsheet-parseexcel-perl libx11-protocol-perl libxml2-utils libyaml-tiny-perl lsb-release lynx ruby shared-mime-info tex-gyre tipa tk wget x11-utils x11-xserver-utils xdg-user-dirs 0 packages upgraded, 163 newly installed, 0 to remove and 0 not upgraded. Need to get 437 MB of archives. After unpacking 1186 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main i386 autoconf-archive all 20220903-3 [775 kB] Get: 2 http://deb.debian.org/debian bookworm/main i386 m4 i386 1.4.19-3 [294 kB] Get: 3 http://deb.debian.org/debian bookworm/main i386 flex i386 2.6.4-8.2 [412 kB] Get: 4 http://deb.debian.org/debian bookworm/main i386 libpython3.11-minimal i386 3.11.2-6 [813 kB] Get: 5 http://deb.debian.org/debian bookworm/main i386 libexpat1 i386 2.5.0-1 [103 kB] Get: 6 http://deb.debian.org/debian bookworm/main i386 python3.11-minimal i386 3.11.2-6 [2130 kB] Get: 7 http://deb.debian.org/debian bookworm/main i386 python3-minimal i386 3.11.2-1+b1 [26.3 kB] Get: 8 http://deb.debian.org/debian bookworm/main i386 media-types all 10.0.0 [26.1 kB] Get: 9 http://deb.debian.org/debian bookworm/main i386 readline-common all 8.2-1.3 [69.0 kB] Get: 10 http://deb.debian.org/debian bookworm/main i386 libreadline8 i386 8.2-1.3 [171 kB] Get: 11 http://deb.debian.org/debian bookworm/main i386 libpython3.11-stdlib i386 3.11.2-6 [1799 kB] Get: 12 http://deb.debian.org/debian bookworm/main i386 python3.11 i386 3.11.2-6 [572 kB] Get: 13 http://deb.debian.org/debian bookworm/main i386 libpython3-stdlib i386 3.11.2-1+b1 [9308 B] Get: 14 http://deb.debian.org/debian bookworm/main i386 python3 i386 3.11.2-1+b1 [26.3 kB] Get: 15 http://deb.debian.org/debian bookworm/main i386 sgml-base all 1.31 [15.4 kB] Get: 16 http://deb.debian.org/debian bookworm/main i386 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 17 http://deb.debian.org/debian bookworm/main i386 libmagic-mgc i386 1:5.44-3 [305 kB] Get: 18 http://deb.debian.org/debian bookworm/main i386 libmagic1 i386 1:5.44-3 [114 kB] Get: 19 http://deb.debian.org/debian bookworm/main i386 file i386 1:5.44-3 [42.5 kB] Get: 20 http://deb.debian.org/debian bookworm/main i386 gettext-base i386 0.21-12 [162 kB] Get: 21 http://deb.debian.org/debian bookworm/main i386 libuchardet0 i386 0.0.7-1 [67.9 kB] Get: 22 http://deb.debian.org/debian bookworm/main i386 groff-base i386 1.22.4-10 [932 kB] Get: 23 http://deb.debian.org/debian bookworm/main i386 bsdextrautils i386 2.38.1-5+b1 [90.3 kB] Get: 24 http://deb.debian.org/debian bookworm/main i386 libpipeline1 i386 1.5.7-1 [40.0 kB] Get: 25 http://deb.debian.org/debian bookworm/main i386 man-db i386 2.11.2-2 [1397 kB] Get: 26 http://deb.debian.org/debian bookworm/main i386 ucf all 3.0043+nmu1 [55.2 kB] Get: 27 http://deb.debian.org/debian bookworm/main i386 autoconf all 2.71-3 [332 kB] Get: 28 http://deb.debian.org/debian bookworm/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 29 http://deb.debian.org/debian bookworm/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 30 http://deb.debian.org/debian bookworm/main i386 autopoint all 0.21-12 [495 kB] Get: 31 http://deb.debian.org/debian bookworm/main i386 xml-core all 0.18+nmu1 [23.8 kB] Get: 32 http://deb.debian.org/debian bookworm/main i386 sgml-data all 2.0.11+nmu1 [179 kB] Get: 33 http://deb.debian.org/debian bookworm/main i386 docbook-xml all 4.5-12 [85.2 kB] Get: 34 http://deb.debian.org/debian bookworm/main i386 python-apt-common all 2.6.0 [64.3 kB] Get: 35 http://deb.debian.org/debian bookworm/main i386 distro-info-data all 0.58+deb12u1 [6072 B] Get: 36 http://deb.debian.org/debian bookworm/main i386 python3-apt i386 2.6.0 [163 kB] Get: 37 http://deb.debian.org/debian bookworm/main i386 tex-common all 6.18 [32.5 kB] Get: 38 http://deb.debian.org/debian bookworm/main i386 libpaper1 i386 1.1.29 [12.7 kB] Get: 39 http://deb.debian.org/debian bookworm/main i386 libpaper-utils i386 1.1.29 [8972 B] Get: 40 http://deb.debian.org/debian bookworm/main i386 libkpathsea6 i386 2022.20220321.62855-5.1+deb12u1 [155 kB] Get: 41 http://deb.debian.org/debian bookworm/main i386 libptexenc1 i386 2022.20220321.62855-5.1+deb12u1 [44.8 kB] Get: 42 http://deb.debian.org/debian bookworm/main i386 libsynctex2 i386 2022.20220321.62855-5.1+deb12u1 [62.5 kB] Get: 43 http://deb.debian.org/debian bookworm/main i386 libtexlua53-5 i386 2022.20220321.62855-5.1+deb12u1 [126 kB] Get: 44 http://deb.debian.org/debian bookworm/main i386 t1utils i386 1.41-4 [62.3 kB] Get: 45 http://deb.debian.org/debian bookworm/main i386 libbrotli1 i386 1.0.9-2+b6 [275 kB] Get: 46 http://deb.debian.org/debian bookworm/main i386 libpng16-16 i386 1.6.39-2 [283 kB] Get: 47 http://deb.debian.org/debian bookworm/main i386 libfreetype6 i386 2.12.1+dfsg-5 [410 kB] Get: 48 http://deb.debian.org/debian bookworm/main i386 fonts-dejavu-core all 2.37-6 [1068 kB] Get: 49 http://deb.debian.org/debian bookworm/main i386 fontconfig-config i386 2.14.1-4 [315 kB] Get: 50 http://deb.debian.org/debian bookworm/main i386 libfontconfig1 i386 2.14.1-4 [398 kB] Get: 51 http://deb.debian.org/debian bookworm/main i386 libpixman-1-0 i386 0.42.2-1 [548 kB] Get: 52 http://deb.debian.org/debian bookworm/main i386 libxau6 i386 1:1.0.9-1 [20.0 kB] Get: 53 http://deb.debian.org/debian bookworm/main i386 libbsd0 i386 0.11.7-2 [121 kB] Get: 54 http://deb.debian.org/debian bookworm/main i386 libxdmcp6 i386 1:1.1.2-3 [26.7 kB] Get: 55 http://deb.debian.org/debian bookworm/main i386 libxcb1 i386 1.15-1 [148 kB] Get: 56 http://deb.debian.org/debian bookworm/main i386 libx11-data all 2:1.8.4-2+deb12u2 [292 kB] Get: 57 http://deb.debian.org/debian bookworm/main i386 libx11-6 i386 2:1.8.4-2+deb12u2 [782 kB] Get: 58 http://deb.debian.org/debian bookworm/main i386 libxcb-render0 i386 1.15-1 [116 kB] Get: 59 http://deb.debian.org/debian bookworm/main i386 libxcb-shm0 i386 1.15-1 [106 kB] Get: 60 http://deb.debian.org/debian bookworm/main i386 libxext6 i386 2:1.3.4-1+b1 [55.3 kB] Get: 61 http://deb.debian.org/debian bookworm/main i386 libxrender1 i386 1:0.9.10-1.1 [34.1 kB] Get: 62 http://deb.debian.org/debian bookworm/main i386 libcairo2 i386 1.16.0-7 [627 kB] Get: 63 http://deb.debian.org/debian bookworm/main i386 libgraphite2-3 i386 1.3.14-1 [84.0 kB] Get: 64 http://deb.debian.org/debian bookworm/main i386 libglib2.0-0 i386 2.74.6-2 [1467 kB] Get: 65 http://deb.debian.org/debian bookworm/main i386 libharfbuzz0b i386 6.0.0+dfsg-3 [1966 kB] Get: 66 http://deb.debian.org/debian bookworm/main i386 libicu72 i386 72.1-3 [9541 kB] Get: 67 http://deb.debian.org/debian bookworm/main i386 libteckit0 i386 2.5.11+ds1-1+b1 [282 kB] Get: 68 http://deb.debian.org/debian bookworm/main i386 x11-common all 1:7.7+23 [252 kB] Get: 69 http://deb.debian.org/debian bookworm/main i386 libice6 i386 2:1.0.10-1 [60.8 kB] Get: 70 http://deb.debian.org/debian bookworm/main i386 libsm6 i386 2:1.2.3-1 [35.7 kB] Get: 71 http://deb.debian.org/debian bookworm/main i386 libxt6 i386 1:1.2.1-1.1 [192 kB] Get: 72 http://deb.debian.org/debian bookworm/main i386 libxmu6 i386 2:1.1.3-3 [62.5 kB] Get: 73 http://deb.debian.org/debian bookworm/main i386 libxpm4 i386 1:3.5.12-1.1+deb12u1 [50.4 kB] Get: 74 http://deb.debian.org/debian bookworm/main i386 libxaw7 i386 2:1.0.14-1 [209 kB] Get: 75 http://deb.debian.org/debian bookworm/main i386 libxi6 i386 2:1.8-1+b1 [86.2 kB] Get: 76 http://deb.debian.org/debian bookworm/main i386 libzzip-0-13 i386 0.13.72+dfsg.1-1.1 [60.1 kB] Get: 77 http://deb.debian.org/debian bookworm/main i386 texlive-binaries i386 2022.20220321.62855-5.1+deb12u1 [8537 kB] Get: 78 http://deb.debian.org/debian bookworm/main i386 xdg-utils all 1.1.3-4.1 [75.5 kB] Get: 79 http://deb.debian.org/debian bookworm/main i386 texlive-base all 2022.20230122-3 [21.9 MB] Get: 80 http://deb.debian.org/debian bookworm/main i386 texlive-fonts-recommended all 2022.20230122-3 [4988 kB] Get: 81 http://deb.debian.org/debian bookworm/main i386 fonts-lmodern all 2.005-1 [4540 kB] Get: 82 http://deb.debian.org/debian bookworm/main i386 texlive-latex-base all 2022.20230122-3 [1182 kB] Get: 83 http://deb.debian.org/debian bookworm/main i386 texlive-latex-recommended all 2022.20230122-3 [8880 kB] Get: 84 http://deb.debian.org/debian bookworm/main i386 texlive all 2022.20230122-3 [18.2 kB] Get: 85 http://deb.debian.org/debian bookworm/main i386 texlive-bibtex-extra all 2022.20230122-4 [75.6 MB] Get: 86 http://deb.debian.org/debian bookworm/main i386 libthai-data all 0.1.29-1 [176 kB] Get: 87 http://deb.debian.org/debian bookworm/main i386 libdatrie1 i386 0.2.13-2+b1 [45.0 kB] Get: 88 http://deb.debian.org/debian bookworm/main i386 libthai0 i386 0.1.29-1 [58.6 kB] Get: 89 http://deb.debian.org/debian bookworm/main i386 libsombok3 i386 2.4.0-2+b1 [33.2 kB] Get: 90 http://deb.debian.org/debian bookworm/main i386 libmime-charset-perl all 1.013.1-2 [34.0 kB] Get: 91 http://deb.debian.org/debian bookworm/main i386 libunicode-linebreak-perl i386 0.0.20190101-1+b4 [99.1 kB] Get: 92 http://deb.debian.org/debian bookworm/main i386 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 93 http://deb.debian.org/debian bookworm/main i386 libfontenc1 i386 1:1.1.4-1 [24.5 kB] Get: 94 http://deb.debian.org/debian bookworm/main i386 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 95 http://deb.debian.org/debian bookworm/main i386 xfonts-utils i386 1:7.7+6 [95.2 kB] Get: 96 http://deb.debian.org/debian bookworm/main i386 lmodern all 2.005-1 [9480 kB] Get: 97 http://deb.debian.org/debian bookworm/main i386 texlive-luatex all 2022.20230122-3 [22.7 MB] Get: 98 http://deb.debian.org/debian bookworm/main i386 texlive-plain-generic all 2022.20230122-4 [28.9 MB] Get: 99 http://deb.debian.org/debian bookworm/main i386 texlive-extra-utils all 2022.20230122-4 [59.0 MB] Get: 100 http://deb.debian.org/debian bookworm/main i386 libapache-pom-java all 29-2 [5276 B] Get: 101 http://deb.debian.org/debian bookworm/main i386 libcommons-parent-java all 56-1 [10.8 kB] Get: 102 http://deb.debian.org/debian bookworm/main i386 libcommons-logging-java all 1.2-3 [62.4 kB] Get: 103 http://deb.debian.org/debian bookworm/main i386 libfontbox-java all 1:1.8.16-2 [211 kB] Get: 104 http://deb.debian.org/debian bookworm/main i386 libpdfbox-java all 1:1.8.16-2 [5205 kB] Get: 105 http://deb.debian.org/debian bookworm/main i386 preview-latex-style all 12.2-1 [201 kB] Get: 106 http://deb.debian.org/debian bookworm/main i386 texlive-pictures all 2022.20230122-3 [15.8 MB] Get: 107 http://deb.debian.org/debian bookworm/main i386 texlive-latex-extra all 2022.20230122-4 [19.2 MB] Get: 108 http://deb.debian.org/debian bookworm/main i386 fonts-gfs-baskerville all 1.1-6 [43.7 kB] Get: 109 http://deb.debian.org/debian bookworm/main i386 fonts-gfs-porson all 1.1-7 [33.8 kB] Get: 110 http://deb.debian.org/debian bookworm/main i386 texlive-lang-greek all 2022.20230122-1 [78.1 MB] Get: 111 http://deb.debian.org/debian bookworm/main i386 texlive-science all 2022.20230122-4 [3722 kB] Get: 112 http://deb.debian.org/debian bookworm/main i386 libxml2 i386 2.9.14+dfsg-1.3~deb12u1 [720 kB] Get: 113 http://deb.debian.org/debian bookworm/main i386 libxslt1.1 i386 1.1.35-1 [253 kB] Get: 114 http://deb.debian.org/debian bookworm/main i386 xsltproc i386 1.1.35-1 [127 kB] Get: 115 http://deb.debian.org/debian bookworm/main i386 dblatex all 0.3.12py3-2 [371 kB] Get: 116 http://deb.debian.org/debian bookworm/main i386 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 117 http://deb.debian.org/debian bookworm/main i386 libtool all 2.4.7-5 [517 kB] Get: 118 http://deb.debian.org/debian bookworm/main i386 dh-autoreconf all 20 [17.1 kB] Get: 119 http://deb.debian.org/debian bookworm/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 120 http://deb.debian.org/debian bookworm/main i386 libsub-override-perl all 0.09-4 [9304 B] Get: 121 http://deb.debian.org/debian bookworm/main i386 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 122 http://deb.debian.org/debian bookworm/main i386 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 123 http://deb.debian.org/debian bookworm/main i386 libelf1 i386 0.188-2.1 [179 kB] Get: 124 http://deb.debian.org/debian bookworm/main i386 dwz i386 0.15-1 [118 kB] Get: 125 http://deb.debian.org/debian bookworm/main i386 gettext i386 0.21-12 [1311 kB] Get: 126 http://deb.debian.org/debian bookworm/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 127 http://deb.debian.org/debian bookworm/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 128 http://deb.debian.org/debian bookworm/main i386 debhelper all 13.11.4 [942 kB] Get: 129 http://deb.debian.org/debian bookworm/main i386 docbook-xsl all 1.79.2+dfsg-2 [1237 kB] Get: 130 http://deb.debian.org/debian bookworm/main i386 icu-devtools i386 72.1-3 [214 kB] Get: 131 http://deb.debian.org/debian bookworm/main i386 libboost1.74-dev i386 1.74.0+ds1-21 [9508 kB] Get: 132 http://deb.debian.org/debian bookworm/main i386 libboost-atomic1.74.0 i386 1.74.0+ds1-21 [221 kB] Get: 133 http://deb.debian.org/debian bookworm/main i386 libboost-atomic1.74-dev i386 1.74.0+ds1-21 [222 kB] Get: 134 http://deb.debian.org/debian bookworm/main i386 libboost-chrono1.74.0 i386 1.74.0+ds1-21 [230 kB] Get: 135 http://deb.debian.org/debian bookworm/main i386 libboost-chrono1.74-dev i386 1.74.0+ds1-21 [237 kB] Get: 136 http://deb.debian.org/debian bookworm/main i386 libboost-date-time1.74.0 i386 1.74.0+ds1-21 [218 kB] Get: 137 http://deb.debian.org/debian bookworm/main i386 libboost-serialization1.74.0 i386 1.74.0+ds1-21 [325 kB] Get: 138 http://deb.debian.org/debian bookworm/main i386 libboost-serialization1.74-dev i386 1.74.0+ds1-21 [368 kB] Get: 139 http://deb.debian.org/debian bookworm/main i386 libboost-date-time1.74-dev i386 1.74.0+ds1-21 [226 kB] Get: 140 http://deb.debian.org/debian bookworm/main i386 libboost-filesystem1.74.0 i386 1.74.0+ds1-21 [264 kB] Get: 141 http://deb.debian.org/debian bookworm/main i386 libboost-system1.74.0 i386 1.74.0+ds1-21 [218 kB] Get: 142 http://deb.debian.org/debian bookworm/main i386 libboost-system1.74-dev i386 1.74.0+ds1-21 [219 kB] Get: 143 http://deb.debian.org/debian bookworm/main i386 libboost-filesystem1.74-dev i386 1.74.0+ds1-21 [286 kB] Get: 144 http://deb.debian.org/debian bookworm/main i386 libboost-filesystem-dev i386 1.74.0.3 [4368 B] Get: 145 http://deb.debian.org/debian bookworm/main i386 libboost-regex1.74.0 i386 1.74.0+ds1-21 [509 kB] Get: 146 http://deb.debian.org/debian bookworm/main i386 libicu-dev i386 72.1-3 [10.6 MB] Get: 147 http://deb.debian.org/debian bookworm/main i386 libboost-regex1.74-dev i386 1.74.0+ds1-21 [585 kB] Get: 148 http://deb.debian.org/debian bookworm/main i386 libboost-iostreams1.74-dev i386 1.74.0+ds1-21 [250 kB] Get: 149 http://deb.debian.org/debian bookworm/main i386 libboost-iostreams-dev i386 1.74.0.3 [4320 B] Get: 150 http://deb.debian.org/debian bookworm/main i386 libboost-regex-dev i386 1.74.0.3 [4596 B] Get: 151 http://deb.debian.org/debian bookworm/main i386 libboost-system-dev i386 1.74.0.3 [4472 B] Get: 152 http://deb.debian.org/debian bookworm/main i386 libboost-thread1.74.0 i386 1.74.0+ds1-21 [259 kB] Get: 153 http://deb.debian.org/debian bookworm/main i386 libboost-thread1.74-dev i386 1.74.0+ds1-21 [270 kB] Get: 154 http://deb.debian.org/debian bookworm/main i386 libboost-thread-dev i386 1.74.0.3 [4356 B] Get: 155 http://deb.debian.org/debian bookworm/main i386 libbz2-dev i386 1.0.8-5+b1 [31.5 kB] Get: 156 http://deb.debian.org/debian bookworm/main i386 libexpat1-dev i386 2.5.0-1 [158 kB] Get: 157 http://deb.debian.org/debian bookworm/main i386 libfl2 i386 2.6.4-8.2 [84.0 kB] Get: 158 http://deb.debian.org/debian bookworm/main i386 libfl-dev i386 2.6.4-8.2 [85.4 kB] Get: 159 http://deb.debian.org/debian bookworm/main i386 libtcmalloc-minimal4 i386 2.10-1 [94.5 kB] Get: 160 http://deb.debian.org/debian bookworm/main i386 libgoogle-perftools4 i386 2.10-1 [205 kB] Get: 161 http://deb.debian.org/debian bookworm/main i386 libgoogle-perftools-dev i386 2.10-1 [466 kB] Get: 162 http://deb.debian.org/debian bookworm/main i386 xxd i386 2:9.0.1378-2 [83.7 kB] Get: 163 http://deb.debian.org/debian bookworm/main i386 zlib1g-dev i386 1:1.2.13.dfsg-1 [913 kB] Fetched 437 MB in 2min 6s (3475 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package autoconf-archive. (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 ... 18156 files and directories currently installed.) Preparing to unpack .../0-autoconf-archive_20220903-3_all.deb ... Unpacking autoconf-archive (20220903-3) ... Selecting previously unselected package m4. Preparing to unpack .../1-m4_1.4.19-3_i386.deb ... Unpacking m4 (1.4.19-3) ... Selecting previously unselected package flex. Preparing to unpack .../2-flex_2.6.4-8.2_i386.deb ... Unpacking flex (2.6.4-8.2) ... Selecting previously unselected package libpython3.11-minimal:i386. Preparing to unpack .../3-libpython3.11-minimal_3.11.2-6_i386.deb ... Unpacking libpython3.11-minimal:i386 (3.11.2-6) ... Selecting previously unselected package libexpat1:i386. Preparing to unpack .../4-libexpat1_2.5.0-1_i386.deb ... Unpacking libexpat1:i386 (2.5.0-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../5-python3.11-minimal_3.11.2-6_i386.deb ... Unpacking python3.11-minimal (3.11.2-6) ... Setting up libpython3.11-minimal:i386 (3.11.2-6) ... Setting up libexpat1:i386 (2.5.0-1) ... Setting up python3.11-minimal (3.11.2-6) ... 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 ... 19836 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.2-1+b1_i386.deb ... Unpacking python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.0.0_all.deb ... Unpacking media-types (10.0.0) ... Selecting previously unselected package readline-common. Preparing to unpack .../2-readline-common_8.2-1.3_all.deb ... Unpacking readline-common (8.2-1.3) ... Selecting previously unselected package libreadline8:i386. Preparing to unpack .../3-libreadline8_8.2-1.3_i386.deb ... Unpacking libreadline8:i386 (8.2-1.3) ... Selecting previously unselected package libpython3.11-stdlib:i386. Preparing to unpack .../4-libpython3.11-stdlib_3.11.2-6_i386.deb ... Unpacking libpython3.11-stdlib:i386 (3.11.2-6) ... Selecting previously unselected package python3.11. Preparing to unpack .../5-python3.11_3.11.2-6_i386.deb ... Unpacking python3.11 (3.11.2-6) ... Selecting previously unselected package libpython3-stdlib:i386. Preparing to unpack .../6-libpython3-stdlib_3.11.2-1+b1_i386.deb ... Unpacking libpython3-stdlib:i386 (3.11.2-1+b1) ... Setting up python3-minimal (3.11.2-1+b1) ... 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 ... 20270 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.2-1+b1_i386.deb ... Unpacking python3 (3.11.2-1+b1) ... Selecting previously unselected package sgml-base. Preparing to unpack .../001-sgml-base_1.31_all.deb ... Unpacking sgml-base (1.31) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../002-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../003-libmagic-mgc_1%3a5.44-3_i386.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:i386. Preparing to unpack .../004-libmagic1_1%3a5.44-3_i386.deb ... Unpacking libmagic1:i386 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../005-file_1%3a5.44-3_i386.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../006-gettext-base_0.21-12_i386.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../007-libuchardet0_0.0.7-1_i386.deb ... Unpacking libuchardet0:i386 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../008-groff-base_1.22.4-10_i386.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../009-bsdextrautils_2.38.1-5+b1_i386.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../010-libpipeline1_1.5.7-1_i386.deb ... Unpacking libpipeline1:i386 (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../011-man-db_2.11.2-2_i386.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package ucf. Preparing to unpack .../012-ucf_3.0043+nmu1_all.deb ... Moving old data out of the way Unpacking ucf (3.0043+nmu1) ... Selecting previously unselected package autoconf. Preparing to unpack .../013-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../014-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../015-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../016-autopoint_0.21-12_all.deb ... Unpacking autopoint (0.21-12) ... Selecting previously unselected package xml-core. Preparing to unpack .../017-xml-core_0.18+nmu1_all.deb ... Unpacking xml-core (0.18+nmu1) ... Selecting previously unselected package sgml-data. Preparing to unpack .../018-sgml-data_2.0.11+nmu1_all.deb ... Unpacking sgml-data (2.0.11+nmu1) ... Selecting previously unselected package docbook-xml. Preparing to unpack .../019-docbook-xml_4.5-12_all.deb ... Unpacking docbook-xml (4.5-12) ... Selecting previously unselected package python-apt-common. Preparing to unpack .../020-python-apt-common_2.6.0_all.deb ... Unpacking python-apt-common (2.6.0) ... Selecting previously unselected package distro-info-data. Preparing to unpack .../021-distro-info-data_0.58+deb12u1_all.deb ... Unpacking distro-info-data (0.58+deb12u1) ... Selecting previously unselected package python3-apt. Preparing to unpack .../022-python3-apt_2.6.0_i386.deb ... Unpacking python3-apt (2.6.0) ... Selecting previously unselected package tex-common. Preparing to unpack .../023-tex-common_6.18_all.deb ... Unpacking tex-common (6.18) ... Selecting previously unselected package libpaper1:i386. Preparing to unpack .../024-libpaper1_1.1.29_i386.deb ... Unpacking libpaper1:i386 (1.1.29) ... Selecting previously unselected package libpaper-utils. Preparing to unpack .../025-libpaper-utils_1.1.29_i386.deb ... Unpacking libpaper-utils (1.1.29) ... Selecting previously unselected package libkpathsea6:i386. Preparing to unpack .../026-libkpathsea6_2022.20220321.62855-5.1+deb12u1_i386.deb ... Unpacking libkpathsea6:i386 (2022.20220321.62855-5.1+deb12u1) ... Selecting previously unselected package libptexenc1:i386. Preparing to unpack .../027-libptexenc1_2022.20220321.62855-5.1+deb12u1_i386.deb ... Unpacking libptexenc1:i386 (2022.20220321.62855-5.1+deb12u1) ... Selecting previously unselected package libsynctex2:i386. Preparing to unpack .../028-libsynctex2_2022.20220321.62855-5.1+deb12u1_i386.deb ... Unpacking libsynctex2:i386 (2022.20220321.62855-5.1+deb12u1) ... Selecting previously unselected package libtexlua53-5:i386. Preparing to unpack .../029-libtexlua53-5_2022.20220321.62855-5.1+deb12u1_i386.deb ... Unpacking libtexlua53-5:i386 (2022.20220321.62855-5.1+deb12u1) ... Selecting previously unselected package t1utils. Preparing to unpack .../030-t1utils_1.41-4_i386.deb ... Unpacking t1utils (1.41-4) ... Selecting previously unselected package libbrotli1:i386. Preparing to unpack .../031-libbrotli1_1.0.9-2+b6_i386.deb ... Unpacking libbrotli1:i386 (1.0.9-2+b6) ... Selecting previously unselected package libpng16-16:i386. Preparing to unpack .../032-libpng16-16_1.6.39-2_i386.deb ... Unpacking libpng16-16:i386 (1.6.39-2) ... Selecting previously unselected package libfreetype6:i386. Preparing to unpack .../033-libfreetype6_2.12.1+dfsg-5_i386.deb ... Unpacking libfreetype6:i386 (2.12.1+dfsg-5) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../034-fonts-dejavu-core_2.37-6_all.deb ... Unpacking fonts-dejavu-core (2.37-6) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../035-fontconfig-config_2.14.1-4_i386.deb ... Unpacking fontconfig-config (2.14.1-4) ... Selecting previously unselected package libfontconfig1:i386. Preparing to unpack .../036-libfontconfig1_2.14.1-4_i386.deb ... Unpacking libfontconfig1:i386 (2.14.1-4) ... Selecting previously unselected package libpixman-1-0:i386. Preparing to unpack .../037-libpixman-1-0_0.42.2-1_i386.deb ... Unpacking libpixman-1-0:i386 (0.42.2-1) ... Selecting previously unselected package libxau6:i386. Preparing to unpack .../038-libxau6_1%3a1.0.9-1_i386.deb ... Unpacking libxau6:i386 (1:1.0.9-1) ... Selecting previously unselected package libbsd0:i386. Preparing to unpack .../039-libbsd0_0.11.7-2_i386.deb ... Unpacking libbsd0:i386 (0.11.7-2) ... Selecting previously unselected package libxdmcp6:i386. Preparing to unpack .../040-libxdmcp6_1%3a1.1.2-3_i386.deb ... Unpacking libxdmcp6:i386 (1:1.1.2-3) ... Selecting previously unselected package libxcb1:i386. Preparing to unpack .../041-libxcb1_1.15-1_i386.deb ... Unpacking libxcb1:i386 (1.15-1) ... Selecting previously unselected package libx11-data. Preparing to unpack .../042-libx11-data_2%3a1.8.4-2+deb12u2_all.deb ... Unpacking libx11-data (2:1.8.4-2+deb12u2) ... Selecting previously unselected package libx11-6:i386. Preparing to unpack .../043-libx11-6_2%3a1.8.4-2+deb12u2_i386.deb ... Unpacking libx11-6:i386 (2:1.8.4-2+deb12u2) ... Selecting previously unselected package libxcb-render0:i386. Preparing to unpack .../044-libxcb-render0_1.15-1_i386.deb ... Unpacking libxcb-render0:i386 (1.15-1) ... Selecting previously unselected package libxcb-shm0:i386. Preparing to unpack .../045-libxcb-shm0_1.15-1_i386.deb ... Unpacking libxcb-shm0:i386 (1.15-1) ... Selecting previously unselected package libxext6:i386. Preparing to unpack .../046-libxext6_2%3a1.3.4-1+b1_i386.deb ... Unpacking libxext6:i386 (2:1.3.4-1+b1) ... Selecting previously unselected package libxrender1:i386. Preparing to unpack .../047-libxrender1_1%3a0.9.10-1.1_i386.deb ... Unpacking libxrender1:i386 (1:0.9.10-1.1) ... Selecting previously unselected package libcairo2:i386. Preparing to unpack .../048-libcairo2_1.16.0-7_i386.deb ... Unpacking libcairo2:i386 (1.16.0-7) ... Selecting previously unselected package libgraphite2-3:i386. Preparing to unpack .../049-libgraphite2-3_1.3.14-1_i386.deb ... Unpacking libgraphite2-3:i386 (1.3.14-1) ... Selecting previously unselected package libglib2.0-0:i386. Preparing to unpack .../050-libglib2.0-0_2.74.6-2_i386.deb ... Unpacking libglib2.0-0:i386 (2.74.6-2) ... Selecting previously unselected package libharfbuzz0b:i386. Preparing to unpack .../051-libharfbuzz0b_6.0.0+dfsg-3_i386.deb ... Unpacking libharfbuzz0b:i386 (6.0.0+dfsg-3) ... Selecting previously unselected package libicu72:i386. Preparing to unpack .../052-libicu72_72.1-3_i386.deb ... Unpacking libicu72:i386 (72.1-3) ... Selecting previously unselected package libteckit0:i386. Preparing to unpack .../053-libteckit0_2.5.11+ds1-1+b1_i386.deb ... Unpacking libteckit0:i386 (2.5.11+ds1-1+b1) ... Selecting previously unselected package x11-common. Preparing to unpack .../054-x11-common_1%3a7.7+23_all.deb ... Unpacking x11-common (1:7.7+23) ... Selecting previously unselected package libice6:i386. Preparing to unpack .../055-libice6_2%3a1.0.10-1_i386.deb ... Unpacking libice6:i386 (2:1.0.10-1) ... Selecting previously unselected package libsm6:i386. Preparing to unpack .../056-libsm6_2%3a1.2.3-1_i386.deb ... Unpacking libsm6:i386 (2:1.2.3-1) ... Selecting previously unselected package libxt6:i386. Preparing to unpack .../057-libxt6_1%3a1.2.1-1.1_i386.deb ... Unpacking libxt6:i386 (1:1.2.1-1.1) ... Selecting previously unselected package libxmu6:i386. Preparing to unpack .../058-libxmu6_2%3a1.1.3-3_i386.deb ... Unpacking libxmu6:i386 (2:1.1.3-3) ... Selecting previously unselected package libxpm4:i386. Preparing to unpack .../059-libxpm4_1%3a3.5.12-1.1+deb12u1_i386.deb ... Unpacking libxpm4:i386 (1:3.5.12-1.1+deb12u1) ... Selecting previously unselected package libxaw7:i386. Preparing to unpack .../060-libxaw7_2%3a1.0.14-1_i386.deb ... Unpacking libxaw7:i386 (2:1.0.14-1) ... Selecting previously unselected package libxi6:i386. Preparing to unpack .../061-libxi6_2%3a1.8-1+b1_i386.deb ... Unpacking libxi6:i386 (2:1.8-1+b1) ... Selecting previously unselected package libzzip-0-13:i386. Preparing to unpack .../062-libzzip-0-13_0.13.72+dfsg.1-1.1_i386.deb ... Unpacking libzzip-0-13:i386 (0.13.72+dfsg.1-1.1) ... Selecting previously unselected package texlive-binaries. Preparing to unpack .../063-texlive-binaries_2022.20220321.62855-5.1+deb12u1_i386.deb ... Unpacking texlive-binaries (2022.20220321.62855-5.1+deb12u1) ... Selecting previously unselected package xdg-utils. Preparing to unpack .../064-xdg-utils_1.1.3-4.1_all.deb ... Unpacking xdg-utils (1.1.3-4.1) ... Selecting previously unselected package texlive-base. Preparing to unpack .../065-texlive-base_2022.20230122-3_all.deb ... Unpacking texlive-base (2022.20230122-3) ... Selecting previously unselected package texlive-fonts-recommended. Preparing to unpack .../066-texlive-fonts-recommended_2022.20230122-3_all.deb ... Unpacking texlive-fonts-recommended (2022.20230122-3) ... Selecting previously unselected package fonts-lmodern. Preparing to unpack .../067-fonts-lmodern_2.005-1_all.deb ... Unpacking fonts-lmodern (2.005-1) ... Selecting previously unselected package texlive-latex-base. Preparing to unpack .../068-texlive-latex-base_2022.20230122-3_all.deb ... Unpacking texlive-latex-base (2022.20230122-3) ... Selecting previously unselected package texlive-latex-recommended. Preparing to unpack .../069-texlive-latex-recommended_2022.20230122-3_all.deb ... Unpacking texlive-latex-recommended (2022.20230122-3) ... Selecting previously unselected package texlive. Preparing to unpack .../070-texlive_2022.20230122-3_all.deb ... Unpacking texlive (2022.20230122-3) ... Selecting previously unselected package texlive-bibtex-extra. Preparing to unpack .../071-texlive-bibtex-extra_2022.20230122-4_all.deb ... Unpacking texlive-bibtex-extra (2022.20230122-4) ... Selecting previously unselected package libthai-data. Preparing to unpack .../072-libthai-data_0.1.29-1_all.deb ... Unpacking libthai-data (0.1.29-1) ... Selecting previously unselected package libdatrie1:i386. Preparing to unpack .../073-libdatrie1_0.2.13-2+b1_i386.deb ... Unpacking libdatrie1:i386 (0.2.13-2+b1) ... Selecting previously unselected package libthai0:i386. Preparing to unpack .../074-libthai0_0.1.29-1_i386.deb ... Unpacking libthai0:i386 (0.1.29-1) ... Selecting previously unselected package libsombok3:i386. Preparing to unpack .../075-libsombok3_2.4.0-2+b1_i386.deb ... Unpacking libsombok3:i386 (2.4.0-2+b1) ... Selecting previously unselected package libmime-charset-perl. Preparing to unpack .../076-libmime-charset-perl_1.013.1-2_all.deb ... Unpacking libmime-charset-perl (1.013.1-2) ... Selecting previously unselected package libunicode-linebreak-perl. Preparing to unpack .../077-libunicode-linebreak-perl_0.0.20190101-1+b4_i386.deb ... Unpacking libunicode-linebreak-perl (0.0.20190101-1+b4) ... Selecting previously unselected package libjs-jquery. Preparing to unpack .../078-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Selecting previously unselected package libfontenc1:i386. Preparing to unpack .../079-libfontenc1_1%3a1.1.4-1_i386.deb ... Unpacking libfontenc1:i386 (1:1.1.4-1) ... Selecting previously unselected package xfonts-encodings. Preparing to unpack .../080-xfonts-encodings_1%3a1.0.4-2.2_all.deb ... Unpacking xfonts-encodings (1:1.0.4-2.2) ... Selecting previously unselected package xfonts-utils. Preparing to unpack .../081-xfonts-utils_1%3a7.7+6_i386.deb ... Unpacking xfonts-utils (1:7.7+6) ... Selecting previously unselected package lmodern. Preparing to unpack .../082-lmodern_2.005-1_all.deb ... Unpacking lmodern (2.005-1) ... Selecting previously unselected package texlive-luatex. Preparing to unpack .../083-texlive-luatex_2022.20230122-3_all.deb ... Unpacking texlive-luatex (2022.20230122-3) ... Selecting previously unselected package texlive-plain-generic. Preparing to unpack .../084-texlive-plain-generic_2022.20230122-4_all.deb ... Unpacking texlive-plain-generic (2022.20230122-4) ... Selecting previously unselected package texlive-extra-utils. Preparing to unpack .../085-texlive-extra-utils_2022.20230122-4_all.deb ... Unpacking texlive-extra-utils (2022.20230122-4) ... Selecting previously unselected package libapache-pom-java. Preparing to unpack .../086-libapache-pom-java_29-2_all.deb ... Unpacking libapache-pom-java (29-2) ... Selecting previously unselected package libcommons-parent-java. Preparing to unpack .../087-libcommons-parent-java_56-1_all.deb ... Unpacking libcommons-parent-java (56-1) ... Selecting previously unselected package libcommons-logging-java. Preparing to unpack .../088-libcommons-logging-java_1.2-3_all.deb ... Unpacking libcommons-logging-java (1.2-3) ... Selecting previously unselected package libfontbox-java. Preparing to unpack .../089-libfontbox-java_1%3a1.8.16-2_all.deb ... Unpacking libfontbox-java (1:1.8.16-2) ... Selecting previously unselected package libpdfbox-java. Preparing to unpack .../090-libpdfbox-java_1%3a1.8.16-2_all.deb ... Unpacking libpdfbox-java (1:1.8.16-2) ... Selecting previously unselected package preview-latex-style. Preparing to unpack .../091-preview-latex-style_12.2-1_all.deb ... Unpacking preview-latex-style (12.2-1) ... Selecting previously unselected package texlive-pictures. Preparing to unpack .../092-texlive-pictures_2022.20230122-3_all.deb ... Unpacking texlive-pictures (2022.20230122-3) ... Selecting previously unselected package texlive-latex-extra. Preparing to unpack .../093-texlive-latex-extra_2022.20230122-4_all.deb ... Unpacking texlive-latex-extra (2022.20230122-4) ... Selecting previously unselected package fonts-gfs-baskerville. Preparing to unpack .../094-fonts-gfs-baskerville_1.1-6_all.deb ... Unpacking fonts-gfs-baskerville (1.1-6) ... Selecting previously unselected package fonts-gfs-porson. Preparing to unpack .../095-fonts-gfs-porson_1.1-7_all.deb ... Unpacking fonts-gfs-porson (1.1-7) ... Selecting previously unselected package texlive-lang-greek. Preparing to unpack .../096-texlive-lang-greek_2022.20230122-1_all.deb ... Unpacking texlive-lang-greek (2022.20230122-1) ... Selecting previously unselected package texlive-science. Preparing to unpack .../097-texlive-science_2022.20230122-4_all.deb ... Unpacking texlive-science (2022.20230122-4) ... Selecting previously unselected package libxml2:i386. Preparing to unpack .../098-libxml2_2.9.14+dfsg-1.3~deb12u1_i386.deb ... Unpacking libxml2:i386 (2.9.14+dfsg-1.3~deb12u1) ... Selecting previously unselected package libxslt1.1:i386. Preparing to unpack .../099-libxslt1.1_1.1.35-1_i386.deb ... Unpacking libxslt1.1:i386 (1.1.35-1) ... Selecting previously unselected package xsltproc. Preparing to unpack .../100-xsltproc_1.1.35-1_i386.deb ... Unpacking xsltproc (1.1.35-1) ... Selecting previously unselected package dblatex. Preparing to unpack .../101-dblatex_0.3.12py3-2_all.deb ... Unpacking dblatex (0.3.12py3-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../102-libdebhelper-perl_13.11.4_all.deb ... Unpacking libdebhelper-perl (13.11.4) ... Selecting previously unselected package libtool. Preparing to unpack .../103-libtool_2.4.7-5_all.deb ... Unpacking libtool (2.4.7-5) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../104-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../105-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../106-libsub-override-perl_0.09-4_all.deb ... Unpacking libsub-override-perl (0.09-4) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../107-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../108-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1:i386. Preparing to unpack .../109-libelf1_0.188-2.1_i386.deb ... Unpacking libelf1:i386 (0.188-2.1) ... Selecting previously unselected package dwz. Preparing to unpack .../110-dwz_0.15-1_i386.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package gettext. Preparing to unpack .../111-gettext_0.21-12_i386.deb ... Unpacking gettext (0.21-12) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../112-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../113-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../114-debhelper_13.11.4_all.deb ... Unpacking debhelper (13.11.4) ... Selecting previously unselected package docbook-xsl. Preparing to unpack .../115-docbook-xsl_1.79.2+dfsg-2_all.deb ... Unpacking docbook-xsl (1.79.2+dfsg-2) ... Selecting previously unselected package icu-devtools. Preparing to unpack .../116-icu-devtools_72.1-3_i386.deb ... Unpacking icu-devtools (72.1-3) ... Selecting previously unselected package libboost1.74-dev:i386. Preparing to unpack .../117-libboost1.74-dev_1.74.0+ds1-21_i386.deb ... Unpacking libboost1.74-dev:i386 (1.74.0+ds1-21) ... Selecting previously unselected package libboost-atomic1.74.0:i386. Preparing to unpack .../118-libboost-atomic1.74.0_1.74.0+ds1-21_i386.deb ... Unpacking libboost-atomic1.74.0:i386 (1.74.0+ds1-21) ... Selecting previously unselected package libboost-atomic1.74-dev:i386. Preparing to unpack .../119-libboost-atomic1.74-dev_1.74.0+ds1-21_i386.deb ... Unpacking libboost-atomic1.74-dev:i386 (1.74.0+ds1-21) ... Selecting previously unselected package libboost-chrono1.74.0:i386. Preparing to unpack .../120-libboost-chrono1.74.0_1.74.0+ds1-21_i386.deb ... Unpacking libboost-chrono1.74.0:i386 (1.74.0+ds1-21) ... Selecting previously unselected package libboost-chrono1.74-dev:i386. Preparing to unpack .../121-libboost-chrono1.74-dev_1.74.0+ds1-21_i386.deb ... Unpacking libboost-chrono1.74-dev:i386 (1.74.0+ds1-21) ... Selecting previously unselected package libboost-date-time1.74.0:i386. Preparing to unpack .../122-libboost-date-time1.74.0_1.74.0+ds1-21_i386.deb ... Unpacking libboost-date-time1.74.0:i386 (1.74.0+ds1-21) ... Selecting previously unselected package libboost-serialization1.74.0:i386. Preparing to unpack .../123-libboost-serialization1.74.0_1.74.0+ds1-21_i386.deb ... Unpacking libboost-serialization1.74.0:i386 (1.74.0+ds1-21) ... Selecting previously unselected package libboost-serialization1.74-dev:i386. Preparing to unpack .../124-libboost-serialization1.74-dev_1.74.0+ds1-21_i386.deb ... Unpacking libboost-serialization1.74-dev:i386 (1.74.0+ds1-21) ... Selecting previously unselected package libboost-date-time1.74-dev:i386. Preparing to unpack .../125-libboost-date-time1.74-dev_1.74.0+ds1-21_i386.deb ... Unpacking libboost-date-time1.74-dev:i386 (1.74.0+ds1-21) ... Selecting previously unselected package libboost-filesystem1.74.0:i386. Preparing to unpack .../126-libboost-filesystem1.74.0_1.74.0+ds1-21_i386.deb ... Unpacking libboost-filesystem1.74.0:i386 (1.74.0+ds1-21) ... Selecting previously unselected package libboost-system1.74.0:i386. Preparing to unpack .../127-libboost-system1.74.0_1.74.0+ds1-21_i386.deb ... Unpacking libboost-system1.74.0:i386 (1.74.0+ds1-21) ... Selecting previously unselected package libboost-system1.74-dev:i386. Preparing to unpack .../128-libboost-system1.74-dev_1.74.0+ds1-21_i386.deb ... Unpacking libboost-system1.74-dev:i386 (1.74.0+ds1-21) ... Selecting previously unselected package libboost-filesystem1.74-dev:i386. Preparing to unpack .../129-libboost-filesystem1.74-dev_1.74.0+ds1-21_i386.deb ... Unpacking libboost-filesystem1.74-dev:i386 (1.74.0+ds1-21) ... Selecting previously unselected package libboost-filesystem-dev:i386. Preparing to unpack .../130-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 .../131-libboost-regex1.74.0_1.74.0+ds1-21_i386.deb ... Unpacking libboost-regex1.74.0:i386 (1.74.0+ds1-21) ... Selecting previously unselected package libicu-dev:i386. Preparing to unpack .../132-libicu-dev_72.1-3_i386.deb ... Unpacking libicu-dev:i386 (72.1-3) ... Selecting previously unselected package libboost-regex1.74-dev:i386. Preparing to unpack .../133-libboost-regex1.74-dev_1.74.0+ds1-21_i386.deb ... Unpacking libboost-regex1.74-dev:i386 (1.74.0+ds1-21) ... Selecting previously unselected package libboost-iostreams1.74-dev:i386. Preparing to unpack .../134-libboost-iostreams1.74-dev_1.74.0+ds1-21_i386.deb ... Unpacking libboost-iostreams1.74-dev:i386 (1.74.0+ds1-21) ... Selecting previously unselected package libboost-iostreams-dev:i386. Preparing to unpack .../135-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 .../136-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 .../137-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 .../138-libboost-thread1.74.0_1.74.0+ds1-21_i386.deb ... Unpacking libboost-thread1.74.0:i386 (1.74.0+ds1-21) ... Selecting previously unselected package libboost-thread1.74-dev:i386. Preparing to unpack .../139-libboost-thread1.74-dev_1.74.0+ds1-21_i386.deb ... Unpacking libboost-thread1.74-dev:i386 (1.74.0+ds1-21) ... Selecting previously unselected package libboost-thread-dev:i386. Preparing to unpack .../140-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 .../141-libbz2-dev_1.0.8-5+b1_i386.deb ... Unpacking libbz2-dev:i386 (1.0.8-5+b1) ... Selecting previously unselected package libexpat1-dev:i386. Preparing to unpack .../142-libexpat1-dev_2.5.0-1_i386.deb ... Unpacking libexpat1-dev:i386 (2.5.0-1) ... Selecting previously unselected package libfl2:i386. Preparing to unpack .../143-libfl2_2.6.4-8.2_i386.deb ... Unpacking libfl2:i386 (2.6.4-8.2) ... Selecting previously unselected package libfl-dev:i386. Preparing to unpack .../144-libfl-dev_2.6.4-8.2_i386.deb ... Unpacking libfl-dev:i386 (2.6.4-8.2) ... Selecting previously unselected package libtcmalloc-minimal4:i386. Preparing to unpack .../145-libtcmalloc-minimal4_2.10-1_i386.deb ... Unpacking libtcmalloc-minimal4:i386 (2.10-1) ... Selecting previously unselected package libgoogle-perftools4:i386. Preparing to unpack .../146-libgoogle-perftools4_2.10-1_i386.deb ... Unpacking libgoogle-perftools4:i386 (2.10-1) ... Selecting previously unselected package libgoogle-perftools-dev:i386. Preparing to unpack .../147-libgoogle-perftools-dev_2.10-1_i386.deb ... Unpacking libgoogle-perftools-dev:i386 (2.10-1) ... Selecting previously unselected package xxd. Preparing to unpack .../148-xxd_2%3a9.0.1378-2_i386.deb ... Unpacking xxd (2:9.0.1378-2) ... Selecting previously unselected package zlib1g-dev:i386. Preparing to unpack .../149-zlib1g-dev_1%3a1.2.13.dfsg-1_i386.deb ... Unpacking zlib1g-dev:i386 (1:1.2.13.dfsg-1) ... Setting up libboost-chrono1.74.0:i386 (1.74.0+ds1-21) ... Setting up media-types (10.0.0) ... Setting up libpipeline1:i386 (1.5.7-1) ... Setting up libboost-system1.74.0:i386 (1.74.0+ds1-21) ... Setting up libgraphite2-3:i386 (1.3.14-1) ... Setting up libpixman-1-0:i386 (0.42.2-1) ... Setting up libxau6:i386 (1:1.0.9-1) ... Setting up libboost1.74-dev:i386 (1.74.0+ds1-21) ... Setting up libicu72:i386 (72.1-3) ... Setting up libboost-atomic1.74.0:i386 (1.74.0+ds1-21) ... Setting up bsdextrautils (2.38.1-5+b1) ... Setting up fonts-gfs-porson (1.1-7) ... Setting up libdatrie1:i386 (0.2.13-2+b1) ... Setting up libmagic-mgc (1:5.44-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libglib2.0-0:i386 (2.74.6-2) ... No schema files found: doing nothing. Setting up distro-info-data (0.58+deb12u1) ... Setting up libdebhelper-perl (13.11.4) ... Setting up libbrotli1:i386 (1.0.9-2+b6) ... Setting up libfontbox-java (1:1.8.16-2) ... Setting up libboost-chrono1.74-dev:i386 (1.74.0+ds1-21) ... Setting up x11-common (1:7.7+23) ... invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libtcmalloc-minimal4:i386 (2.10-1) ... Setting up libmagic1:i386 (1:5.44-3) ... Setting up gettext-base (0.21-12) ... Setting up m4 (1.4.19-3) ... Setting up libboost-filesystem1.74.0:i386 (1.74.0+ds1-21) ... Setting up autoconf-archive (20220903-3) ... Setting up libzzip-0-13:i386 (0.13.72+dfsg.1-1.1) ... Setting up file (1:5.44-3) ... Setting up xxd (2:9.0.1378-2) ... Setting up libfontenc1:i386 (1:1.1.4-1) ... Setting up autotools-dev (20220109.1) ... Setting up libexpat1-dev:i386 (2.5.0-1) ... Setting up libx11-data (2:1.8.4-2+deb12u2) ... Setting up libteckit0:i386 (2.5.11+ds1-1+b1) ... Setting up libapache-pom-java (29-2) ... Setting up libboost-system1.74-dev:i386 (1.74.0+ds1-21) ... Setting up xfonts-encodings (1:1.0.4-2.2) ... Setting up libboost-regex1.74.0:i386 (1.74.0+ds1-21) ... Setting up t1utils (1.41-4) ... Setting up libtexlua53-5:i386 (2022.20220321.62855-5.1+deb12u1) ... Setting up libpng16-16:i386 (1.6.39-2) ... Setting up autopoint (0.21-12) ... Setting up icu-devtools (72.1-3) ... Setting up fonts-dejavu-core (2.37-6) ... Setting up libfl2:i386 (2.6.4-8.2) ... Setting up libkpathsea6:i386 (2022.20220321.62855-5.1+deb12u1) ... Setting up autoconf (2.71-3) ... Setting up libboost-atomic1.74-dev:i386 (1.74.0+ds1-21) ... Setting up libboost-serialization1.74.0:i386 (1.74.0+ds1-21) ... Setting up zlib1g-dev:i386 (1:1.2.13.dfsg-1) ... Setting up python-apt-common (2.6.0) ... Setting up fonts-gfs-baskerville (1.1-6) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up libmime-charset-perl (1.013.1-2) ... Setting up libuchardet0:i386 (0.0.7-1) ... Setting up fonts-lmodern (2.005-1) ... Setting up libsub-override-perl (0.09-4) ... Setting up libthai-data (0.1.29-1) ... Setting up sgml-base (1.31) ... Setting up libboost-filesystem1.74-dev:i386 (1.74.0+ds1-21) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libboost-date-time1.74.0:i386 (1.74.0+ds1-21) ... Setting up libbsd0:i386 (0.11.7-2) ... Setting up libelf1:i386 (0.188-2.1) ... Setting up readline-common (8.2-1.3) ... Setting up libicu-dev:i386 (72.1-3) ... Setting up libxml2:i386 (2.9.14+dfsg-1.3~deb12u1) ... 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 (2.10-1) ... Setting up libsynctex2:i386 (2022.20220321.62855-5.1+deb12u1) ... Setting up libboost-thread1.74.0:i386 (1.74.0+ds1-21) ... Setting up libbz2-dev:i386 (1.0.8-5+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up libice6:i386 (2:1.0.10-1) ... Setting up libxdmcp6:i386 (1:1.1.2-3) ... Setting up flex (2.6.4-8.2) ... Setting up libxcb1:i386 (1.15-1) ... Setting up gettext (0.21-12) ... Setting up libpdfbox-java (1:1.8.16-2) ... Setting up libtool (2.4.7-5) ... Setting up libxcb-render0:i386 (1.15-1) ... Setting up fontconfig-config (2.14.1-4) ... Setting up libgoogle-perftools-dev:i386 (2.10-1) ... Setting up libreadline8:i386 (8.2-1.3) ... Setting up libboost-system-dev:i386 (1.74.0.3) ... Setting up libcommons-parent-java (56-1) ... Setting up libcommons-logging-java (1.2-3) ... Setting up libxcb-shm0:i386 (1.15-1) ... Setting up libfl-dev:i386 (2.6.4-8.2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libthai0:i386 (0.1.29-1) ... Setting up libptexenc1:i386 (2022.20220321.62855-5.1+deb12u1) ... Setting up libfreetype6:i386 (2.12.1+dfsg-5) ... Setting up ucf (3.0043+nmu1) ... Setting up libboost-serialization1.74-dev:i386 (1.74.0+ds1-21) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up libboost-regex1.74-dev:i386 (1.74.0+ds1-21) ... Setting up groff-base (1.22.4-10) ... Setting up xml-core (0.18+nmu1) ... Setting up libxslt1.1:i386 (1.1.35-1) ... Setting up libx11-6:i386 (2:1.8.4-2+deb12u2) ... Setting up libharfbuzz0b:i386 (6.0.0+dfsg-3) ... Setting up libfontconfig1:i386 (2.14.1-4) ... Setting up libboost-regex-dev:i386 (1.74.0.3) ... Setting up libsm6:i386 (2:1.2.3-1) ... Setting up libpaper1:i386 (1.1.29) ... Creating config file /etc/papersize with new version Setting up libxpm4:i386 (1:3.5.12-1.1+deb12u1) ... Setting up libxrender1:i386 (1:0.9.10-1.1) ... Setting up libsombok3:i386 (2.4.0-2+b1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:i386 (3.11.2-6) ... Setting up xsltproc (1.1.35-1) ... Setting up libxext6:i386 (2:1.3.4-1+b1) ... Setting up libpaper-utils (1.1.29) ... Setting up xfonts-utils (1:7.7+6) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:i386 (1.16.0-7) ... Setting up libboost-iostreams1.74-dev:i386 (1.74.0+ds1-21) ... Setting up tex-common (6.18) ... update-language: texlive-base not installed and configured, doing nothing! Setting up libboost-date-time1.74-dev:i386 (1.74.0+ds1-21) ... Setting up libunicode-linebreak-perl (0.0.20190101-1+b4) ... Setting up libxt6:i386 (1:1.2.1-1.1) ... Setting up lmodern (2.005-1) ... Setting up libboost-thread1.74-dev:i386 (1.74.0+ds1-21) ... Setting up libboost-thread-dev:i386 (1.74.0.3) ... Setting up libpython3-stdlib:i386 (3.11.2-1+b1) ... Setting up python3.11 (3.11.2-6) ... Setting up libxmu6:i386 (2:1.1.3-3) ... Setting up libxi6:i386 (2:1.8-1+b1) ... Setting up preview-latex-style (12.2-1) ... Setting up debhelper (13.11.4) ... Setting up python3 (3.11.2-1+b1) ... Setting up libxaw7:i386 (2:1.0.14-1) ... Setting up libboost-iostreams-dev:i386 (1.74.0.3) ... Setting up texlive-binaries (2022.20220321.62855-5.1+deb12u1) ... 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 (2022.20230122-3) ... 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 (2022.20230122-3) ... Setting up python3-apt (2.6.0) ... Setting up texlive-plain-generic (2022.20230122-4) ... Setting up texlive-lang-greek (2022.20230122-1) ... Setting up texlive-latex-base (2022.20230122-3) ... Setting up texlive-extra-utils (2022.20230122-4) ... Setting up texlive-latex-recommended (2022.20230122-3) ... Setting up texlive-pictures (2022.20230122-3) ... Setting up texlive-fonts-recommended (2022.20230122-3) ... Setting up texlive (2022.20230122-3) ... Setting up texlive-science (2022.20230122-4) ... Setting up texlive-latex-extra (2022.20230122-4) ... Setting up texlive-bibtex-extra (2022.20230122-4) ... Processing triggers for libc-bin (2.36-9+deb12u3) ... Processing triggers for sgml-base (1.31) ... Setting up docbook-xsl (1.79.2+dfsg-2) ... Setting up sgml-data (2.0.11+nmu1) ... Processing triggers for sgml-base (1.31) ... Setting up docbook-xml (4.5-12) ... Processing triggers for sgml-base (1.31) ... Setting up dblatex (0.3.12py3-2) ... Processing triggers for tex-common (6.18) ... Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Building format(s) --all. This may take some time... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/mira-4.9.6/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../mira_4.9.6-7_source.changes dpkg-buildpackage: info: source package mira dpkg-buildpackage: info: source version 4.9.6-7 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 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 cp -an --reflink=auto config.guess debian/.debhelper/bucket/files/9be3de218833c076786b919dc34aab691611f4cd73316e7705f2673e2c41921b.tmp mv debian/.debhelper/bucket/files/9be3de218833c076786b919dc34aab691611f4cd73316e7705f2673e2c41921b.tmp debian/.debhelper/bucket/files/9be3de218833c076786b919dc34aab691611f4cd73316e7705f2673e2c41921b cp -f /usr/share/misc/config.guess ./config.guess cp -an --reflink=auto config.sub debian/.debhelper/bucket/files/e308ae7f7f524bd790f8d4457c7c0a30f8403ffff4dd0b7d4388daca24275db4.tmp mv debian/.debhelper/bucket/files/e308ae7f7f524bd790f8d4457c7c0a30f8403ffff4dd0b7d4388daca24275db4.tmp debian/.debhelper/bucket/files/e308ae7f7f524bd790f8d4457c7c0a30f8403ffff4dd0b7d4388daca24275db4 cp -f /usr/share/misc/config.sub ./config.sub dh_autoreconf find ! -ipath "./debian/*" -a ! \( -path '*/.git/*' -o -path '*/.hg/*' -o -path '*/.bzr/*' -o -path '*/.svn/*' -o -path '*/CVS/*' \) -a -type f -exec md5sum {} + -o -type l -printf "symlink %p " > debian/autoreconf.before grep -q ^XDT_ configure.ac autoreconf -f -i libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'. libtoolize: copying file 'm4/libtool.m4' libtoolize: copying file 'm4/ltoptions.m4' libtoolize: copying file 'm4/ltsugar.m4' libtoolize: copying file 'm4/ltversion.m4' libtoolize: copying file 'm4/lt~obsolete.m4' configure.ac:38: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:38: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:38: the top level configure.ac:46: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:46: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:46: the top level configure.ac:190: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:190: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:190: the top level configure.ac:328: warning: The macro `AC_TRY_COMPILE' is obsolete. configure.ac:328: You should run autoupdate. ./lib/autoconf/general.m4:2847: AC_TRY_COMPILE is expanded from... configure.ac:328: the top level configure.ac:419: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:419: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:419: the top level configure.ac:423: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:423: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:423: the top level configure.ac:663: warning: AC_PROG_LEX without either yywrap or noyywrap is obsolete ./lib/autoconf/programs.m4:716: _AC_PROG_LEX is expanded from... ./lib/autoconf/programs.m4:709: AC_PROG_LEX is expanded from... configure.ac:663: the top level configure.ac:670: warning: The macro `AC_HEADER_STDC' is obsolete. configure.ac:670: You should run autoupdate. ./lib/autoconf/headers.m4:704: AC_HEADER_STDC is expanded from... configure.ac:670: the top level configure.ac:715: warning: The macro `AC_TRY_LINK' is obsolete. configure.ac:715: You should run autoupdate. ./lib/autoconf/general.m4:2920: AC_TRY_LINK is expanded from... lib/m4sugar/m4sh.m4:692: _AS_IF_ELSE is expanded from... lib/m4sugar/m4sh.m4:699: AS_IF is expanded from... ./lib/autoconf/general.m4:2249: AC_CACHE_VAL is expanded from... ./lib/autoconf/general.m4:2270: AC_CACHE_CHECK is expanded from... configure.ac:702: SUDO_FUNC_ISBLANK is expanded from... configure.ac:715: the top level configure.ac:1033: warning: The macro `AC_LANG_C' is obsolete. configure.ac:1033: You should run autoupdate. ./lib/autoconf/c.m4:72: AC_LANG_C is expanded from... m4/ax_check_zlib.m4:63: AX_CHECK_ZLIB is expanded from... configure.ac:1033: the top level configure.ac:1045: warning: The macro `AC_LANG_C' is obsolete. configure.ac:1045: You should run autoupdate. ./lib/autoconf/c.m4:72: AC_LANG_C is expanded from... configure.ac:1045: the top level configure.ac:1134: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:1134: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:1134: the top level configure.ac:1143: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:1143: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:1143: the top level configure.ac:1154: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:1154: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:1154: the top level configure.ac:1197: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:1197: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:1197: the top level configure.ac:1248: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:1248: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:1248: the top level configure.ac:1347: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:1347: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:1347: the top level configure.ac:1366: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:1366: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:1366: the top level configure.ac:1383: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:1383: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:1383: the top level configure.ac:1401: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:1401: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:1401: the top level configure.ac:1417: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:1417: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:1417: the top level configure.ac:1428: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:1428: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.ac:1428: the top level configure.ac:1466: warning: AC_OUTPUT should be used without arguments. configure.ac:1466: You should run autoupdate. configure.ac:103: installing './compile' configure.ac:9: installing './missing' doc/docbook/Makefile.am:22: warning: '%'-style pattern rules are a GNU make extension src/caf/Makefile.am: installing './depcomp' src/io/Makefile.am:12: warning: '%'-style pattern rules are a GNU make extension src/mira/Makefile.am:10: warning: '%'-style pattern rules are a GNU make extension find ! -ipath "./debian/*" -a ! \( -path '*/.git/*' -o -path '*/.hg/*' -o -path '*/.bzr/*' -o -path '*/.svn/*' -o -path '*/CVS/*' \) -a -type f -exec md5sum {} + -o -type l -printf "symlink %p " > debian/autoreconf.after dh_auto_configure ./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 race-free 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 '1111' is supported by ustar format... yes checking whether GID '1111' 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 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include CXXFLAGS now: -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include LDFLAGS now: -Wl,-z,relro -Wl,-z,now -L/usr/lib +++++++++++++++++++++++++++++++++++++ checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of gcc... none checking for g++... g++ checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking dependency style of g++... none checking for OpenMP flag of C compiler... -fopenmp Rescuing C++ flags for OpenMP +++++++++++++++++++++++++++++++++++++ OpenMP CFLAGS: -fopenmp OpenMP CXXFLAGS: -fopenmp +++++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++++++++++++++ systemuname: Linux CFLAGS now: -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include CXXFLAGS now: -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include LDFLAGS now: -Wl,-z,relro -Wl,-z,now -L/usr/lib +++++++++++++++++++++++++++++++++++++ checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for int64_t... yes +++++++++++++++++++++++++++++++++++++ CFLAGS now: -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include CXXFLAGS now: -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include LDFLAGS now: -Wl,-z,relro -Wl,-z,now -L/usr/lib +++++++++++++++++++++++++++++++++++++ checking whether long has 64bit... no checking whether enabling 64bit compilation support... no checking build system type... i686-pc-linux-gnu checking for compiler optimisation settings... -O3 -funroll-loops +++++++++++++++++++++++++++++++++++++ CFLAGS now: -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops CXXFLAGS now: -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops LDFLAGS now: -Wl,-z,relro -Wl,-z,now -L/usr/lib +++++++++++++++++++++++++++++++++++++ checking host system type... i686-pc-linux-gnu checking how to print strings... printf checking for a sed that does not truncate output... (cached) /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E 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 file... file checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /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 for lex output file root... lex.yy checking for lex library... none needed checking for library containing yywrap... -ll checking whether yytext is a pointer... yes checking for flex++... yes checking for xxd... yes checking for egrep... (cached) /bin/grep -E checking for _Bool... yes checking for stdbool.h that conforms to C99... yes checking for an ANSI C-conforming const... yes checking for inline... inline checking for C/C++ restrict keyword... __restrict__ checking whether struct tm is in sys/time.h or time.h... time.h checking for GNU libc compatible malloc... yes checking for GNU libc compatible realloc... yes checking whether lstat correctly handles trailing slash... yes checking whether stat accepts an empty string... no checking for strftime... yes checking for floor... no checking for memset... yes checking for pow... no checking for sqrt... no checking for 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 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops CXXFLAGS now: -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops LDFLAGS now: -Wl,-z,relro -Wl,-z,now -L/usr/lib +++++++++++++++++++++++++++++++++++++ checking for boostlib >= 1.48.0... yes +++++++++++++++++++++++++++++++++++++ BOOST_CPPFLAGS: -I/usr/include BOOST LDFLAGS: -L/usr/lib/i386-linux-gnu ac_boost_path: ac_boost_lib_path: CFLAGS now: -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops CXXFLAGS now: -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops LDFLAGS now: -Wl,-z,relro -Wl,-z,now -L/usr/lib +++++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++++++++++++++ BOOST_CPPFLAGS: -I/usr/include BOOST LDFLAGS: -L/usr/lib/i386-linux-gnu CFLAGS now: -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -Wl,-rpath, CXXFLAGS now: -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops LDFLAGS now: -Wl,-z,relro -Wl,-z,now -L/usr/lib +++++++++++++++++++++++++++++++++++++ checking whether the Boost::Thread library is available... yes checking for exit in -lboost_thread... yes +++++++++++++++++++++++++++++++++++++ BOOST_CPPFLAGS: -pthread -I/usr/include BOOST LDFLAGS: -L/usr/lib/i386-linux-gnu ac_boost_path: ac_boost_lib_path: BOOST_THREAD_LIB: -lboost_thread CFLAGS now: -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -Wl,-rpath, CXXFLAGS now: -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops LDFLAGS now: -Wl,-z,relro -Wl,-z,now -L/usr/lib +++++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++++++++++++++ BOOST_CPPFLAGS: -pthread -I/usr/include BOOST LDFLAGS: -L/usr/lib/i386-linux-gnu ac_boost_path: ac_boost_lib_path: BOOST_THREAD_LIB: -lboost_thread CFLAGS now: -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -Wl,-rpath, CXXFLAGS now: -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include LDFLAGS now: -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/i386-linux-gnu LIBS now: -lboost_thread +++++++++++++++++++++++++++++++++++++ checking whether the Boost::Regex library is available... yes checking for exit in -lboost_regex... yes +++++++++++++++++++++++++++++++++++++ BOOST_CPPFLAGS: -pthread -I/usr/include BOOST LDFLAGS: -L/usr/lib/i386-linux-gnu ac_boost_path: ac_boost_lib_path: BOOST_REGEX_LIB: -lboost_regex CFLAGS now: -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -Wl,-rpath, CXXFLAGS now: -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include LIBS now: -lboost_thread -lboost_regex +++++++++++++++++++++++++++++++++++++ checking whether the Boost::System library is available... yes checking for exit in -lboost_system... yes +++++++++++++++++++++++++++++++++++++ BOOST_CPPFLAGS: -pthread -I/usr/include BOOST LDFLAGS: -L/usr/lib/i386-linux-gnu ac_boost_path: ac_boost_lib_path: BOOST_SYSTEM_LIB: -lboost_system CFLAGS now: -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -Wl,-rpath, CXXFLAGS now: -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include LIBS now: -lboost_thread -lboost_regex -lboost_system +++++++++++++++++++++++++++++++++++++ checking whether the Boost::Filesystem library is available... yes checking for exit in -lboost_filesystem... yes +++++++++++++++++++++++++++++++++++++ BOOST_CPPFLAGS: -pthread -I/usr/include BOOST LDFLAGS: -L/usr/lib/i386-linux-gnu ac_boost_path: ac_boost_lib_path: BOOST_FILESYSTEM_LIB: -lboost_filesystem CFLAGS now: -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -Wl,-rpath, CXXFLAGS now: -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include LIBS now: -lboost_thread -lboost_regex -lboost_system -lboost_filesystem +++++++++++++++++++++++++++++++++++++ checking whether the Boost::IOStreams library is available... yes checking for exit in -lboost_iostreams... yes +++++++++++++++++++++++++++++++++++++ BOOST_CPPFLAGS: -pthread -I/usr/include BOOST LDFLAGS: -L/usr/lib/i386-linux-gnu ac_boost_path: ac_boost_lib_path: BOOST_IOSTREAMS_LIB: -lboost_iostreams CFLAGS now: -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -Wl,-rpath, CXXFLAGS now: -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include LIBS now: -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams +++++++++++++++++++++++++++++++++++++ checking for clock_gettime in -lrt... yes +++++++++++++++++++++++++++++++++++++ Need to specifically use rt library LIBS now: -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt +++++++++++++++++++++++++++++++++++++ BOOST is through, yay. +++++++++++++++++++++++++++++++++++++ CFLAGS now: -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops CXXFLAGS now: -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include LDFLAGS now: -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/i386-linux-gnu LIBS now: -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt +++++++++++++++++++++++++++++++++++++ checking for Expat XML Parser headers in /usr/include... found checking for Expat XML Parser libraries... found checking for Expat XML Parser... yes +++++++++++++++++++++++++++++++++++++ CFLAGS now: -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -I/usr/include CXXFLAGS now: -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include LDFLAGS now: -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/i386-linux-gnu -L/usr/lib LIBS now: -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt -lexpat +++++++++++++++++++++++++++++++++++++ checking if zlib is wanted... yes +++++++++++++++++++++++++++++++++++++ CFLAGS now: -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -I/usr/include CXXFLAGS now: -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include LDFLAGS now: -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/i386-linux-gnu -L/usr/lib LIBS now: -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt -lexpat -lm -lz +++++++++++++++++++++++++++++++++++++ checking for gzoffset in -lz... yes checking for BZ2_bzRead in -lbz2... yes checking for flex version compatible with MIRA... yes checking for profiling settings... no checking for purify... no checking whether mira should compile in public quiet mode... yes checking whether mira should compile with bound tracking... yes checking whether mira should compile with bug tracking... yes checking whether mira should compile with extended bug tracking... no checking whether mira should compile with function trace... no checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating src/other/Makefile config.status: creating src/other/sls/Makefile config.status: creating src/other/sls/mira-createsls/Makefile config.status: creating src/other/sls/mira-createsls/bin/Makefile config.status: creating src/stdinc/Makefile config.status: creating src/debuggersupport/Makefile config.status: creating src/memorc/Makefile config.status: creating src/errorhandling/Makefile config.status: creating src/util/Makefile config.status: creating src/io/Makefile config.status: creating src/mira/Makefile config.status: creating src/caf/Makefile config.status: creating src/support/Makefile config.status: creating src/scripts/Makefile config.status: creating src/modules/Makefile config.status: creating src/version/Makefile config.status: creating src/progs/Makefile config.status: creating man/Makefile config.status: creating doc/Makefile config.status: creating doc/docbook/Makefile config.status: creating distribution/Makefile config.status: executing depfiles commands config.status: executing libtool commands -------------------------------------------------------------------------------- Summary of MIRA configuration -------------------------------------------------------------------------------- Building version ................................. 4.9.6_linux-gnu_i686_32_dynamic We are building on ............................... Linux CPU supports 64 bit? ............................. no Compiler family .................................. gcc Compiler optimisation flags used ................. -O3 -funroll-loops Building completely static? ...................... no BOOST expected to compile and link? .............. yes Have OpenMP? ..................................... yes Have complete zlib support? ...................... yes Can MIRA be built on this system? ................ yes Using CFLAGS : -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -I/usr/include -Werror=uninitialized -Werror=return-type -fopenmp Using CXXFLAGS : -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp Using LDFLAGS : -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/i386-linux-gnu -L/usr/lib Using LIBS : -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt -lexpat -lm -lz -lbz2 Looks good, we do not expect compilation problems. -------------------------------------------------------------------------------- Type 'make' to make the binaries and then 'make install' to install binaries and man pages. Type 'make docinstall' to install extensive documentation as HTML and PDF. 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 -j8 make[2]: Entering directory '/build/reproducible-path/mira-4.9.6' make all-recursive make[3]: Entering directory '/build/reproducible-path/mira-4.9.6' Making all in man make[4]: Entering directory '/build/reproducible-path/mira-4.9.6/man' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/reproducible-path/mira-4.9.6/man' Making all in src make[4]: Entering directory '/build/reproducible-path/mira-4.9.6/src' Making all in debuggersupport make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/debuggersupport' g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o dbgsupport.o dbgsupport.C rm -f libmiradebuggersupport.a ar cru libmiradebuggersupport.a dbgsupport.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libmiradebuggersupport.a make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/debuggersupport' Making all in io make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/io' Making .H out of .xxd mira_ft_set.xxd.H Making .H out of .xxd gap4_ft_so_map.xxd.H Reducing so.obo for smaller so.obo.xxd Making .H out of .xxd so2xgap4map.xxd.H Making .H out of .xxd oldso2so.xxd.H Making .H out of .xxd so.obo.xxd.H make all-am make[6]: Entering directory '/build/reproducible-path/mira-4.9.6/src/io' g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o annotationmappings.o annotationmappings.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o exp.o exp.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o generalio.o generalio.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o fasta.o fasta.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o fastq-mira.o fastq-mira.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o phd.o phd.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o scf.o scf.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o ncbiinfoxml.o ncbiinfoxml.C /bin/bash ../../ylwrap exp_flexer.ll lex.yy.c exp_flexer.cc -- flex g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o exp_flexer.o exp_flexer.cc rm -f libmirafio.a ar cru libmirafio.a annotationmappings.o exp.o generalio.o fasta.o fastq-mira.o phd.o scf.o ncbiinfoxml.o exp_flexer.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libmirafio.a make[6]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/io' make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/io' Making all in stdinc make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/stdinc' make[5]: Nothing to be done for 'all'. make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/stdinc' Making all in errorhandling make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/errorhandling' g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o errorhandling.o errorhandling.C rm -f libmiraerrorhandling.a ar cru libmiraerrorhandling.a errorhandling.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libmiraerrorhandling.a make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/errorhandling' Making all in util make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/util' g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o machineinfo.o machineinfo.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o fileanddisk.o fileanddisk.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o misc.o misc.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o dptools.o dptools.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o fmttext.o fmttext.C rm -f libmirafmttext.a ar cru libmirafmttext.a fmttext.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libmirafmttext.a rm -f libmiradptools.a ar cru libmiradptools.a dptools.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libmiradptools.a fileanddisk.C: In function 'int64 myGZRead(gzFile_s*&, void*, uint64)': fileanddisk.C:173:19: warning: ignoring return value of 'char* strerror_r(int, char*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 173 | strerror_r(errno,buf,1024); | ~~~~~~~~~~^~~~~~~~~~~~~~~~ rm -f libmirautil.a ar cru libmirautil.a machineinfo.o fileanddisk.o misc.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libmirautil.a make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/util' Making all in mira make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/mira' Making .H out of .xxd adaptorsforclip.454.xxd.H Making .H out of .xxd adaptorsforclip.solexa.xxd.H Making .H out of .xxd adaptorsforclip.iontor.xxd.H Making .H out of .xxd adaptorsregex.solexa.xxd.H Making .H out of .xxd adaptorsregex.iontor.xxd.H Making .H out of .xxd seqforfilter_phix174.solexa.xxd.H make all-am make[6]: Entering directory '/build/reproducible-path/mira-4.9.6/src/mira' g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o estassembly.o estassembly.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o hashstats_sdbg.o hashstats_sdbg.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o hashstats.o hashstats.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o skim.o skim.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o assembly.o assembly.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o contig.o contig.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o read.o read.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o contig_analysis.o contig_analysis.C 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/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/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 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( | ^~~~~~~~~~~~~~~~~~~~ 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 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 ../../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( | ^~~~~~~~~~~~~~~~~~~~ read.C: In member function 'void Read::dumpAsReadname(std::ostream&)': read.C:1242:25: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'Read*' [-Wformat=] 1242 | sprintf(buffer, "%x", this) ; | ~^ ~~~~ | | | | | Read* | unsigned int read.C: In member function 'void Read::dumpAsFASTA(std::ostream&, bool, bool, bool)': read.C:1273:25: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'Read*' [-Wformat=] 1273 | sprintf(buffer, "%x", this) ; | ~^ ~~~~ | | | | | Read* | unsigned int read.C: In member function 'void Read::dumpAsFASTQ(std::ostream&, bool, bool, bool)': read.C:1357:25: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'Read*' [-Wformat=] 1357 | sprintf(buffer, "%x", this) ; | ~^ ~~~~ | | | | | Read* | unsigned int read.C: In member function 'void Read::dumpAsFASTAQual(std::ostream&, bool, bool, bool)': read.C:1458:25: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'Read*' [-Wformat=] 1458 | sprintf(buffer, "%x", this) ; | ~^ ~~~~ | | | | | Read* | unsigned int read.C: In member function 'void Read::dumpAsCAF(std::ostream&)': read.C:1530:25: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'Read*' [-Wformat=] 1530 | sprintf(buffer, "%x", this) ; | ~^ ~~~~ | | | | | Read* | unsigned int read.C: In member function 'void Read::dumpAsMAF(std::ostream&)': read.C:1945:25: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'Read*' [-Wformat=] 1945 | sprintf(buffer, "%x", this) ; | ~^ ~~~~ | | | | | Read* | unsigned int In file included from /usr/include/boost/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( | ^~~~~~~~~~~~~~~~~~~~ g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o ads.o ads.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o adsfacts.o adsfacts.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o align.o align.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o assembly_info.o assembly_info.C In file included from /usr/include/boost/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( | ^~~~~~~~~~~~~~~~~~~~ g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o assembly_buildcontigs.o assembly_buildcontigs.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o assembly_io.o assembly_io.C 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 ../../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( | ^~~~~~~~~~~~~~~~~~~~ g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o assembly_misc.o assembly_misc.C 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 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o assembly_output.o assembly_output.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o assembly_pbcorrect.o assembly_pbcorrect.C In file included from /usr/include/boost/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( | ^~~~~~~~~~~~~~~~~~~~ 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 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o assembly_reduceskimhits.o assembly_reduceskimhits.C assembly_reduceskimhits.C:1111: 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();} | 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 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o assembly_swalign.o assembly_swalign.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o contig_consensus.o contig_consensus.C 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 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( | ^~~~~~~~~~~~~~~~~~~~ g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o contig_covanalysis.o contig_covanalysis.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o contig_edit.o contig_edit.C In file included from /usr/include/boost/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( | ^~~~~~~~~~~~~~~~~~~~ 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( | ^~~~~~~~~~~~~~~~~~~~ g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o contig_featureinfo.o contig_featureinfo.C contig_featureinfo.C:512: warning: "CEBUGF2" redefined 512 | #define CEBUGF2 | contig_featureinfo.C:473: note: this is the location of the previous definition 473 | #define CEBUGF2(bla) | g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o contig_output.o contig_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 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 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o contig_pairconsistency.o contig_pairconsistency.C contig_pairconsistency.C:313: 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 ../../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( | ^~~~~~~~~~~~~~~~~~~~ g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o dataprocessing.o dataprocessing.C In file included from /usr/include/boost/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 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o dynamic.o dynamic.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o gbf_parse.o gbf_parse.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o gff_parse.o gff_parse.C In file included from /usr/include/boost/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( | ^~~~~~~~~~~~~~~~~~~~ g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o gff_save.o gff_save.C In file included from /usr/include/boost/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 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o maf_parse.o maf_parse.C 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 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o manifest.o manifest.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o multitag.o multitag.C /bin/bash ../../ylwrap parameters_flexer.ll lex.yy.c parameters_flexer.cc -- flex g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o parameters.o parameters.C In file included from /usr/include/boost/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 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o pcrcontainer.o pcrcontainer.C In file included from /usr/include/boost/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 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o ppathfinder.o ppathfinder.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o preventinitfiasco.o preventinitfiasco.C 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( | ^~~~~~~~~~~~~~~~~~~~ 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 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o readgrouplib.o readgrouplib.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o readlotstat.o readlotstat.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o readpool.o readpool.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o readpool_io.o readpool_io.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o sam_collect.o sam_collect.C 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 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o scaffolder.o scaffolder.C 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/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 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o seqtohash.o seqtohash.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o simplebloomfilter.o simplebloomfilter.C 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 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o skim_lowbph.o skim_lowbph.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o warnings.o warnings.C rm -f libmiraestass.a ar cru libmiraestass.a estassembly.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libmiraestass.a g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o parameters_flexer.o parameters_flexer.cc In file included from /usr/include/boost/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 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o caf.o caf.C /bin/bash ../../ylwrap caf_flexer.ll lex.yy.c caf_flexer.cc -- flex g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o caf_flexer.o caf_flexer.cc In file included from /usr/include/boost/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 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o memorc.o memorc.C memorc.C: In static member function 'static void MemORC::statistics()': memorc.C:155:39: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 2 has type 'std::map::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:311:42: warning: format '%d' expects argument of type 'int', but argument 2 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 311 | printf("Nearest memblock above (%d):\t",reinterpret_cast(mbI->first)-reinterpret_cast(usraddr)); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int uint64 {aka long long unsigned int} | %lld memorc.C:318:43: warning: format '%d' expects argument of type 'int', but argument 2 has type 'uint64' {aka 'long long unsigned int'} [-Wformat=] 318 | printf("Nearest memblock below (-%d):\t",reinterpret_cast(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 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o main.o main.C rm -f libmemorc.a ar cru libmemorc.a memorc.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libmemorc.a /bin/bash ../../libtool --tag=CXX --mode=link g++ -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -L../io/ -L../util/ -L../errorhandling/ -L../mira -L../caf/ -L/usr/lib/i386-linux-gnu -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/i386-linux-gnu -L/usr/lib -o main main.o -lmiraerrorhandling -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt -lexpat -lm -lz -lbz2 libtool: link: g++ -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -Wl,-z -Wl,relro -Wl,-z -Wl,now -o main main.o -L../io/ -L../util/ -L../errorhandling/ -L../mira -L../caf/ -L/usr/lib/i386-linux-gnu -L/usr/lib -lmiraerrorhandling -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt -lexpat -lm -lz -lbz2 -fopenmp -pthread make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/memorc' Making all in modules make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/modules' g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o mod_sigconex.o mod_sigconex.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o mod_scaffold.o mod_scaffold.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o mod_bait.o mod_bait.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o mod_dbgreplay.o mod_dbgreplay.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o mod_diff.o mod_diff.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o mod_mer.o mod_mer.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o mod_mira.o mod_mira.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o mod_convert.o mod_convert.C In file included from /usr/include/boost/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/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/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/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/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( | ^~~~~~~~~~~~~~~~~~~~ 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( | ^~~~~~~~~~~~~~~~~~~~ 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/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( | ^~~~~~~~~~~~~~~~~~~~ mod_mira.C: In function 'void miraMain_extractContigs(int, char**)': mod_mira.C:414:10: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 414 | chdir("../.."); | ~~~~~^~~~~~~~~ mod_mira.C:439:10: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 439 | chdir("../.."); | ~~~~~^~~~~~~~~ g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o mod_memestim.o mod_memestim.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o mod_tagsnp.o mod_tagsnp.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o misc.o misc.C In file included from /usr/include/boost/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( | ^~~~~~~~~~~~~~~~~~~~ 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 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o mversion.o mversion.C rm -f libmiraversion.a ar cru libmiraversion.a mversion.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libmiraversion.a make[6]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/version' make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/version' Making all in progs make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/progs' Making .C out of .xxd compileinfo.itxt make all-am make[6]: Entering directory '/build/reproducible-path/mira-4.9.6/src/progs' g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o mira.o mira.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o quirks.o quirks.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o miratest.o miratest.C Making .C out of .xxd compileinfo.itxt g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o compileinfo.itxt.xxd.o compileinfo.itxt.xxd.C In file included from /usr/include/boost/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/bash ../../libtool --tag=CXX --mode=link g++ -pthread -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -L../version -L../modules -L../debuggersupport -L../memorc -L../io/ -L../util/ -L../errorhandling/ -L../mira -L../caf -L/usr/lib/i386-linux-gnu -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/i386-linux-gnu -L/usr/lib -o miratest miratest.o compileinfo.itxt.xxd.o -lmiraversion -lmiramodules -lmiradebuggersupport -lmira -lmiraestass -lmiracaf -lmirautil -lmiradptools -lmirafio -lmiraerrorhandling -lmiradebuggersupport -lmirafmttext -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt -lexpat -lm -lz -lbz2 /bin/bash ../../libtool --tag=CXX --mode=link g++ -pthread -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -L../version -L../modules -L../debuggersupport -L../memorc -L../io/ -L../util/ -L../errorhandling/ -L../mira -L../caf -L/usr/lib/i386-linux-gnu -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/i386-linux-gnu -L/usr/lib -o mira mira.o quirks.o compileinfo.itxt.xxd.o -lmiraversion -lmiramodules -lmiradebuggersupport -lmira -lmiraestass -lmiracaf -lmirautil -lmiradptools -lmirafio -lmiraerrorhandling -lmiradebuggersupport -lmirafmttext -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt -lexpat -lm -lz -lbz2 libtool: link: g++ -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -Wl,-z -Wl,relro -Wl,-z -Wl,now -o 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 libtool: link: g++ -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -Wl,-z -Wl,relro -Wl,-z -Wl,now -o mira mira.o quirks.o compileinfo.itxt.xxd.o -L../version -L../modules -L../debuggersupport -L../memorc -L../io/ -L../util/ -L../errorhandling/ -L../mira -L../caf -L/usr/lib/i386-linux-gnu -L/usr/lib -lmiraversion -lmiramodules -lmira -lmiraestass -lmiracaf -lmirautil -lmiradptools -lmirafio -lmiraerrorhandling -lmiradebuggersupport -lmirafmttext -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt -lexpat -lm -lz -lbz2 -fopenmp -pthread 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 -j8 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/mira-4.9.6/doc' Making all in docbook make[3]: Entering directory '/build/reproducible-path/mira-4.9.6/doc/docbook' Making versionfile xsltproc --nonet --xinclude --output DefinitiveGuideToMIRA.html ../../doc/docbook/book.xsl ../../doc/docbook/book_definitiveguide.xml xsltproc --nonet --xinclude --output 3rdparty_MIRA.html ../../doc/docbook/book.xsl ../../doc/docbook/book_3rdparty.xml dblatex --xslt-opts=--nonet --output=DefinitiveGuideToMIRA.pdf ../../doc/docbook/book_definitiveguide.xml dblatex --xslt-opts=--nonet --output=3rdparty_MIRA.pdf ../../doc/docbook/book_3rdparty.xml Making .html out of _part.xml chap_bitsandpieces_part.html Making .html out of _part.xml chap_mirautils_part.html Making .html out of _part.xml chap_est_part.html Making .html out of _part.xml chap_faq_part.html Build the book set list... 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". Build the book set list... 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_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 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 Making .html out of _part.xml chap_sra_part.html Build the listings... 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 Making .html out of _part.xml chap_preface_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. Build book_3rdparty.pdf 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 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o compileinfo.itxt.xxd.o compileinfo.itxt.xxd.C /bin/bash ../../libtool --tag=CXX --mode=link g++ -pthread -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -L../version -L../modules -L../debuggersupport -L../memorc -L../io/ -L../util/ -L../errorhandling/ -L../mira -L../caf -L/usr/lib/i386-linux-gnu -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/i386-linux-gnu -L/usr/lib -o mira mira.o quirks.o compileinfo.itxt.xxd.o -lmiraversion -lmiramodules -lmiradebuggersupport -lmira -lmiraestass -lmiracaf -lmirautil -lmiradptools -lmirafio -lmiraerrorhandling -lmiradebuggersupport -lmirafmttext -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt -lexpat -lm -lz -lbz2 libtool: link: g++ -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -Wl,-z -Wl,relro -Wl,-z -Wl,now -o mira mira.o quirks.o compileinfo.itxt.xxd.o -L../version -L../modules -L../debuggersupport -L../memorc -L../io/ -L../util/ -L../errorhandling/ -L../mira -L../caf -L/usr/lib/i386-linux-gnu -L/usr/lib -lmiraversion -lmiramodules -lmira -lmiraestass -lmiracaf -lmirautil -lmiradptools -lmirafio -lmiraerrorhandling -lmiradebuggersupport -lmirafmttext -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt -lexpat -lm -lz -lbz2 -fopenmp -pthread /bin/bash ../../libtool --tag=CXX --mode=link g++ -pthread -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -L../version -L../modules -L../debuggersupport -L../memorc -L../io/ -L../util/ -L../errorhandling/ -L../mira -L../caf -L/usr/lib/i386-linux-gnu -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/i386-linux-gnu -L/usr/lib -o miratest miratest.o compileinfo.itxt.xxd.o -lmiraversion -lmiramodules -lmiradebuggersupport -lmira -lmiraestass -lmiracaf -lmirautil -lmiradptools -lmirafio -lmiraerrorhandling -lmiradebuggersupport -lmirafmttext -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt -lexpat -lm -lz -lbz2 libtool: link: g++ -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -Wl,-z -Wl,relro -Wl,-z -Wl,now -o miratest miratest.o compileinfo.itxt.xxd.o -L../version -L../modules -L../debuggersupport -L../memorc -L../io/ -L../util/ -L../errorhandling/ -L../mira -L../caf -L/usr/lib/i386-linux-gnu -L/usr/lib -lmiraversion -lmiramodules -lmira -lmiraestass -lmiracaf -lmirautil -lmiradptools -lmirafio -lmiraerrorhandling -lmiradebuggersupport -lmirafmttext -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt -lexpat -lm -lz -lbz2 -fopenmp -pthread make[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 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o compileinfo.itxt.xxd.o compileinfo.itxt.xxd.C /bin/bash ../../libtool --tag=CXX --mode=link g++ -pthread -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -L../version -L../modules -L../debuggersupport -L../memorc -L../io/ -L../util/ -L../errorhandling/ -L../mira -L../caf -L/usr/lib/i386-linux-gnu -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/i386-linux-gnu -L/usr/lib -o mira mira.o quirks.o compileinfo.itxt.xxd.o -lmiraversion -lmiramodules -lmiradebuggersupport -lmira -lmiraestass -lmiracaf -lmirautil -lmiradptools -lmirafio -lmiraerrorhandling -lmiradebuggersupport -lmirafmttext -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt -lexpat -lm -lz -lbz2 libtool: link: g++ -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -Wl,-z -Wl,relro -Wl,-z -Wl,now -o mira mira.o quirks.o compileinfo.itxt.xxd.o -L../version -L../modules -L../debuggersupport -L../memorc -L../io/ -L../util/ -L../errorhandling/ -L../mira -L../caf -L/usr/lib/i386-linux-gnu -L/usr/lib -lmiraversion -lmiramodules -lmira -lmiraestass -lmiracaf -lmirautil -lmiradptools -lmirafio -lmiraerrorhandling -lmiradebuggersupport -lmirafmttext -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt -lexpat -lm -lz -lbz2 -fopenmp -pthread /bin/bash ../../libtool --tag=CXX --mode=link g++ -pthread -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -L../version -L../modules -L../debuggersupport -L../memorc -L../io/ -L../util/ -L../errorhandling/ -L../mira -L../caf -L/usr/lib/i386-linux-gnu -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/i386-linux-gnu -L/usr/lib -o miratest miratest.o compileinfo.itxt.xxd.o -lmiraversion -lmiramodules -lmiradebuggersupport -lmira -lmiraestass -lmiracaf -lmirautil -lmiradptools -lmirafio -lmiraerrorhandling -lmiradebuggersupport -lmirafmttext -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt -lexpat -lm -lz -lbz2 libtool: link: g++ -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -Wl,-z -Wl,relro -Wl,-z -Wl,now -o miratest miratest.o compileinfo.itxt.xxd.o -L../version -L../modules -L../debuggersupport -L../memorc -L../io/ -L../util/ -L../errorhandling/ -L../mira -L../caf -L/usr/lib/i386-linux-gnu -L/usr/lib -lmiraversion -lmiramodules -lmira -lmiraestass -lmiracaf -lmirautil -lmiradptools -lmirafio -lmiraerrorhandling -lmiradebuggersupport -lmirafmttext -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt -lexpat -lm -lz -lbz2 -fopenmp -pthread make[7]: Entering directory '/build/reproducible-path/mira-4.9.6/src/progs' Making .C out of .xxd compileinfo.itxt /bin/mkdir -p '/build/reproducible-path/mira-4.9.6/debian/mira-assembler/usr/bin' /bin/bash ../../libtool --mode=install /usr/bin/install -c mira '/build/reproducible-path/mira-4.9.6/debian/mira-assembler/usr/bin' libtool: install: /usr/bin/install -c mira /build/reproducible-path/mira-4.9.6/debian/mira-assembler/usr/bin/mira make install-exec-hook make[8]: Entering directory '/build/reproducible-path/mira-4.9.6/src/progs' cd /build/reproducible-path/mira-4.9.6/debian/mira-assembler/usr/bin && \ rm -f miramem && \ ln -s mira miramem && \ rm -f mirabait && \ ln -s mira mirabait &&\ rm -f miraconvert && \ ln -s mira miraconvert && \ rm -f miramer && \ ln -s mira miramer make[8]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/progs' make[7]: Nothing to be done for 'install-data-am'. make[7]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/progs' make[6]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/progs' make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/progs' Making install in other make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/other' Making install in sls make[6]: Entering directory '/build/reproducible-path/mira-4.9.6/src/other/sls' Making install in mira-createsls make[7]: Entering directory '/build/reproducible-path/mira-4.9.6/src/other/sls/mira-createsls' Making install in bin make[8]: Entering directory '/build/reproducible-path/mira-4.9.6/src/other/sls/mira-createsls/bin' make[9]: Entering directory '/build/reproducible-path/mira-4.9.6/src/other/sls/mira-createsls/bin' make[9]: Nothing to be done for 'install-exec-am'. make[9]: Nothing to be done for 'install-data-am'. make[9]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/other/sls/mira-createsls/bin' make[8]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/other/sls/mira-createsls/bin' make[8]: Entering directory '/build/reproducible-path/mira-4.9.6/src/other/sls/mira-createsls' make[9]: Entering directory '/build/reproducible-path/mira-4.9.6/src/other/sls/mira-createsls' make[9]: Nothing to be done for 'install-exec-am'. make[9]: Nothing to be done for 'install-data-am'. make[9]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/other/sls/mira-createsls' make[8]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/other/sls/mira-createsls' make[7]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/other/sls/mira-createsls' make[7]: Entering directory '/build/reproducible-path/mira-4.9.6/src/other/sls' make[8]: Entering directory '/build/reproducible-path/mira-4.9.6/src/other/sls' make[8]: Nothing to be done for 'install-exec-am'. make[8]: Nothing to be done for 'install-data-am'. make[8]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/other/sls' make[7]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/other/sls' make[6]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/other/sls' make[6]: Entering directory '/build/reproducible-path/mira-4.9.6/src/other' make[7]: Entering directory '/build/reproducible-path/mira-4.9.6/src/other' make[7]: Nothing to be done for 'install-exec-am'. make[7]: Nothing to be done for 'install-data-am'. make[7]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/other' make[6]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/other' make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/other' make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src' make[6]: Entering directory '/build/reproducible-path/mira-4.9.6/src' make[6]: Nothing to be done for 'install-exec-am'. make[6]: Nothing to be done for 'install-data-am'. make[6]: Leaving directory '/build/reproducible-path/mira-4.9.6/src' make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src' make[4]: Leaving directory '/build/reproducible-path/mira-4.9.6/src' make[4]: Entering directory '/build/reproducible-path/mira-4.9.6' make[5]: Entering directory '/build/reproducible-path/mira-4.9.6' make[5]: Nothing to be done for 'install-exec-am'. make[5]: Nothing to be done for 'install-data-am'. make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6' make[4]: Leaving directory '/build/reproducible-path/mira-4.9.6' make[3]: Leaving directory '/build/reproducible-path/mira-4.9.6' make[2]: Leaving directory '/build/reproducible-path/mira-4.9.6' make[1]: Leaving directory '/build/reproducible-path/mira-4.9.6' debian/rules override_dh_auto_install-indep make[1]: Entering directory '/build/reproducible-path/mira-4.9.6' #There is no installation target for the docs mkdir -p /build/reproducible-path/mira-4.9.6/debian/tmp/usr/share/doc/mira-assembler cp -r -t /build/reproducible-path/mira-4.9.6/debian/tmp/usr/share/doc/mira-assembler doc/docbook/bookfigures doc/docbook/images \ doc/docbook/doccss doc/docbook/DefinitiveGuideToMIRA.html || true make[1]: Leaving directory '/build/reproducible-path/mira-4.9.6' dh_install install -m0755 -d debian/mira-rfam-12s-rrna/usr/share/mira/ cp --reflink=auto -a ./src/other/sls/mira-install-sls-rrna.sh ./src/other/sls/rfam_rrna-21-12.sls.gz debian/mira-rfam-12s-rrna/usr/share/mira// install -m0755 -d debian/mira-doc//usr/share cp --reflink=auto -a debian/tmp/usr/share/doc/ debian/mira-doc//usr/share/ dh_installdocs install -m0755 -d debian/mira-assembler/usr/share/doc/mira-assembler install -m0755 -d debian/mira-assembler/usr/share/doc/mira-assembler cp --reflink=auto -a ./NEWS debian/mira-assembler/usr/share/doc/mira-assembler cp --reflink=auto -a ./README debian/mira-assembler/usr/share/doc/mira-assembler cp --reflink=auto -a ./THANKS debian/mira-assembler/usr/share/doc/mira-assembler cp --reflink=auto -a ./HELP_WANTED debian/mira-assembler/usr/share/doc/mira-assembler cp --reflink=auto -a ./debian/README.test debian/mira-assembler/usr/share/doc/mira-assembler cp --reflink=auto -a ./debian/tests/run-unit-test debian/mira-assembler/usr/share/doc/mira-assembler cp --reflink=auto -a ./debian/tests/est_assembly.conf debian/mira-assembler/usr/share/doc/mira-assembler cp --reflink=auto -a ./debian/tests/solexa1.conf debian/mira-assembler/usr/share/doc/mira-assembler cp --reflink=auto -a ./debian/tests/solexa2.conf debian/mira-assembler/usr/share/doc/mira-assembler cd './debian/tests/test_data//..' && find 'test_data' \( -type f -or -type l \) -and ! -empty -print0 | LC_ALL=C sort -z | xargs -0 -I {} cp --reflink=auto --parents -dp {} /build/reproducible-path/mira-4.9.6/debian/mira-assembler/usr/share/doc/mira-assembler chmod -R u\+rw,go=rX debian/mira-assembler/usr/share/doc install -p -m0644 debian/copyright debian/mira-assembler/usr/share/doc/mira-assembler/copyright install -m0755 -d debian/mira-rfam-12s-rrna/usr/share/doc/mira-rfam-12s-rrna install -p -m0644 debian/copyright debian/mira-rfam-12s-rrna/usr/share/doc/mira-rfam-12s-rrna/copyright install -m0755 -d debian/mira-doc/usr/share/doc/mira-doc install -p -m0644 debian/mira-doc.README.Debian debian/mira-doc/usr/share/doc/mira-doc/README.Debian install -p -m0644 debian/copyright debian/mira-doc/usr/share/doc/mira-doc/copyright install -m0755 -d debian/mira-doc/usr/share/doc-base/ install -p -m0644 debian/mira-doc.doc-base debian/mira-doc/usr/share/doc-base/mira-doc.mira-manual debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/reproducible-path/mira-4.9.6' dh_installchangelogs src/mira/CHANGES.txt install -m0755 -d debian/mira-assembler/usr/share/doc/mira-assembler install -p -m0644 debian/.debhelper/generated/mira-assembler/dh_installchangelogs.dch.trimmed debian/mira-assembler/usr/share/doc/mira-assembler/changelog.Debian install -p -m0644 src/mira/CHANGES.txt debian/mira-assembler/usr/share/doc/mira-assembler/changelog install -m0755 -d debian/mira-rfam-12s-rrna/usr/share/doc/mira-rfam-12s-rrna install -p -m0644 debian/.debhelper/generated/mira-rfam-12s-rrna/dh_installchangelogs.dch.trimmed debian/mira-rfam-12s-rrna/usr/share/doc/mira-rfam-12s-rrna/changelog.Debian install -p -m0644 src/mira/CHANGES.txt debian/mira-rfam-12s-rrna/usr/share/doc/mira-rfam-12s-rrna/changelog install -m0755 -d debian/mira-doc/usr/share/doc/mira-doc install -p -m0644 debian/.debhelper/generated/mira-doc/dh_installchangelogs.dch.trimmed debian/mira-doc/usr/share/doc/mira-doc/changelog.Debian install -p -m0644 src/mira/CHANGES.txt debian/mira-doc/usr/share/doc/mira-doc/changelog 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/miramem.1 man-recode --to-code UTF-8 --suffix .dh-new debian/mira-assembler/usr/share/man/man1/miramer.1 mv debian/mira-assembler/usr/share/man/man1/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/miramer.1.dh-new debian/mira-assembler/usr/share/man/man1/miramer.1 chmod 0644 -- debian/mira-assembler/usr/share/man/man1/miramer.1 mv debian/mira-assembler/usr/share/man/man1/miramem.1.dh-new debian/mira-assembler/usr/share/man/man1/miramem.1 chmod 0644 -- debian/mira-assembler/usr/share/man/man1/miramem.1 mv debian/mira-assembler/usr/share/man/man1/miraconvert.1.dh-new debian/mira-assembler/usr/share/man/man1/miraconvert.1 chmod 0644 -- debian/mira-assembler/usr/share/man/man1/miraconvert.1 mv debian/mira-assembler/usr/share/man/man1/mirabait.1.dh-new debian/mira-assembler/usr/share/man/man1/mirabait.1 chmod 0644 -- debian/mira-assembler/usr/share/man/man1/mirabait.1 mv debian/mira-assembler/usr/share/man/man1/miradiff.1.dh-new debian/mira-assembler/usr/share/man/man1/miradiff.1 chmod 0644 -- debian/mira-assembler/usr/share/man/man1/miradiff.1 dh_lintian install -m0755 -d debian/mira-assembler/usr/share/lintian/overrides install -p -m0644 debian/mira-assembler.lintian-overrides debian/mira-assembler/usr/share/lintian/overrides/mira-assembler dh_perl dh_link rm -f debian/mira-assembler/usr/bin/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 1656100895 as canonical time Normalizing debian/mira-rfam-12s-rrna/usr/share/mira/rfam_rrna-21-12.sls.gz using File::StripNondeterminism::handlers::gzip Using 1656100895 as canonical time 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/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 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/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/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/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 dh_compress cd debian/mira-assembler cd debian/mira-rfam-12s-rrna cd debian/mira-doc chmod a-x usr/share/doc/mira-rfam-12s-rrna/changelog usr/share/doc/mira-rfam-12s-rrna/changelog.Debian chmod a-x usr/share/doc/mira-doc/changelog usr/share/doc/mira-doc/changelog.Debian chmod a-x usr/share/doc/mira-assembler/NEWS usr/share/doc/mira-assembler/changelog usr/share/doc/mira-assembler/changelog.Debian usr/share/doc/mira-assembler/test_data/fasta_estset1/tvc_mini.fasta usr/share/doc/mira-assembler/test_data/fasta_estset1/tvc_mini.fasta.qual usr/share/doc/mira-assembler/test_data/solexa_eco_art/ecoli_backbone_in.gbf usr/share/doc/mira-assembler/test_data/solexa_eco_art/ecoli_in.solexa.fasta usr/share/doc/mira-assembler/test_data/solexa_eco_art/ecoli_in.solexa.fasta.qual usr/share/doc/mira-assembler/test_data/solexa_eco_art/ecoli_straindata_in.txt usr/share/man/man1/mira.1 usr/share/man/man1/mirabait.1 usr/share/man/man1/miraconvert.1 usr/share/man/man1/miradiff.1 usr/share/man/man1/miramem.1 usr/share/man/man1/miramer.1 gzip -9nf usr/share/doc/mira-rfam-12s-rrna/changelog usr/share/doc/mira-rfam-12s-rrna/changelog.Debian gzip -9nf usr/share/doc/mira-doc/changelog usr/share/doc/mira-doc/changelog.Debian gzip -9nf usr/share/doc/mira-assembler/NEWS usr/share/doc/mira-assembler/changelog usr/share/doc/mira-assembler/changelog.Debian usr/share/doc/mira-assembler/test_data/fasta_estset1/tvc_mini.fasta usr/share/doc/mira-assembler/test_data/fasta_estset1/tvc_mini.fasta.qual usr/share/doc/mira-assembler/test_data/solexa_eco_art/ecoli_backbone_in.gbf usr/share/doc/mira-assembler/test_data/solexa_eco_art/ecoli_in.solexa.fasta usr/share/doc/mira-assembler/test_data/solexa_eco_art/ecoli_in.solexa.fasta.qual usr/share/doc/mira-assembler/test_data/solexa_eco_art/ecoli_straindata_in.txt usr/share/man/man1/mira.1 usr/share/man/man1/mirabait.1 usr/share/man/man1/miraconvert.1 usr/share/man/man1/miradiff.1 usr/share/man/man1/miramem.1 usr/share/man/man1/miramer.1 cd '/build/reproducible-path/mira-4.9.6' cd '/build/reproducible-path/mira-4.9.6' cd '/build/reproducible-path/mira-4.9.6' dh_fixperms find debian/mira-assembler ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/mira-rfam-12s-rrna ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/mira-doc ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/mira-rfam-12s-rrna/usr/share/doc -type f -a -true -a ! -regex 'debian/mira-rfam-12s-rrna/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/mira-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-doc/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/mira-rfam-12s-rrna -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/mira-doc -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/mira-assembler/usr/share/man debian/mira-assembler/usr/share/lintian/overrides -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/mira-assembler -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/mira-assembler/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x dh_missing dh_dwz -a dwz -- debian/mira-assembler/usr/bin/mira dh_strip -a install -m0755 -d debian/.debhelper/mira-assembler/dbgsym-root/usr/lib/debug/.build-id/6e objcopy --only-keep-debug --compress-debug-sections debian/mira-assembler/usr/bin/mira debian/.debhelper/mira-assembler/dbgsym-root/usr/lib/debug/.build-id/6e/13589b940d36a48b72cefb55552d52cab27897.debug chmod 0644 -- debian/.debhelper/mira-assembler/dbgsym-root/usr/lib/debug/.build-id/6e/13589b940d36a48b72cefb55552d52cab27897.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/6e/13589b940d36a48b72cefb55552d52cab27897.debug debian/mira-assembler/usr/bin/mira install -m0755 -d debian/.debhelper/mira-assembler/dbgsym-root/usr/share/doc ln -s mira-assembler debian/.debhelper/mira-assembler/dbgsym-root/usr/share/doc/mira-assembler-dbgsym install -m0755 -d debian/.debhelper/mira-assembler dh_makeshlibs -a rm -f debian/mira-assembler/DEBIAN/shlibs dh_shlibdeps -a install -m0755 -d debian/mira-assembler/DEBIAN dpkg-shlibdeps -Tdebian/mira-assembler.substvars debian/mira-assembler/usr/bin/mira dh_installdeb install -m0755 -d debian/mira-assembler/DEBIAN install -m0755 -d debian/mira-rfam-12s-rrna/DEBIAN cp -f debian/mira-rfam-12s-rrna.postinst debian/mira-rfam-12s-rrna/DEBIAN/postinst [META] Replace #TOKEN#s in "debian/mira-rfam-12s-rrna/DEBIAN/postinst" chmod 0755 -- debian/mira-rfam-12s-rrna/DEBIAN/postinst cp -f debian/mira-rfam-12s-rrna.postrm debian/mira-rfam-12s-rrna/DEBIAN/postrm [META] Replace #TOKEN#s in "debian/mira-rfam-12s-rrna/DEBIAN/postrm" chmod 0755 -- debian/mira-rfam-12s-rrna/DEBIAN/postrm install -m0755 -d debian/mira-doc/DEBIAN dh_gencontrol install -m0755 -d debian/mira-doc/DEBIAN echo misc:Depends= >> debian/mira-doc.substvars echo misc:Pre-Depends= >> debian/mira-doc.substvars dpkg-gencontrol -pmira-doc -ldebian/changelog -Tdebian/mira-doc.substvars -Pdebian/mira-doc install -m0755 -d debian/mira-rfam-12s-rrna/DEBIAN echo misc:Depends= >> debian/mira-rfam-12s-rrna.substvars echo misc:Pre-Depends= >> debian/mira-rfam-12s-rrna.substvars dpkg-gencontrol -pmira-rfam-12s-rrna -ldebian/changelog -Tdebian/mira-rfam-12s-rrna.substvars -Pdebian/mira-rfam-12s-rrna install -m0755 -d debian/mira-assembler/DEBIAN echo misc:Depends= >> debian/mira-assembler.substvars echo misc:Pre-Depends= >> debian/mira-assembler.substvars install -m0755 -d debian/.debhelper/mira-assembler/dbgsym-root/DEBIAN dpkg-gencontrol -pmira-assembler -ldebian/changelog -Tdebian/mira-assembler.substvars -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=6e13589b940d36a48b72cefb55552d52cab27897 -DSection=debug -UMulti-Arch -UReplaces -UBreaks chmod 0644 -- debian/mira-doc/DEBIAN/control chmod 0644 -- debian/mira-rfam-12s-rrna/DEBIAN/control 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-assembler/DEBIAN/control dh_md5sums install -m0755 -d debian/mira-assembler/DEBIAN install -m0755 -d debian/mira-doc/DEBIAN install -m0755 -d debian/mira-rfam-12s-rrna/DEBIAN cd debian/mira-doc >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/mira-assembler >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/mira-rfam-12s-rrna >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/mira-doc/DEBIAN/md5sums chmod 0644 -- debian/mira-assembler/DEBIAN/md5sums install -m0755 -d debian/.debhelper/mira-assembler/dbgsym-root/DEBIAN cd debian/.debhelper/mira-assembler/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/mira-rfam-12s-rrna/DEBIAN/md5sums chmod 0644 -- debian/.debhelper/mira-assembler/dbgsym-root/DEBIAN/md5sums dh_builddeb dpkg-deb --root-owner-group --build debian/mira-assembler .. dpkg-deb --root-owner-group --build debian/.debhelper/mira-assembler/dbgsym-root .. dpkg-deb --root-owner-group --build debian/mira-rfam-12s-rrna .. dpkg-deb --root-owner-group --build debian/mira-doc .. dpkg-deb: building package 'mira-rfam-12s-rrna' in '../mira-rfam-12s-rrna_4.9.6-7_all.deb'. dpkg-deb: building package 'mira-assembler-dbgsym' in '../mira-assembler-dbgsym_4.9.6-7_i386.deb'. dpkg-deb: building package 'mira-doc' in '../mira-doc_4.9.6-7_all.deb'. dpkg-deb: building package 'mira-assembler' in '../mira-assembler_4.9.6-7_i386.deb'. dpkg-genbuildinfo --build=binary -O../mira_4.9.6-7_i386.buildinfo dpkg-genchanges --build=binary -O../mira_4.9.6-7_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: 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/15184 and its subdirectories I: Current time: Thu Jan 18 01:56:31 -12 2024 I: pbuilder-time-stamp: 1705586191 Thu Jan 18 13:56:33 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos6-i386.debian.net. Thu Jan 18 13:56:33 UTC 2024 I: Preparing to do remote build '2' on ionos6-i386.debian.net. Thu Jan 18 14:05:55 UTC 2024 I: Deleting $TMPDIR on ionos6-i386.debian.net. Thu Jan 18 14:05:55 UTC 2024 I: mira_4.9.6-7_i386.changes: Format: 1.8 Date: Fri, 24 Jun 2022 20:01:35 +0000 Source: mira Binary: mira-assembler mira-assembler-dbgsym mira-doc mira-rfam-12s-rrna Architecture: i386 all Version: 4.9.6-7 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Nilesh Patra Description: mira-assembler - Whole Genome Shotgun and EST Sequence Assembler mira-doc - documentation for the mira assembler mira-rfam-12s-rrna - extract of RFAM 12 rRNA database Closes: 1013000 Changes: mira (4.9.6-7) unstable; urgency=medium . * Team Upload. * Add patch to fix gcc-12 FTBFS (Closes: #1013000) Checksums-Sha1: 721b84888ad5035200df286f888fe5a0e924ec78 33451508 mira-assembler-dbgsym_4.9.6-7_i386.deb c977177c08f495178d8f7f0677ecdbec3db86201 2366172 mira-assembler_4.9.6-7_i386.deb d54ca610fb5a8d111b2ab6f5939cae04b45a1c2d 2798612 mira-doc_4.9.6-7_all.deb e531bca0854d05dd828236b7b7436739eb7122f4 10440692 mira-rfam-12s-rrna_4.9.6-7_all.deb e393c2ff6440b34be4fd80855103f641fc81d462 10350 mira_4.9.6-7_i386.buildinfo Checksums-Sha256: a24657071650c0e97b4169032be55d53f8fb88f6102f7d2d8e59245e3734644b 33451508 mira-assembler-dbgsym_4.9.6-7_i386.deb 32a03cbbd4ce8ab43423a99db62b0000efecd2d723d9ab305aa4bff104861fe0 2366172 mira-assembler_4.9.6-7_i386.deb a9008bdb6f0858884ef542123a731cc4ba32617576a079b61da76a0f83b8c391 2798612 mira-doc_4.9.6-7_all.deb dfe73fec9ab9f17689aa4a944952311cbae1c5d7f90d19a718b462ee804d4af7 10440692 mira-rfam-12s-rrna_4.9.6-7_all.deb 6a486db62b1533e92dd38a08653450adec558af00fb62aac4c87f7ddae30becb 10350 mira_4.9.6-7_i386.buildinfo Files: 2de241ed58f13bc6d310b0196d893690 33451508 debug optional mira-assembler-dbgsym_4.9.6-7_i386.deb cbf6d89e36967245c5218beab3d85e3c 2366172 science optional mira-assembler_4.9.6-7_i386.deb 02332b3323fdb6de1a1b5edba2a3154a 2798612 doc optional mira-doc_4.9.6-7_all.deb 38a9af3854a4d9ad0673c5921733509d 10440692 science optional mira-rfam-12s-rrna_4.9.6-7_all.deb 8a451c0fbfe18b2a76576b032aa29c54 10350 science optional mira_4.9.6-7_i386.buildinfo Thu Jan 18 14:05:56 UTC 2024 I: diffoscope 240 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.ylEm2WXX/mira_4.9.6-7.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.ylEm2WXX/mira_4.9.6-7.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.ylEm2WXX/mira_4.9.6-7.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.ylEm2WXX/b1/mira_4.9.6-7_i386.changes /srv/reproducible-results/rbuild-debian/r-b-build.ylEm2WXX/b2/mira_4.9.6-7_i386.changes ## close_archive (total time: 0.000s) 0.000s 22 calls diffoscope.comparators.xz.XzContainer 0.000s 16 calls diffoscope.comparators.tar.TarContainer 0.000s 12 calls diffoscope.comparators.deb.DebContainer 0.000s 6 calls diffoscope.comparators.deb.DebTarContainer ## command (total time: 1430.313s) 704.060s 1043 calls readelf 570.545s 123 calls diff 142.504s 209 calls objdump 6.178s 22 calls xz 5.574s 2 calls objcopy 1.122s 22 calls strings 0.163s 2 calls cmp 0.163s 2 calls cmp (external) 0.004s 23 calls cmp (internal) ## compare_files (cumulative) (total time: 12908.287s) 2256.820s 1 call abc.DotChangesFile 2256.139s 2 calls abc.DebFile 2253.845s 4 calls abc.XzFile 2250.360s 2 calls abc.DebDataTarFile 2247.620s 2 calls abc.ElfFile 1636.647s 10 calls diffoscope.comparators.elf.ElfCodeSection 3.686s 35 calls diffoscope.comparators.elf.ElfSection 3.077s 3 calls diffoscope.comparators.elf.ElfStringSection 0.062s 2 calls abc.TarFile 0.013s 1 call abc.TextFile 0.009s 2 calls abc.Md5sumsFile 0.008s 1 call diffoscope.comparators.elf.MonkeyPatchedElfSection ## container_extract (total time: 8.986s) 6.179s 22 calls diffoscope.comparators.xz.XzContainer 2.451s 26 calls diffoscope.comparators.deb.DebContainer 0.346s 64 calls diffoscope.comparators.deb.DebTarContainer 0.011s 20 calls diffoscope.comparators.tar.TarContainer ## diff (total time: 0.544s) 0.544s 170 calls linediff ## has_same_content_as (total time: 0.170s) 0.164s 4 calls abc.DebFile 0.003s 5 calls diffoscope.comparators.utils.libarchive.LibarchiveSymlink 0.000s 4 calls abc.TextFile 0.000s 2 calls abc.DebDataTarFile 0.000s 4 calls abc.Md5sumsFile 0.000s 4 calls abc.XzFile 0.000s 2 calls abc.ElfFile 0.000s 35 calls diffoscope.comparators.elf.ElfSection 0.000s 2 calls abc.TarFile 0.000s 1 call abc.DotChangesFile 0.000s 10 calls diffoscope.comparators.elf.ElfCodeSection 0.000s 3 calls diffoscope.comparators.elf.ElfStringSection 0.000s 1 call diffoscope.comparators.elf.MonkeyPatchedElfSection ## main (total time: 2260.125s) 2260.124s 2 calls outputs 0.001s 1 call cleanup ## open_archive (total time: 0.001s) 0.000s 16 calls diffoscope.comparators.tar.TarContainer 0.000s 22 calls diffoscope.comparators.xz.XzContainer 0.000s 12 calls diffoscope.comparators.deb.DebContainer 0.000s 6 calls diffoscope.comparators.deb.DebTarContainer ## output (total time: 2.509s) 2.490s 1 call html 0.011s 1 call text 0.008s 1 call json ## recognizes (total time: 5.006s) 2.848s 1004 calls diffoscope.comparators.utils.archive.ArchiveMember 0.541s 432 calls diffoscope.comparators.debian.DebControlMember 0.509s 12 calls diffoscope.comparators.binary.FilesystemFile 0.505s 1956 calls diffoscope.comparators.utils.libarchive.LibarchiveMember 0.385s 770 calls diffoscope.comparators.elf.ElfSection 0.187s 220 calls diffoscope.comparators.elf.ElfCodeSection 0.029s 66 calls diffoscope.comparators.elf.ElfStringSection 0.002s 22 calls diffoscope.comparators.elf.MonkeyPatchedElfSection 0.000s 32 calls abc.Md5sumsFile 0.000s 10 calls abc.DotChangesFile 0.000s 20 calls diffoscope.comparators.utils.libarchive.LibarchiveSymlink ## specialize (total time: 1.241s) 1.241s 77 calls specialize Thu Jan 18 14:43:37 UTC 2024 E: mira failed to build reproducibly in bookworm on i386. Thu Jan 18 14:43:37 UTC 2024 E: diffoscope 240 found issues, please check https://tests.reproducible-builds.org/debian/dbd/bookworm/i386/mira_4.9.6-7.diffoscope.html Thu Jan 18 14:43:40 UTC 2024 I: Submitting .buildinfo files to external archives: Thu Jan 18 14:43:40 UTC 2024 I: Submitting 12K b1/mira_4.9.6-7_i386.buildinfo.asc Thu Jan 18 14:43:41 UTC 2024 I: Submitting 12K b2/mira_4.9.6-7_i386.buildinfo.asc Thu Jan 18 14:43:42 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Thu Jan 18 14:43:42 UTC 2024 I: Done submitting .buildinfo files. Thu Jan 18 14:43:42 UTC 2024 I: Removing signed mira_4.9.6-7_i386.buildinfo.asc files: removed './b1/mira_4.9.6-7_i386.buildinfo.asc' removed './b2/mira_4.9.6-7_i386.buildinfo.asc'