https://launchpad.net/ubuntu/+source/mira/4.9.6-4build7/+build/19742897 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux lcy01-amd64-002 4.4.0-186-generic #216-Ubuntu SMP Wed Jul 1 05:34:05 UTC 2020 x86_64 Buildd toolchain package versions: launchpad-buildd_189 python-lpbuildd_189 sbuild_0.67.0-2ubuntu7.1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu14.10.1 bzr_2.7.0-2ubuntu3.1 git-build-recipe_0.3.6~git201906051340.ff11471~ubuntu16.04.1 git_1:2.7.4-0ubuntu1.9 dpkg-dev_1.18.4ubuntu1.6 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 28 Jul 19:25:34 ntpdate[1884]: adjust time server 10.211.37.1 offset 0.000403 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=groovy --arch=amd64 PACKAGEBUILD-19742897 --image-type chroot /home/buildd/filecache-default/20f824f72d640d2ced4a53a84e89958befe66512 Creating target for build PACKAGEBUILD-19742897 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=groovy --arch=amd64 PACKAGEBUILD-19742897 Starting target for build PACKAGEBUILD-19742897 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=groovy --arch=amd64 PACKAGEBUILD-19742897 'deb http://ftpmaster.internal/ubuntu groovy main universe' 'deb http://ftpmaster.internal/ubuntu groovy-security main universe' 'deb http://ftpmaster.internal/ubuntu groovy-updates main universe' 'deb http://ftpmaster.internal/ubuntu groovy-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-19742897 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=groovy --arch=amd64 PACKAGEBUILD-19742897 Updating target for build PACKAGEBUILD-19742897 Get:1 http://ftpmaster.internal/ubuntu groovy InRelease [267 kB] Get:2 http://ftpmaster.internal/ubuntu groovy-security InRelease [89.1 kB] Get:3 http://ftpmaster.internal/ubuntu groovy-updates InRelease [89.1 kB] Get:4 http://ftpmaster.internal/ubuntu groovy-proposed InRelease [118 kB] Get:5 http://ftpmaster.internal/ubuntu groovy/main amd64 Packages [983 kB] Get:6 http://ftpmaster.internal/ubuntu groovy/main Translation-en [513 kB] Get:7 http://ftpmaster.internal/ubuntu groovy/universe amd64 Packages [8810 kB] Get:8 http://ftpmaster.internal/ubuntu groovy/universe Translation-en [5242 kB] Get:9 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 Packages [102 kB] Get:10 http://ftpmaster.internal/ubuntu groovy-proposed/main Translation-en [54.8 kB] Get:11 http://ftpmaster.internal/ubuntu groovy-proposed/universe amd64 Packages [339 kB] Get:12 http://ftpmaster.internal/ubuntu groovy-proposed/universe Translation-en [204 kB] Fetched 16.8 MB in 3s (6215 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: base-files bsdutils build-essential ca-certificates dpkg dpkg-dev libblkid1 libdpkg-perl liblzma5 libmount1 libmpfr6 libselinux1 libsemanage-common libsemanage1 libsmartcols1 libuuid1 mount util-linux xz-utils 19 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 5763 kB of archives. After this operation, 2548 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu groovy/main amd64 base-files amd64 11ubuntu10 [60.3 kB] Get:2 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 bsdutils amd64 1:2.35.2-9ubuntu1 [86.6 kB] Get:3 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 libselinux1 amd64 3.1-2 [68.8 kB] Get:4 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 dpkg amd64 1.20.5ubuntu1 [1172 kB] Get:5 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 util-linux amd64 2.35.2-9ubuntu1 [1048 kB] Get:6 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 mount amd64 2.35.2-9ubuntu1 [118 kB] Get:7 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 libblkid1 amd64 2.35.2-9ubuntu1 [133 kB] Get:8 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 liblzma5 amd64 5.2.4-1ubuntu1 [91.7 kB] Get:9 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 libmount1 amd64 2.35.2-9ubuntu1 [146 kB] Get:10 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 libsemanage-common all 3.1-1 [10.2 kB] Get:11 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 libsemanage1 amd64 3.1-1 [86.2 kB] Get:12 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 libsmartcols1 amd64 2.35.2-9ubuntu1 [95.7 kB] Get:13 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 libuuid1 amd64 2.35.2-9ubuntu1 [22.0 kB] Get:14 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 ca-certificates all 20200601 [147 kB] Get:15 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 xz-utils amd64 5.2.4-1ubuntu1 [82.5 kB] Get:16 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 dpkg-dev all 1.20.5ubuntu1 [758 kB] Get:17 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 libdpkg-perl all 1.20.5ubuntu1 [231 kB] Get:18 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 build-essential amd64 12.8ubuntu3 [4640 B] Get:19 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 libmpfr6 amd64 4.1.0-3 [1401 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 5763 kB in 1s (10.3 MB/s) (Reading database ... 12787 files and directories currently installed.) Preparing to unpack .../base-files_11ubuntu10_amd64.deb ... Unpacking base-files (11ubuntu10) over (11ubuntu9) ... Setting up base-files (11ubuntu10) ... Installing new version of config file /etc/update-motd.d/50-motd-news ... (Reading database ... 12787 files and directories currently installed.) Preparing to unpack .../bsdutils_1%3a2.35.2-9ubuntu1_amd64.deb ... Unpacking bsdutils (1:2.35.2-9ubuntu1) over (1:2.35.2-7ubuntu3) ... Setting up bsdutils (1:2.35.2-9ubuntu1) ... (Reading database ... 12787 files and directories currently installed.) Preparing to unpack .../libselinux1_3.1-2_amd64.deb ... Unpacking libselinux1:amd64 (3.1-2) over (3.0-1build2) ... Setting up libselinux1:amd64 (3.1-2) ... (Reading database ... 12787 files and directories currently installed.) Preparing to unpack .../dpkg_1.20.5ubuntu1_amd64.deb ... Unpacking dpkg (1.20.5ubuntu1) over (1.19.7ubuntu4) ... Setting up dpkg (1.20.5ubuntu1) ... Installing new version of config file /etc/cron.daily/dpkg ... (Reading database ... 12796 files and directories currently installed.) Preparing to unpack .../util-linux_2.35.2-9ubuntu1_amd64.deb ... Unpacking util-linux (2.35.2-9ubuntu1) over (2.35.2-7ubuntu3) ... Setting up util-linux (2.35.2-9ubuntu1) ... (Reading database ... 12796 files and directories currently installed.) Preparing to unpack .../mount_2.35.2-9ubuntu1_amd64.deb ... Unpacking mount (2.35.2-9ubuntu1) over (2.35.2-7ubuntu3) ... Preparing to unpack .../libblkid1_2.35.2-9ubuntu1_amd64.deb ... Unpacking libblkid1:amd64 (2.35.2-9ubuntu1) over (2.35.2-7ubuntu3) ... Setting up libblkid1:amd64 (2.35.2-9ubuntu1) ... (Reading database ... 12796 files and directories currently installed.) Preparing to unpack .../liblzma5_5.2.4-1ubuntu1_amd64.deb ... Unpacking liblzma5:amd64 (5.2.4-1ubuntu1) over (5.2.4-1) ... Setting up liblzma5:amd64 (5.2.4-1ubuntu1) ... (Reading database ... 12796 files and directories currently installed.) Preparing to unpack .../libmount1_2.35.2-9ubuntu1_amd64.deb ... Unpacking libmount1:amd64 (2.35.2-9ubuntu1) over (2.35.2-7ubuntu3) ... Setting up libmount1:amd64 (2.35.2-9ubuntu1) ... (Reading database ... 12796 files and directories currently installed.) Preparing to unpack .../libsemanage-common_3.1-1_all.deb ... Unpacking libsemanage-common (3.1-1) over (3.0-1build2) ... Setting up libsemanage-common (3.1-1) ... (Reading database ... 12796 files and directories currently installed.) Preparing to unpack .../libsemanage1_3.1-1_amd64.deb ... Unpacking libsemanage1:amd64 (3.1-1) over (3.0-1build2) ... Setting up libsemanage1:amd64 (3.1-1) ... (Reading database ... 12796 files and directories currently installed.) Preparing to unpack .../libsmartcols1_2.35.2-9ubuntu1_amd64.deb ... Unpacking libsmartcols1:amd64 (2.35.2-9ubuntu1) over (2.35.2-7ubuntu3) ... Setting up libsmartcols1:amd64 (2.35.2-9ubuntu1) ... (Reading database ... 12796 files and directories currently installed.) Preparing to unpack .../libuuid1_2.35.2-9ubuntu1_amd64.deb ... Unpacking libuuid1:amd64 (2.35.2-9ubuntu1) over (2.35.2-7ubuntu3) ... Setting up libuuid1:amd64 (2.35.2-9ubuntu1) ... (Reading database ... 12796 files and directories currently installed.) Preparing to unpack .../0-ca-certificates_20200601_all.deb ... Unpacking ca-certificates (20200601) over (20190110ubuntu2) ... Preparing to unpack .../1-xz-utils_5.2.4-1ubuntu1_amd64.deb ... Unpacking xz-utils (5.2.4-1ubuntu1) over (5.2.4-1) ... Preparing to unpack .../2-dpkg-dev_1.20.5ubuntu1_all.deb ... Unpacking dpkg-dev (1.20.5ubuntu1) over (1.19.7ubuntu4) ... Preparing to unpack .../3-libdpkg-perl_1.20.5ubuntu1_all.deb ... Unpacking libdpkg-perl (1.20.5ubuntu1) over (1.19.7ubuntu4) ... Preparing to unpack .../4-build-essential_12.8ubuntu3_amd64.deb ... Unpacking build-essential (12.8ubuntu3) over (12.8ubuntu1) ... Preparing to unpack .../5-libmpfr6_4.1.0-3_amd64.deb ... Unpacking libmpfr6:amd64 (4.1.0-3) over (4.0.2-1build1) ... Setting up ca-certificates (20200601) ... Updating certificates in /etc/ssl/certs... 13 added, 14 removed; done. Setting up libmpfr6:amd64 (4.1.0-3) ... Setting up xz-utils (5.2.4-1ubuntu1) ... Setting up libdpkg-perl (1.20.5ubuntu1) ... Setting up mount (2.35.2-9ubuntu1) ... Setting up dpkg-dev (1.20.5ubuntu1) ... Setting up build-essential (12.8ubuntu3) ... Processing triggers for systemd (245.6-3ubuntu3) ... Processing triggers for libc-bin (2.31-0ubuntu10) ... Processing triggers for ca-certificates (20200601) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-19742897 amd64 groovy-proposed -c chroot:build-PACKAGEBUILD-19742897 --arch=amd64 --dist=groovy-proposed --nolog -A mira_4.9.6-4build7.dsc Initiating build PACKAGEBUILD-19742897 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-186-generic #216-Ubuntu SMP Wed Jul 1 05:34:05 UTC 2020 x86_64 sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on lcy01-amd64-002.buildd +==============================================================================+ | mira 4.9.6-4build7 (amd64) 28 Jul 2020 19:25 | +==============================================================================+ Package: mira Version: 4.9.6-4build7 Source Version: 4.9.6-4build7 Distribution: groovy-proposed Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 I: NOTICE: Log filtering will replace 'build/mira-3PiO6B/mira-4.9.6' with '<>' I: NOTICE: Log filtering will replace 'build/mira-3PiO6B' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-19742897/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- mira_4.9.6-4build7.dsc exists in .; copying to chroot Check architectures ------------------- Check dependencies ------------------ Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-z9orn5/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-z9orn5/apt_archive ./ InRelease Get:2 copy:/<>/resolver-z9orn5/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-z9orn5/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-z9orn5/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-z9orn5/apt_archive ./ Packages [528 B] Fetched 2861 B in 0s (249 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install core build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 852 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-z9orn5/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 852 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 12775 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: debhelper (>= 11~), autoconf-archive, libbz2-dev, libexpat1-dev, libgoogle-perftools-dev, perl, flex, libfl-dev, vim-common, zlib1g-dev, libboost-thread-dev, libboost-regex-dev, libboost-filesystem-dev, libboost-system-dev, libboost-iostreams-dev, docbook-xsl, dblatex Filtered Build-Depends: debhelper (>= 11~), autoconf-archive, libbz2-dev, libexpat1-dev, libgoogle-perftools-dev, perl, flex, libfl-dev, vim-common, zlib1g-dev, libboost-thread-dev, libboost-regex-dev, libboost-filesystem-dev, libboost-system-dev, libboost-iostreams-dev, docbook-xsl, dblatex dpkg-deb: building package 'sbuild-build-depends-mira-dummy' in '/<>/resolver-qhOdYA/apt_archive/sbuild-build-depends-mira-dummy.deb'. Ign:1 copy:/<>/resolver-qhOdYA/apt_archive ./ InRelease Get:2 copy:/<>/resolver-qhOdYA/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-qhOdYA/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-qhOdYA/apt_archive ./ Sources [342 B] Get:5 copy:/<>/resolver-qhOdYA/apt_archive ./ Packages [639 B] Fetched 3100 B in 0s (238 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install mira build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf autoconf-archive automake autopoint autotools-dev bsdextrautils dblatex debhelper dh-autoreconf dh-strip-nondeterminism docbook-xml docbook-xsl dwz file flex fontconfig-config fonts-dejavu-core fonts-gfs-baskerville fonts-gfs-porson fonts-lmodern gettext gettext-base groff-base icu-devtools intltool-debian libapache-pom-java libarchive-zip-perl libboost-atomic1.71-dev libboost-atomic1.71.0 libboost-chrono1.71-dev libboost-chrono1.71.0 libboost-date-time1.71-dev libboost-date-time1.71.0 libboost-filesystem-dev libboost-filesystem1.71-dev libboost-filesystem1.71.0 libboost-iostreams-dev libboost-iostreams1.71-dev libboost-iostreams1.71.0 libboost-regex-dev libboost-regex1.71-dev libboost-regex1.71.0 libboost-serialization1.71-dev libboost-serialization1.71.0 libboost-system-dev libboost-system1.71-dev libboost-system1.71.0 libboost-thread-dev libboost-thread1.71-dev libboost-thread1.71.0 libboost1.71-dev libbrotli1 libbsd0 libbz2-dev libcairo2 libcommons-logging-java libcommons-parent-java libcroco3 libdatrie1 libdebhelper-perl libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libfl-dev libfl2 libfontbox-java libfontconfig1 libfontenc1 libfreetype6 libglib2.0-0 libgoogle-perftools-dev libgoogle-perftools4 libgraphite2-3 libharfbuzz0b libice6 libicu-dev libicu66 libicu67 libjs-jquery libkpathsea6 liblzma-dev libmagic-mgc libmagic1 libmime-charset-perl libmpdec2 libpaper-utils libpaper1 libpdfbox-java libpipeline1 libpixman-1-0 libptexenc1 libpython3-stdlib libpython3.8-minimal libpython3.8-stdlib libsigsegv2 libsm6 libsombok3 libsub-override-perl libsynctex2 libtcmalloc-minimal4 libteckit0 libtexlua53 libtexluajit2 libthai-data libthai0 libtool libuchardet0 libunicode-linebreak-perl libunwind-dev libunwind8 libx11-6 libx11-data libxau6 libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxi6 libxml2 libxmu6 libxpm4 libxrender1 libxslt1.1 libxt6 libzzip-0-13 lmodern m4 man-db mime-support node-jquery po-debconf preview-latex-style python-apt-common python3 python3-apt python3-minimal python3.8 python3.8-minimal sgml-base sgml-data t1utils tex-common texlive texlive-base texlive-bibtex-extra texlive-binaries texlive-extra-utils texlive-fonts-recommended texlive-lang-greek texlive-latex-base texlive-latex-extra texlive-latex-recommended texlive-luatex texlive-pictures texlive-plain-generic texlive-science ucf vim-common x11-common xdg-utils xfonts-encodings xfonts-utils xml-core xsltproc xxd zlib1g-dev Suggested packages: gnu-standards autoconf-doc docbook ghostscript graphicsmagick-imagemagick-compat | imagemagick inkscape latex-cjk-all opensp pdf-viewer texlive-lang-all texlive-lang-cyrillic texlive-xetex transfig xindy dh-make docbook-dsssl docbook-defguide dbtoepub docbook-xsl-doc-html | docbook-xsl-doc-pdf | docbook-xsl-doc-text | docbook-xsl-doc docbook-xsl-saxon fop libsaxon-java libxalan2-java libxslthl-java xalan bison flex-doc gettext-doc libasprintf-dev libgettextpo-dev groff libboost1.71-doc libboost-container1.71-dev libboost-context1.71-dev libboost-contract1.71-dev libboost-coroutine1.71-dev libboost-exception1.71-dev libboost-fiber1.71-dev libboost-graph1.71-dev libboost-graph-parallel1.71-dev libboost-locale1.71-dev libboost-log1.71-dev libboost-math1.71-dev libboost-mpi1.71-dev libboost-mpi-python1.71-dev libboost-numpy1.71-dev libboost-program-options1.71-dev libboost-python1.71-dev libboost-random1.71-dev libboost-stacktrace1.71-dev libboost-test1.71-dev libboost-timer1.71-dev libboost-type-erasure1.71-dev libboost-wave1.71-dev libboost1.71-tools-dev libmpfrc++-dev libntl-dev libavalon-framework-java libcommons-logging-java-doc libexcalibur-logkit-java liblog4j1.2-java icu-doc liblzma-doc libencode-hanextra-perl libpod2-base-perl libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl python3-doc python3-tk python3-venv python3-apt-dbg python-apt-doc python3.8-venv python3.8-doc binfmt-support sgml-base-doc perlsgml w3-recs libxml2-utils gv | postscript-viewer perl-tk xpdf | pdf-viewer xzdec chktex default-jre-headless dvidvi dvipng fragmaster lacheck latexdiff latexmk purifyeps texlive-fonts-recommended-doc texlive-latex-base-doc python3-pygments icc-profiles libfile-which-perl libspreadsheet-parseexcel-perl texlive-latex-extra-doc texlive-latex-recommended-doc texlive-pstricks dot2tex prerex ruby-tcltk | libtcltk-ruby texlive-pictures-doc vprerex texlive-science-doc Recommended packages: libxml2-utils dblatex-doc curl | wget | lynx bzip2-doc libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs javascript-common libltdl-dev libmail-sendmail-perl lsb-release iso-codes dvisvgm ghostscript libfile-homedir-perl liblog-log4perl-perl libyaml-tiny-perl ruby | ruby-interpreter tex-gyre tipa tk vim | vim-gtk3 | vim-athena | vim-nox | vim-tiny libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils The following NEW packages will be installed: autoconf autoconf-archive automake autopoint autotools-dev bsdextrautils dblatex debhelper dh-autoreconf dh-strip-nondeterminism docbook-xml docbook-xsl dwz file flex fontconfig-config fonts-dejavu-core fonts-gfs-baskerville fonts-gfs-porson fonts-lmodern gettext gettext-base groff-base icu-devtools intltool-debian libapache-pom-java libarchive-zip-perl libboost-atomic1.71-dev libboost-atomic1.71.0 libboost-chrono1.71-dev libboost-chrono1.71.0 libboost-date-time1.71-dev libboost-date-time1.71.0 libboost-filesystem-dev libboost-filesystem1.71-dev libboost-filesystem1.71.0 libboost-iostreams-dev libboost-iostreams1.71-dev libboost-iostreams1.71.0 libboost-regex-dev libboost-regex1.71-dev libboost-regex1.71.0 libboost-serialization1.71-dev libboost-serialization1.71.0 libboost-system-dev libboost-system1.71-dev libboost-system1.71.0 libboost-thread-dev libboost-thread1.71-dev libboost-thread1.71.0 libboost1.71-dev libbrotli1 libbsd0 libbz2-dev libcairo2 libcommons-logging-java libcommons-parent-java libcroco3 libdatrie1 libdebhelper-perl libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libfl-dev libfl2 libfontbox-java libfontconfig1 libfontenc1 libfreetype6 libglib2.0-0 libgoogle-perftools-dev libgoogle-perftools4 libgraphite2-3 libharfbuzz0b libice6 libicu-dev libicu66 libicu67 libjs-jquery libkpathsea6 liblzma-dev libmagic-mgc libmagic1 libmime-charset-perl libmpdec2 libpaper-utils libpaper1 libpdfbox-java libpipeline1 libpixman-1-0 libptexenc1 libpython3-stdlib libpython3.8-minimal libpython3.8-stdlib libsigsegv2 libsm6 libsombok3 libsub-override-perl libsynctex2 libtcmalloc-minimal4 libteckit0 libtexlua53 libtexluajit2 libthai-data libthai0 libtool libuchardet0 libunicode-linebreak-perl libunwind-dev libunwind8 libx11-6 libx11-data libxau6 libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxi6 libxml2 libxmu6 libxpm4 libxrender1 libxslt1.1 libxt6 libzzip-0-13 lmodern m4 man-db mime-support node-jquery po-debconf preview-latex-style python-apt-common python3 python3-apt python3-minimal python3.8 python3.8-minimal sbuild-build-depends-mira-dummy sgml-base sgml-data t1utils tex-common texlive texlive-base texlive-bibtex-extra texlive-binaries texlive-extra-utils texlive-fonts-recommended texlive-lang-greek texlive-latex-base texlive-latex-extra texlive-latex-recommended texlive-luatex texlive-pictures texlive-plain-generic texlive-science ucf vim-common x11-common xdg-utils xfonts-encodings xfonts-utils xml-core xsltproc xxd zlib1g-dev 0 upgraded, 170 newly installed, 0 to remove and 0 not upgraded. Need to get 394 MB of archives. After this operation, 1125 MB of additional disk space will be used. Get:1 copy:/<>/resolver-qhOdYA/apt_archive ./ sbuild-build-depends-mira-dummy 0.invalid.0 [972 B] Get:2 http://ftpmaster.internal/ubuntu groovy/main amd64 libpython3.8-minimal amd64 3.8.5-1 [714 kB] Get:3 http://ftpmaster.internal/ubuntu groovy/main amd64 libexpat1 amd64 2.2.9-1build1 [73.3 kB] Get:4 http://ftpmaster.internal/ubuntu groovy/main amd64 python3.8-minimal amd64 3.8.5-1 [1900 kB] Get:5 http://ftpmaster.internal/ubuntu groovy/main amd64 python3-minimal amd64 3.8.2-0ubuntu2 [23.6 kB] Get:6 http://ftpmaster.internal/ubuntu groovy/main amd64 mime-support all 3.64ubuntu1 [30.6 kB] Get:7 http://ftpmaster.internal/ubuntu groovy/main amd64 libmpdec2 amd64 2.4.2-3 [81.1 kB] Get:8 http://ftpmaster.internal/ubuntu groovy/main amd64 libpython3.8-stdlib amd64 3.8.5-1 [1671 kB] Get:9 http://ftpmaster.internal/ubuntu groovy/main amd64 python3.8 amd64 3.8.5-1 [373 kB] Get:10 http://ftpmaster.internal/ubuntu groovy/main amd64 libpython3-stdlib amd64 3.8.2-0ubuntu2 [7068 B] Get:11 http://ftpmaster.internal/ubuntu groovy/main amd64 python3 amd64 3.8.2-0ubuntu2 [47.6 kB] Get:12 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 bsdextrautils amd64 2.35.2-9ubuntu1 [77.3 kB] Get:13 http://ftpmaster.internal/ubuntu groovy/main amd64 libuchardet0 amd64 0.0.7-1 [68.0 kB] Get:14 http://ftpmaster.internal/ubuntu groovy/main amd64 groff-base amd64 1.22.4-5 [847 kB] Get:15 http://ftpmaster.internal/ubuntu groovy/main amd64 libpipeline1 amd64 1.5.2-2build1 [27.7 kB] Get:16 http://ftpmaster.internal/ubuntu groovy/main amd64 man-db amd64 2.9.3-2 [1117 kB] Get:17 http://ftpmaster.internal/ubuntu groovy/universe amd64 autoconf-archive all 20190106-2.1ubuntu1 [665 kB] Get:18 http://ftpmaster.internal/ubuntu groovy/main amd64 libsigsegv2 amd64 2.12-2build1 [13.9 kB] Get:19 http://ftpmaster.internal/ubuntu groovy/main amd64 m4 amd64 1.4.18-4 [199 kB] Get:20 http://ftpmaster.internal/ubuntu groovy/main amd64 flex amd64 2.6.4-8 [298 kB] Get:21 http://ftpmaster.internal/ubuntu groovy/main amd64 sgml-base all 1.30 [12.5 kB] Get:22 http://ftpmaster.internal/ubuntu groovy/main amd64 ucf all 3.0043 [56.1 kB] Get:23 http://ftpmaster.internal/ubuntu groovy/universe amd64 tex-common all 6.15 [33.0 kB] Get:24 http://ftpmaster.internal/ubuntu groovy/main amd64 libmagic-mgc amd64 1:5.38-5 [218 kB] Get:25 http://ftpmaster.internal/ubuntu groovy/main amd64 libmagic1 amd64 1:5.38-5 [76.0 kB] Get:26 http://ftpmaster.internal/ubuntu groovy/main amd64 file amd64 1:5.38-5 [23.3 kB] Get:27 http://ftpmaster.internal/ubuntu groovy/main amd64 libbsd0 amd64 0.10.0-1 [45.4 kB] Get:28 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 libelf1 amd64 0.180-1 [44.2 kB] Get:29 http://ftpmaster.internal/ubuntu groovy/main amd64 libglib2.0-0 amd64 2.64.4-1 [1286 kB] Get:30 http://ftpmaster.internal/ubuntu groovy/main amd64 libicu66 amd64 66.1-2ubuntu3 [8515 kB] Get:31 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 libicu67 amd64 67.1-3ubuntu1 [8619 kB] Get:32 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 libxml2 amd64 2.9.10+dfsg-5build1 [623 kB] Get:33 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 xxd amd64 2:8.2.0716-3ubuntu1 [49.8 kB] Get:34 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 vim-common all 2:8.2.0716-3ubuntu1 [80.8 kB] Get:35 http://ftpmaster.internal/ubuntu groovy/main amd64 gettext-base amd64 0.19.8.1-10build1 [50.2 kB] Get:36 http://ftpmaster.internal/ubuntu groovy/main amd64 libxau6 amd64 1:1.0.9-0ubuntu1 [7488 B] Get:37 http://ftpmaster.internal/ubuntu groovy/main amd64 libxdmcp6 amd64 1:1.1.3-0ubuntu1 [10.6 kB] Get:38 http://ftpmaster.internal/ubuntu groovy/main amd64 libxcb1 amd64 1.14-2 [44.7 kB] Get:39 http://ftpmaster.internal/ubuntu groovy/main amd64 libx11-data all 2:1.6.9-2ubuntu1 [113 kB] Get:40 http://ftpmaster.internal/ubuntu groovy/main amd64 libx11-6 amd64 2:1.6.9-2ubuntu1 [573 kB] Get:41 http://ftpmaster.internal/ubuntu groovy/main amd64 libxext6 amd64 2:1.3.4-0ubuntu1 [29.1 kB] Get:42 http://ftpmaster.internal/ubuntu groovy/main amd64 python-apt-common all 2.1.3 [17.1 kB] Get:43 http://ftpmaster.internal/ubuntu groovy/main amd64 python3-apt amd64 2.1.3 [153 kB] Get:44 http://ftpmaster.internal/ubuntu groovy/main amd64 autoconf all 2.69-11.1 [321 kB] Get:45 http://ftpmaster.internal/ubuntu groovy/main amd64 autotools-dev all 20180224.1 [39.6 kB] Get:46 http://ftpmaster.internal/ubuntu groovy/main amd64 automake all 1:1.16.2-3ubuntu1 [548 kB] Get:47 http://ftpmaster.internal/ubuntu groovy/main amd64 autopoint all 0.19.8.1-10build1 [412 kB] Get:48 http://ftpmaster.internal/ubuntu groovy/main amd64 xml-core all 0.18+nmu1 [21.6 kB] Get:49 http://ftpmaster.internal/ubuntu groovy/main amd64 sgml-data all 2.0.11 [171 kB] Get:50 http://ftpmaster.internal/ubuntu groovy/main amd64 docbook-xml all 4.5-9 [71.2 kB] Get:51 http://ftpmaster.internal/ubuntu groovy/main amd64 libpaper1 amd64 1.1.28 [13.0 kB] Get:52 http://ftpmaster.internal/ubuntu groovy/main amd64 libpaper-utils amd64 1.1.28 [8400 B] Get:53 http://ftpmaster.internal/ubuntu groovy/main amd64 libkpathsea6 amd64 2020.20200327.54578-4 [57.9 kB] Get:54 http://ftpmaster.internal/ubuntu groovy/main amd64 libptexenc1 amd64 2020.20200327.54578-4 [35.5 kB] Get:55 http://ftpmaster.internal/ubuntu groovy/main amd64 libsynctex2 amd64 2020.20200327.54578-4 [55.3 kB] Get:56 http://ftpmaster.internal/ubuntu groovy/main amd64 libtexlua53 amd64 2020.20200327.54578-4 [105 kB] Get:57 http://ftpmaster.internal/ubuntu groovy/main amd64 libtexluajit2 amd64 2020.20200327.54578-4 [236 kB] Get:58 http://ftpmaster.internal/ubuntu groovy/main amd64 t1utils amd64 1.41-4 [56.0 kB] Get:59 http://ftpmaster.internal/ubuntu groovy/main amd64 libbrotli1 amd64 1.0.7-7 [270 kB] Get:60 http://ftpmaster.internal/ubuntu groovy/main amd64 libfreetype6 amd64 2.10.2+dfsg-3 [348 kB] Get:61 http://ftpmaster.internal/ubuntu groovy/main amd64 fonts-dejavu-core all 2.37-2 [1041 kB] Get:62 http://ftpmaster.internal/ubuntu groovy/main amd64 fontconfig-config all 2.13.1-2ubuntu3 [28.8 kB] Get:63 http://ftpmaster.internal/ubuntu groovy/main amd64 libfontconfig1 amd64 2.13.1-2ubuntu3 [114 kB] Get:64 http://ftpmaster.internal/ubuntu groovy/main amd64 libpixman-1-0 amd64 0.38.4-0ubuntu1 [227 kB] Get:65 http://ftpmaster.internal/ubuntu groovy/main amd64 libxcb-render0 amd64 1.14-2 [14.8 kB] Get:66 http://ftpmaster.internal/ubuntu groovy/main amd64 libxcb-shm0 amd64 1.14-2 [5584 B] Get:67 http://ftpmaster.internal/ubuntu groovy/main amd64 libxrender1 amd64 1:0.9.10-1 [18.7 kB] Get:68 http://ftpmaster.internal/ubuntu groovy/main amd64 libcairo2 amd64 1.16.0-4ubuntu1 [583 kB] Get:69 http://ftpmaster.internal/ubuntu groovy/main amd64 libgraphite2-3 amd64 1.3.14-1 [73.7 kB] Get:70 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 libharfbuzz0b amd64 2.6.4-1ubuntu5 [331 kB] Get:71 http://ftpmaster.internal/ubuntu groovy/universe amd64 libteckit0 amd64 2.5.8+ds2-5ubuntu2 [320 kB] Get:72 http://ftpmaster.internal/ubuntu groovy/main amd64 x11-common all 1:7.7+19ubuntu14 [22.3 kB] Get:73 http://ftpmaster.internal/ubuntu groovy/main amd64 libice6 amd64 2:1.0.10-0ubuntu1 [41.0 kB] Get:74 http://ftpmaster.internal/ubuntu groovy/main amd64 libsm6 amd64 2:1.2.3-1 [16.1 kB] Get:75 http://ftpmaster.internal/ubuntu groovy/main amd64 libxt6 amd64 1:1.1.5-1 [160 kB] Get:76 http://ftpmaster.internal/ubuntu groovy/main amd64 libxmu6 amd64 2:1.1.3-0ubuntu1 [45.8 kB] Get:77 http://ftpmaster.internal/ubuntu groovy/main amd64 libxpm4 amd64 1:3.5.12-1 [34.0 kB] Get:78 http://ftpmaster.internal/ubuntu groovy/main amd64 libxaw7 amd64 2:1.0.13-1 [173 kB] Get:79 http://ftpmaster.internal/ubuntu groovy/main amd64 libxi6 amd64 2:1.7.10-1 [29.9 kB] Get:80 http://ftpmaster.internal/ubuntu groovy/universe amd64 libzzip-0-13 amd64 0.13.62-3.2ubuntu1 [26.2 kB] Get:81 http://ftpmaster.internal/ubuntu groovy/universe amd64 texlive-binaries amd64 2020.20200327.54578-4 [9697 kB] Get:82 http://ftpmaster.internal/ubuntu groovy/main amd64 xdg-utils all 1.1.3-2ubuntu1 [61.6 kB] Get:83 http://ftpmaster.internal/ubuntu groovy/universe amd64 texlive-base all 2020.20200629-1 [21.4 MB] Get:84 http://ftpmaster.internal/ubuntu groovy/universe amd64 texlive-fonts-recommended all 2020.20200629-1 [4972 kB] Get:85 http://ftpmaster.internal/ubuntu groovy/universe amd64 fonts-lmodern all 2.004.5-6 [4532 kB] Get:86 http://ftpmaster.internal/ubuntu groovy/universe amd64 texlive-latex-base all 2020.20200629-1 [1035 kB] Get:87 http://ftpmaster.internal/ubuntu groovy/universe amd64 texlive-latex-recommended all 2020.20200629-1 [14.7 MB] Get:88 http://ftpmaster.internal/ubuntu groovy/universe amd64 texlive all 2020.20200629-1 [14.4 kB] Get:89 http://ftpmaster.internal/ubuntu groovy/universe amd64 texlive-bibtex-extra all 2020.20200629-1 [67.1 MB] Get:90 http://ftpmaster.internal/ubuntu groovy/main amd64 libthai-data all 0.1.28-3 [134 kB] Get:91 http://ftpmaster.internal/ubuntu groovy/main amd64 libdatrie1 amd64 0.2.12-3 [18.7 kB] Get:92 http://ftpmaster.internal/ubuntu groovy/main amd64 libthai0 amd64 0.1.28-3 [18.1 kB] Get:93 http://ftpmaster.internal/ubuntu groovy/universe amd64 libsombok3 amd64 2.4.0-2 [26.9 kB] Get:94 http://ftpmaster.internal/ubuntu groovy/universe amd64 libmime-charset-perl all 1.012.2-1 [30.9 kB] Get:95 http://ftpmaster.internal/ubuntu groovy/universe amd64 libunicode-linebreak-perl amd64 0.0.20190101-1build1 [96.9 kB] Get:96 http://ftpmaster.internal/ubuntu groovy-proposed/universe amd64 node-jquery all 3.5.1+dfsg-4 [309 kB] Get:97 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 libjs-jquery all 3.5.1+dfsg-4 [2308 B] Get:98 http://ftpmaster.internal/ubuntu groovy/main amd64 libfontenc1 amd64 1:1.1.4-0ubuntu1 [14.0 kB] Get:99 http://ftpmaster.internal/ubuntu groovy/main amd64 xfonts-encodings all 1:1.0.5-0ubuntu1 [573 kB] Get:100 http://ftpmaster.internal/ubuntu groovy/main amd64 xfonts-utils amd64 1:7.7+6 [91.5 kB] Get:101 http://ftpmaster.internal/ubuntu groovy/universe amd64 lmodern all 2.004.5-6 [9474 kB] Get:102 http://ftpmaster.internal/ubuntu groovy/universe amd64 texlive-luatex all 2020.20200629-1 [12.1 MB] Get:103 http://ftpmaster.internal/ubuntu groovy/universe amd64 texlive-plain-generic all 2020.20200629-1 [25.7 MB] Get:104 http://ftpmaster.internal/ubuntu groovy/universe amd64 texlive-extra-utils all 2020.20200629-1 [53.5 MB] Get:105 http://ftpmaster.internal/ubuntu groovy/universe amd64 libapache-pom-java all 18-1 [4720 B] Get:106 http://ftpmaster.internal/ubuntu groovy/universe amd64 libcommons-parent-java all 43-1 [10.8 kB] Get:107 http://ftpmaster.internal/ubuntu groovy/universe amd64 libcommons-logging-java all 1.2-2 [60.3 kB] Get:108 http://ftpmaster.internal/ubuntu groovy/universe amd64 libfontbox-java all 1:1.8.16-2 [207 kB] Get:109 http://ftpmaster.internal/ubuntu groovy/universe amd64 libpdfbox-java all 1:1.8.16-2 [5199 kB] Get:110 http://ftpmaster.internal/ubuntu groovy/universe amd64 preview-latex-style all 11.91-2ubuntu2 [184 kB] Get:111 http://ftpmaster.internal/ubuntu groovy/universe amd64 texlive-pictures all 2020.20200629-1 [4636 kB] Get:112 http://ftpmaster.internal/ubuntu groovy/universe amd64 texlive-latex-extra all 2020.20200629-1 [12.7 MB] Get:113 http://ftpmaster.internal/ubuntu groovy/universe amd64 fonts-gfs-baskerville all 1.1-6 [43.7 kB] Get:114 http://ftpmaster.internal/ubuntu groovy/universe amd64 fonts-gfs-porson all 1.1-6 [33.7 kB] Get:115 http://ftpmaster.internal/ubuntu groovy/universe amd64 texlive-lang-greek all 2020.20200629-1 [77.0 MB] Get:116 http://ftpmaster.internal/ubuntu groovy/universe amd64 texlive-science all 2020.20200629-1 [3289 kB] Get:117 http://ftpmaster.internal/ubuntu groovy/main amd64 libxslt1.1 amd64 1.1.34-4 [152 kB] Get:118 http://ftpmaster.internal/ubuntu groovy/main amd64 xsltproc amd64 1.1.34-4 [14.3 kB] Get:119 http://ftpmaster.internal/ubuntu groovy/universe amd64 dblatex all 0.3.11py3-1 [346 kB] Get:120 http://ftpmaster.internal/ubuntu groovy/main amd64 libtool all 2.4.6-14 [161 kB] Get:121 http://ftpmaster.internal/ubuntu groovy/main amd64 dh-autoreconf all 19 [16.1 kB] Get:122 http://ftpmaster.internal/ubuntu groovy/main amd64 libdebhelper-perl all 13.2ubuntu1 [64.2 kB] Get:123 http://ftpmaster.internal/ubuntu groovy/main amd64 libarchive-zip-perl all 1.68-1 [90.2 kB] Get:124 http://ftpmaster.internal/ubuntu groovy/main amd64 libsub-override-perl all 0.09-2 [9532 B] Get:125 http://ftpmaster.internal/ubuntu groovy/main amd64 libfile-stripnondeterminism-perl all 1.9.0-1 [17.2 kB] Get:126 http://ftpmaster.internal/ubuntu groovy/main amd64 dh-strip-nondeterminism all 1.9.0-1 [5192 B] Get:127 http://ftpmaster.internal/ubuntu groovy/main amd64 dwz amd64 0.13-5 [151 kB] Get:128 http://ftpmaster.internal/ubuntu groovy/main amd64 libcroco3 amd64 0.6.13-1 [82.5 kB] Get:129 http://ftpmaster.internal/ubuntu groovy/main amd64 gettext amd64 0.19.8.1-10build1 [895 kB] Get:130 http://ftpmaster.internal/ubuntu groovy/main amd64 intltool-debian all 0.35.0+20060710.5 [24.9 kB] Get:131 http://ftpmaster.internal/ubuntu groovy/main amd64 po-debconf all 1.0.21 [233 kB] Get:132 http://ftpmaster.internal/ubuntu groovy/main amd64 debhelper all 13.2ubuntu1 [878 kB] Get:133 http://ftpmaster.internal/ubuntu groovy/universe amd64 docbook-xsl all 1.79.2+dfsg-1 [1063 kB] Get:134 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 icu-devtools amd64 67.1-3ubuntu1 [190 kB] Get:135 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 libboost1.71-dev amd64 1.71.0-6ubuntu9 [9070 kB] Get:136 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 libboost-atomic1.71.0 amd64 1.71.0-6ubuntu9 [205 kB] Get:137 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 libboost-atomic1.71-dev amd64 1.71.0-6ubuntu9 [205 kB] Get:138 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 libboost-chrono1.71.0 amd64 1.71.0-6ubuntu9 [217 kB] Get:139 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 libboost-chrono1.71-dev amd64 1.71.0-6ubuntu9 [225 kB] Get:140 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 libboost-date-time1.71.0 amd64 1.71.0-6ubuntu9 [217 kB] Get:141 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 libboost-serialization1.71.0 amd64 1.71.0-6ubuntu9 [303 kB] Get:142 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 libboost-serialization1.71-dev amd64 1.71.0-6ubuntu9 [345 kB] Get:143 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 libboost-date-time1.71-dev amd64 1.71.0-6ubuntu9 [229 kB] Get:144 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 libboost-filesystem1.71.0 amd64 1.71.0-6ubuntu9 [242 kB] Get:145 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 libboost-system1.71.0 amd64 1.71.0-6ubuntu9 [205 kB] Get:146 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 libboost-system1.71-dev amd64 1.71.0-6ubuntu9 [205 kB] Get:147 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 libboost-filesystem1.71-dev amd64 1.71.0-6ubuntu9 [258 kB] Get:148 http://ftpmaster.internal/ubuntu groovy/main amd64 libboost-filesystem-dev amd64 1.71.0.0ubuntu4 [3336 B] Get:149 http://ftpmaster.internal/ubuntu groovy-proposed/universe amd64 libboost-regex1.71.0 amd64 1.71.0-6ubuntu9 [481 kB] Get:150 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 libicu-dev amd64 67.1-3ubuntu1 [9595 kB] Get:151 http://ftpmaster.internal/ubuntu groovy-proposed/universe amd64 libboost-regex1.71-dev amd64 1.71.0-6ubuntu9 [569 kB] Get:152 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 libboost-iostreams1.71.0 amd64 1.71.0-6ubuntu9 [234 kB] Get:153 http://ftpmaster.internal/ubuntu groovy-proposed/universe amd64 libboost-iostreams1.71-dev amd64 1.71.0-6ubuntu9 [246 kB] Get:154 http://ftpmaster.internal/ubuntu groovy/universe amd64 libboost-iostreams-dev amd64 1.71.0.0ubuntu4 [3288 B] Get:155 http://ftpmaster.internal/ubuntu groovy/universe amd64 libboost-regex-dev amd64 1.71.0.0ubuntu4 [3560 B] Get:156 http://ftpmaster.internal/ubuntu groovy/main amd64 libboost-system-dev amd64 1.71.0.0ubuntu4 [3440 B] Get:157 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 libboost-thread1.71.0 amd64 1.71.0-6ubuntu9 [246 kB] Get:158 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 libboost-thread1.71-dev amd64 1.71.0-6ubuntu9 [258 kB] Get:159 http://ftpmaster.internal/ubuntu groovy/main amd64 libboost-thread-dev amd64 1.71.0.0ubuntu4 [3324 B] Get:160 http://ftpmaster.internal/ubuntu groovy/main amd64 libbz2-dev amd64 1.0.8-4ubuntu2 [30.2 kB] Get:161 http://ftpmaster.internal/ubuntu groovy/main amd64 libexpat1-dev amd64 2.2.9-1build1 [116 kB] Get:162 http://ftpmaster.internal/ubuntu groovy/main amd64 libfl2 amd64 2.6.4-8 [11.4 kB] Get:163 http://ftpmaster.internal/ubuntu groovy/main amd64 libfl-dev amd64 2.6.4-8 [6376 B] Get:164 http://ftpmaster.internal/ubuntu groovy/main amd64 libtcmalloc-minimal4 amd64 2.7-1ubuntu2 [93.0 kB] Get:165 http://ftpmaster.internal/ubuntu groovy/main amd64 libunwind8 amd64 1.2.1-11 [47.7 kB] Get:166 http://ftpmaster.internal/ubuntu groovy/main amd64 libgoogle-perftools4 amd64 2.7-1ubuntu2 [195 kB] Get:167 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 liblzma-dev amd64 5.2.4-1ubuntu1 [147 kB] Get:168 http://ftpmaster.internal/ubuntu groovy/main amd64 libunwind-dev amd64 1.2.1-11 [473 kB] Get:169 http://ftpmaster.internal/ubuntu groovy/main amd64 libgoogle-perftools-dev amd64 2.7-1ubuntu2 [445 kB] Get:170 http://ftpmaster.internal/ubuntu groovy/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-2ubuntu1 [156 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 394 MB in 6s (69.5 MB/s) Selecting previously unselected package libpython3.8-minimal:amd64. (Reading database ... 12775 files and directories currently installed.) Preparing to unpack .../libpython3.8-minimal_3.8.5-1_amd64.deb ... Unpacking libpython3.8-minimal:amd64 (3.8.5-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.2.9-1build1_amd64.deb ... Unpacking libexpat1:amd64 (2.2.9-1build1) ... Selecting previously unselected package python3.8-minimal. Preparing to unpack .../python3.8-minimal_3.8.5-1_amd64.deb ... Unpacking python3.8-minimal (3.8.5-1) ... Setting up libpython3.8-minimal:amd64 (3.8.5-1) ... Setting up libexpat1:amd64 (2.2.9-1build1) ... Setting up python3.8-minimal (3.8.5-1) ... Selecting previously unselected package python3-minimal. (Reading database ... 13066 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.8.2-0ubuntu2_amd64.deb ... Unpacking python3-minimal (3.8.2-0ubuntu2) ... Selecting previously unselected package mime-support. 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This may take some time... done. +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-186-generic amd64 (x86_64) Toolchain package versions: binutils_2.35-1ubuntu1 dpkg-dev_1.20.5ubuntu1 g++-10_10.2.0-3ubuntu1 gcc-10_10.2.0-3ubuntu1 libc6-dev_2.31-0ubuntu10 libstdc++-10-dev_10.2.0-3ubuntu1 libstdc++6_10.2.0-3ubuntu1 linux-libc-dev_5.4.0-42.46 Package versions: adduser_3.118ubuntu2 advancecomp_2.1-2.1build1 apt_2.1.7 autoconf_2.69-11.1 autoconf-archive_20190106-2.1ubuntu1 automake_1:1.16.2-3ubuntu1 autopoint_0.19.8.1-10build1 autotools-dev_20180224.1 base-files_11ubuntu10 base-passwd_3.5.47 bash_5.0-6ubuntu2 binutils_2.35-1ubuntu1 binutils-common_2.35-1ubuntu1 binutils-x86-64-linux-gnu_2.35-1ubuntu1 bsdextrautils_2.35.2-9ubuntu1 bsdutils_1:2.35.2-9ubuntu1 build-essential_12.8ubuntu3 bzip2_1.0.8-4ubuntu2 ca-certificates_20200601 coreutils_8.30-3ubuntu3 cpp_4:10.1.0-1ubuntu1 cpp-10_10.2.0-3ubuntu1 dash_0.5.10.2-7 dblatex_0.3.11py3-1 debconf_1.5.74 debhelper_13.2ubuntu1 debianutils_4.11 dh-autoreconf_19 dh-strip-nondeterminism_1.9.0-1 diffutils_1:3.7-3build1 docbook-xml_4.5-9 docbook-xsl_1.79.2+dfsg-1 dpkg_1.20.5ubuntu1 dpkg-dev_1.20.5ubuntu1 dwz_0.13-5 e2fsprogs_1.45.6-1ubuntu1 fakeroot_1.24-1 file_1:5.38-5 findutils_4.7.0-1ubuntu1 flex_2.6.4-8 fontconfig-config_2.13.1-2ubuntu3 fonts-dejavu-core_2.37-2 fonts-gfs-baskerville_1.1-6 fonts-gfs-porson_1.1-6 fonts-lmodern_2.004.5-6 g++_4:10.1.0-1ubuntu1 g++-10_10.2.0-3ubuntu1 gcc_4:10.1.0-1ubuntu1 gcc-10_10.2.0-3ubuntu1 gcc-10-base_10.2.0-3ubuntu1 gettext_0.19.8.1-10build1 gettext-base_0.19.8.1-10build1 gpg_2.2.20-1ubuntu1 gpg-agent_2.2.20-1ubuntu1 gpgconf_2.2.20-1ubuntu1 gpgv_2.2.20-1ubuntu1 grep_3.4-1 groff-base_1.22.4-5 gzip_1.10-2ubuntu1 hostname_3.23 icu-devtools_67.1-3ubuntu1 init_1.58 init-system-helpers_1.58 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-8 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libdpkg-perl_1.20.5ubuntu1 libelf1_0.180-1 libexpat1_2.2.9-1build1 libexpat1-dev_2.2.9-1build1 libext2fs2_1.45.6-1ubuntu1 libfakeroot_1.24-1 libffi7_3.3-4 libfile-stripnondeterminism-perl_1.9.0-1 libfl-dev_2.6.4-8 libfl2_2.6.4-8 libfontbox-java_1:1.8.16-2 libfontconfig1_2.13.1-2ubuntu3 libfontenc1_1:1.1.4-0ubuntu1 libfreetype6_2.10.2+dfsg-3 libgcc-10-dev_10.2.0-3ubuntu1 libgcc-s1_10.2.0-3ubuntu1 libgcrypt20_1.8.5-5ubuntu2 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libglib2.0-0_2.64.4-1 libgmp10_2:6.2.0+dfsg-6 libgnutls30_3.6.13-4ubuntu4 libgomp1_10.2.0-3ubuntu1 libgoogle-perftools-dev_2.7-1ubuntu2 libgoogle-perftools4_2.7-1ubuntu2 libgpg-error0_1.38-2 libgraphite2-3_1.3.14-1 libharfbuzz0b_2.6.4-1ubuntu5 libhogweed6_3.6-2 libice6_2:1.0.10-0ubuntu1 libicu-dev_67.1-3ubuntu1 libicu66_66.1-2ubuntu3 libicu67_67.1-3ubuntu1 libidn2-0_2.3.0-1 libip4tc2_1.8.4-3ubuntu2 libisl22_0.22.1-1 libitm1_10.2.0-3ubuntu1 libjs-jquery_3.5.1+dfsg-4 libjson-c4_0.13.1+dfsg-9 libkmod2_27+20200310-2ubuntu1 libkpathsea6_2020.20200327.54578-4 liblockfile-bin_1.16-1.1 liblockfile1_1.16-1.1 liblsan0_10.2.0-3ubuntu1 liblz4-1_1.9.2-2 liblzma-dev_5.2.4-1ubuntu1 liblzma5_5.2.4-1ubuntu1 libmagic-mgc_1:5.38-5 libmagic1_1:5.38-5 libmime-charset-perl_1.012.2-1 libmount1_2.35.2-9ubuntu1 libmpc3_1.1.0-1 libmpdec2_2.4.2-3 libmpfr6_4.1.0-3 libncurses6_6.2-1 libncursesw6_6.2-1 libnettle8_3.6-2 libnpth0_1.6-2 libp11-kit0_0.23.20-1build1 libpam-modules_1.3.1-5ubuntu5 libpam-modules-bin_1.3.1-5ubuntu5 libpam-runtime_1.3.1-5ubuntu5 libpam0g_1.3.1-5ubuntu5 libpaper-utils_1.1.28 libpaper1_1.1.28 libpcre2-8-0_10.34-7 libpcre3_2:8.39-13 libpdfbox-java_1:1.8.16-2 libperl5.30_5.30.3-4 libpipeline1_1.5.2-2build1 libpixman-1-0_0.38.4-0ubuntu1 libpng16-16_1.6.37-2 libprocps8_2:3.3.16-5ubuntu1 libptexenc1_2020.20200327.54578-4 libpython3-stdlib_3.8.2-0ubuntu2 libpython3.8-minimal_3.8.5-1 libpython3.8-stdlib_3.8.5-1 libquadmath0_10.2.0-3ubuntu1 libreadline8_8.0-4 libseccomp2_2.4.3-1ubuntu4 libselinux1_3.1-2 libsemanage-common_3.1-1 libsemanage1_3.1-1 libsepol1_3.1-1 libsigsegv2_2.12-2build1 libsm6_2:1.2.3-1 libsmartcols1_2.35.2-9ubuntu1 libsombok3_2.4.0-2 libsqlite3-0_3.32.3-1 libss2_1.45.6-1ubuntu1 libssl1.1_1.1.1f-1ubuntu3 libstdc++-10-dev_10.2.0-3ubuntu1 libstdc++6_10.2.0-3ubuntu1 libsub-override-perl_0.09-2 libsynctex2_2020.20200327.54578-4 libsystemd0_245.6-3ubuntu3 libtasn1-6_4.16.0-2 libtcmalloc-minimal4_2.7-1ubuntu2 libteckit0_2.5.8+ds2-5ubuntu2 libtexlua53_2020.20200327.54578-4 libtexluajit2_2020.20200327.54578-4 libthai-data_0.1.28-3 libthai0_0.1.28-3 libtinfo6_6.2-1 libtool_2.4.6-14 libtsan0_10.2.0-3ubuntu1 libubsan1_10.2.0-3ubuntu1 libuchardet0_0.0.7-1 libudev1_245.6-3ubuntu3 libunicode-linebreak-perl_0.0.20190101-1build1 libunistring2_0.9.10-4 libunwind-dev_1.2.1-11 libunwind8_1.2.1-11 libuuid1_2.35.2-9ubuntu1 libx11-6_2:1.6.9-2ubuntu1 libx11-data_2:1.6.9-2ubuntu1 libxau6_1:1.0.9-0ubuntu1 libxaw7_2:1.0.13-1 libxcb-render0_1.14-2 libxcb-shm0_1.14-2 libxcb1_1.14-2 libxdmcp6_1:1.1.3-0ubuntu1 libxext6_2:1.3.4-0ubuntu1 libxi6_2:1.7.10-1 libxml2_2.9.10+dfsg-5build1 libxmu6_2:1.1.3-0ubuntu1 libxpm4_1:3.5.12-1 libxrender1_1:0.9.10-1 libxslt1.1_1.1.34-4 libxt6_1:1.1.5-1 libzstd1_1.4.5+dfsg-3 libzzip-0-13_0.13.62-3.2ubuntu1 linux-libc-dev_5.4.0-42.46 lmodern_2.004.5-6 lockfile-progs_0.1.18 login_1:4.8.1-1ubuntu6 logsave_1.45.6-1ubuntu1 lsb-base_11.1.0ubuntu2 m4_1.4.18-4 make_4.3-4ubuntu1 man-db_2.9.3-2 mawk_1.3.4.20200120-2 mime-support_3.64ubuntu1 mount_2.35.2-9ubuntu1 ncurses-base_6.2-1 ncurses-bin_6.2-1 node-jquery_3.5.1+dfsg-4 openssl_1.1.1f-1ubuntu3 optipng_0.7.7-1 passwd_1:4.8.1-1ubuntu6 patch_2.7.6-6 perl_5.30.3-4 perl-base_5.30.3-4 perl-modules-5.30_5.30.3-4 pinentry-curses_1.1.0-4build1 pkgbinarymangler_146 po-debconf_1.0.21 policyrcd-script-zg2_0.1-3 preview-latex-style_11.91-2ubuntu2 procps_2:3.3.16-5ubuntu1 python-apt-common_2.1.3 python3_3.8.2-0ubuntu2 python3-apt_2.1.3 python3-minimal_3.8.2-0ubuntu2 python3.8_3.8.5-1 python3.8-minimal_3.8.5-1 readline-common_8.0-4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-mira-dummy_0.invalid.0 sed_4.7-1build1 sensible-utils_0.0.12+nmu1 sgml-base_1.30 sgml-data_2.0.11 systemd_245.6-3ubuntu3 systemd-sysv_245.6-3ubuntu3 systemd-timesyncd_245.6-3ubuntu3 sysvinit-utils_2.96-3ubuntu1 t1utils_1.41-4 tar_1.30+dfsg-7 tex-common_6.15 texlive_2020.20200629-1 texlive-base_2020.20200629-1 texlive-bibtex-extra_2020.20200629-1 texlive-binaries_2020.20200327.54578-4 texlive-extra-utils_2020.20200629-1 texlive-fonts-recommended_2020.20200629-1 texlive-lang-greek_2020.20200629-1 texlive-latex-base_2020.20200629-1 texlive-latex-extra_2020.20200629-1 texlive-latex-recommended_2020.20200629-1 texlive-luatex_2020.20200629-1 texlive-pictures_2020.20200629-1 texlive-plain-generic_2020.20200629-1 texlive-science_2020.20200629-1 tzdata_2020a-0ubuntu1 ubuntu-keyring_2020.06.17.1 ucf_3.0043 util-linux_2.35.2-9ubuntu1 vim-common_2:8.2.0716-3ubuntu1 x11-common_1:7.7+19ubuntu14 xdg-utils_1.1.3-2ubuntu1 xfonts-encodings_1:1.0.5-0ubuntu1 xfonts-utils_1:7.7+6 xml-core_0.18+nmu1 xsltproc_1.1.34-4 xxd_2:8.2.0716-3ubuntu1 xz-utils_5.2.4-1ubuntu1 zlib1g_1:1.2.11.dfsg-2ubuntu1 zlib1g-dev_1:1.2.11.dfsg-2ubuntu1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Tue Jul 28 19:21:04 2020 UTC gpgv: using RSA key AC483F68DE728F43F2202FCA568D30F321B2133D gpgv: issuer "steve.langasek@ubuntu.com" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./mira_4.9.6-4build7.dsc dpkg-source: info: extracting mira in mira-4.9.6 dpkg-source: info: unpacking mira_4.9.6.orig.tar.bz2 dpkg-source: info: unpacking mira_4.9.6-4build7.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 Check disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-19742897 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-19742897 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-19742897 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package mira dpkg-buildpackage: info: source version 4.9.6-4build7 dpkg-buildpackage: info: source distribution groovy dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' ( cd doc ; make clean ) || true make[2]: Entering directory '/<>/doc' cd .. && make am--refresh make[3]: Entering directory '/<>' make[3]: *** No rule to make target 'am--refresh'. Stop. make[3]: Leaving directory '/<>' make[2]: *** [Makefile:263: ../config.status] Error 2 make[2]: Leaving directory '/<>/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 '/<>' 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 build dh build dh_update_autotools_config install -d debian/.debhelper/bucket/files cp -an --reflink=auto config.guess debian/.debhelper/bucket/files/9be3de218833c076786b919dc34aab691611f4cd73316e7705f2673e2c41921b.tmp mv debian/.debhelper/bucket/files/9be3de218833c076786b919dc34aab691611f4cd73316e7705f2673e2c41921b.tmp debian/.debhelper/bucket/files/9be3de218833c076786b919dc34aab691611f4cd73316e7705f2673e2c41921b cp -f /usr/share/misc/config.guess ./config.guess cp -an --reflink=auto config.sub debian/.debhelper/bucket/files/e308ae7f7f524bd790f8d4457c7c0a30f8403ffff4dd0b7d4388daca24275db4.tmp mv debian/.debhelper/bucket/files/e308ae7f7f524bd790f8d4457c7c0a30f8403ffff4dd0b7d4388daca24275db4.tmp debian/.debhelper/bucket/files/e308ae7f7f524bd790f8d4457c7c0a30f8403ffff4dd0b7d4388daca24275db4 cp -f /usr/share/misc/config.sub ./config.sub dh_autoreconf find ! -ipath "./debian/*" -a ! \( -path '*/.git/*' -o -path '*/.hg/*' -o -path '*/.bzr/*' -o -path '*/.svn/*' -o -path '*/CVS/*' \) -a -type f -exec md5sum {} + -o -type l -printf "symlink %p " > debian/autoreconf.before grep -q ^XDT_ configure.ac autoreconf -f -i libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'. libtoolize: copying file 'm4/libtool.m4' libtoolize: copying file 'm4/ltoptions.m4' libtoolize: copying file 'm4/ltsugar.m4' libtoolize: copying file 'm4/ltversion.m4' libtoolize: copying file 'm4/lt~obsolete.m4' configure.ac:103: installing './compile' configure.ac:9: installing './missing' doc/docbook/Makefile.am:22: warning: '%'-style pattern rules are a GNU make extension src/caf/Makefile.am: installing './depcomp' src/io/Makefile.am:12: warning: '%'-style pattern rules are a GNU make extension src/mira/Makefile.am:10: warning: '%'-style pattern rules are a GNU make extension find ! -ipath "./debian/*" -a ! \( -path '*/.git/*' -o -path '*/.hg/*' -o -path '*/.bzr/*' -o -path '*/.svn/*' -o -path '*/CVS/*' \) -a -type f -exec md5sum {} + -o -type l -printf "symlink %p " > debian/autoreconf.after dh_auto_configure ./configure --build=x86_64-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/x86_64-linux-gnu --libexecdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether UID '2001' is supported by ustar format... yes checking whether GID '2501' is supported by ustar format... yes checking how to create a ustar tar archive... gnutar checking for a sed that does not truncate output... /bin/sed checking whether to add --prefix as include path... yes +++++++++++++++++++++++++++++++++++++ systemuname: Linux CFLAGS now: -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include CXXFLAGS now: -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include LDFLAGS now: -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -L/usr/lib +++++++++++++++++++++++++++++++++++++ checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of gcc... none checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... none checking for OpenMP flag of C compiler... -fopenmp Rescuing C++ flags for OpenMP +++++++++++++++++++++++++++++++++++++ OpenMP CFLAGS: -fopenmp OpenMP CXXFLAGS: -fopenmp +++++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++++++++++++++ systemuname: Linux CFLAGS now: -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include CXXFLAGS now: -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include LDFLAGS now: -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -L/usr/lib +++++++++++++++++++++++++++++++++++++ checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for int64_t... yes +++++++++++++++++++++++++++++++++++++ CFLAGS now: -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include CXXFLAGS now: -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include LDFLAGS now: -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -L/usr/lib +++++++++++++++++++++++++++++++++++++ checking whether long has 64bit... yes checking whether enabling 64bit compilation support... yes checking build system type... x86_64-pc-linux-gnu checking for compiler optimisation settings... -O3 -funroll-loops +++++++++++++++++++++++++++++++++++++ CFLAGS now: -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops CXXFLAGS now: -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops LDFLAGS now: -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -L/usr/lib +++++++++++++++++++++++++++++++++++++ checking host system type... x86_64-pc-linux-gnu checking how to print strings... printf checking for a sed that does not truncate output... (cached) /bin/sed checking for fgrep... /bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) 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 -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) 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 -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether make sets $(MAKE)... (cached) yes checking whether ln -s works... yes checking for flex... yes checking for flex... flex checking lex output file root... lex.yy checking lex library... -lfl checking whether yytext is a pointer... yes checking for flex++... yes checking for xxd... yes checking for ANSI C header files... (cached) yes checking for stdbool.h that conforms to C99... yes checking for _Bool... yes checking for an ANSI C-conforming const... yes checking for inline... inline checking for C/C++ restrict keyword... __restrict checking whether struct tm is in sys/time.h or time.h... time.h checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible realloc... yes checking whether lstat correctly handles trailing slash... yes checking whether stat accepts an empty string... no checking for strftime... yes checking for floor... no checking for memset... yes checking for pow... no checking for sqrt... no checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking for _LARGEFILE_SOURCE value needed for large files... no checking for isblank... yes +++++++++++++++++++++++++++++++++++++ CFLAGS now: -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops CXXFLAGS now: -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops LDFLAGS now: -Wl,-Bsymbolic-functions -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/x86_64-linux-gnu ac_boost_path: ac_boost_lib_path: CFLAGS now: -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops CXXFLAGS now: -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops LDFLAGS now: -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -L/usr/lib +++++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++++++++++++++ BOOST_CPPFLAGS: -I/usr/include BOOST LDFLAGS: -L/usr/lib/x86_64-linux-gnu CFLAGS now: -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -Wl,-rpath, CXXFLAGS now: -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops LDFLAGS now: -Wl,-Bsymbolic-functions -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/x86_64-linux-gnu ac_boost_path: ac_boost_lib_path: BOOST_THREAD_LIB: -lboost_thread CFLAGS now: -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -Wl,-rpath, CXXFLAGS now: -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops LDFLAGS now: -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -L/usr/lib +++++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++++++++++++++ BOOST_CPPFLAGS: -pthread -I/usr/include BOOST LDFLAGS: -L/usr/lib/x86_64-linux-gnu ac_boost_path: ac_boost_lib_path: BOOST_THREAD_LIB: -lboost_thread CFLAGS now: -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -Wl,-rpath, CXXFLAGS now: -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include LDFLAGS now: -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/x86_64-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/x86_64-linux-gnu ac_boost_path: ac_boost_lib_path: BOOST_REGEX_LIB: -lboost_regex CFLAGS now: -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -Wl,-rpath, CXXFLAGS now: -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -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/x86_64-linux-gnu ac_boost_path: ac_boost_lib_path: BOOST_SYSTEM_LIB: -lboost_system CFLAGS now: -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -Wl,-rpath, CXXFLAGS now: -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -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/x86_64-linux-gnu ac_boost_path: ac_boost_lib_path: BOOST_FILESYSTEM_LIB: -lboost_filesystem CFLAGS now: -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -Wl,-rpath, CXXFLAGS now: -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -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/x86_64-linux-gnu ac_boost_path: ac_boost_lib_path: BOOST_IOSTREAMS_LIB: -lboost_iostreams CFLAGS now: -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -Wl,-rpath, CXXFLAGS now: -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include LIBS now: -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams +++++++++++++++++++++++++++++++++++++ checking for clock_gettime in -lrt... yes +++++++++++++++++++++++++++++++++++++ Need to specifically use rt library LIBS now: -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt +++++++++++++++++++++++++++++++++++++ BOOST is through, yay. +++++++++++++++++++++++++++++++++++++ CFLAGS now: -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops CXXFLAGS now: -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include LDFLAGS now: -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/x86_64-linux-gnu LIBS now: -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt +++++++++++++++++++++++++++++++++++++ checking for Expat XML Parser headers in /usr/include... found checking for Expat XML Parser libraries... found checking for Expat XML Parser... yes +++++++++++++++++++++++++++++++++++++ CFLAGS now: -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -I/usr/include CXXFLAGS now: -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include LDFLAGS now: -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib LIBS now: -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt -lexpat +++++++++++++++++++++++++++++++++++++ checking if zlib is wanted... yes +++++++++++++++++++++++++++++++++++++ CFLAGS now: -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -I/usr/include CXXFLAGS now: -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include LDFLAGS now: -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/x86_64-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_x86_64_dynamic We are building on ............................... Linux CPU supports 64 bit? ............................. yes Compiler family .................................. gcc Compiler optimisation flags used ................. -O3 -funroll-loops Do we compile in 64 bit? ......................... yes Building completely static? ...................... no BOOST expected to compile and link? .............. yes Have OpenMP? ..................................... yes Have complete zlib support? ...................... yes Can MIRA be built on this system? ................ yes Using CFLAGS : -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -I/usr/include -Werror=uninitialized -Werror=return-type -fopenmp Using CXXFLAGS : -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -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,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/x86_64-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 '/<>' # 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 -j4 make[2]: Entering directory '/<>' make all-recursive make[3]: Entering directory '/<>' Making all in man make[4]: Entering directory '/<>/man' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/<>/man' Making all in src make[4]: Entering directory '/<>/src' Making all in debuggersupport make[5]: Entering directory '/<>/src/debuggersupport' g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-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 '/<>/src/debuggersupport' Making all in io make[5]: Entering directory '/<>/src/io' Making .H out of .xxd gap4_ft_so_map.xxd.H Making .H out of .xxd mira_ft_set.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 '/<>/src/io' g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o annotationmappings.o annotationmappings.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o exp.o exp.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o generalio.o generalio.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o fasta.o fasta.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o fastq-mira.o fastq-mira.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o phd.o phd.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o scf.o scf.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-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 '/<>/src/io' make[5]: Leaving directory '/<>/src/io' Making all in stdinc make[5]: Entering directory '/<>/src/stdinc' make[5]: Nothing to be done for 'all'. make[5]: Leaving directory '/<>/src/stdinc' Making all in errorhandling make[5]: Entering directory '/<>/src/errorhandling' g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-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 '/<>/src/errorhandling' Making all in util make[5]: Entering directory '/<>/src/util' g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o machineinfo.o machineinfo.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o fileanddisk.o fileanddisk.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o misc.o misc.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o dptools.o dptools.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-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:173:12: warning: ignoring return value of ‘char* strerror_r(int, char*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 173 | strerror_r(errno,buf,1024); | ~~~~~~~~~~^~~~~~~~~~~~~~~~ rm -f 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 '/<>/src/util' Making all in mira make[5]: Entering directory '/<>/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 '/<>/src/mira' g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o estassembly.o estassembly.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o hashstats_sdbg.o hashstats_sdbg.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o hashstats.o hashstats.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-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 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();} | g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o assembly.o assembly.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o contig.o contig.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-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 read.C: In member function ‘void Read::dumpAsReadname(std::ostream&)’: read.C:1242:25: warning: format ‘%x’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Read*’ [-Wformat=] 1242 | sprintf(buffer, "%x", this) ; | ~^ ~~~~ | | | | | Read* | unsigned int read.C: In member function ‘void Read::dumpAsFASTA(std::ostream&, bool, bool, bool)’: read.C:1273:25: warning: format ‘%x’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Read*’ [-Wformat=] 1273 | sprintf(buffer, "%x", this) ; | ~^ ~~~~ | | | | | Read* | unsigned int read.C: In member function ‘void Read::dumpAsFASTQ(std::ostream&, bool, bool, bool)’: read.C:1357:25: warning: format ‘%x’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Read*’ [-Wformat=] 1357 | sprintf(buffer, "%x", this) ; | ~^ ~~~~ | | | | | Read* | unsigned int read.C: In member function ‘void Read::dumpAsFASTAQual(std::ostream&, bool, bool, bool)’: read.C:1458:25: warning: format ‘%x’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Read*’ [-Wformat=] 1458 | sprintf(buffer, "%x", this) ; | ~^ ~~~~ | | | | | Read* | unsigned int read.C: In member function ‘void Read::dumpAsCAF(std::ostream&)’: read.C:1530:25: warning: format ‘%x’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Read*’ [-Wformat=] 1530 | sprintf(buffer, "%x", this) ; | ~^ ~~~~ | | | | | Read* | unsigned int read.C: In member function ‘void Read::dumpAsMAF(std::ostream&)’: read.C:1945:25: warning: format ‘%x’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Read*’ [-Wformat=] 1945 | sprintf(buffer, "%x", this) ; | ~^ ~~~~ | | | | | Read* | unsigned int g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o contig_analysis.o contig_analysis.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o ads.o ads.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o adsfacts.o adsfacts.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o align.o align.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o assembly_info.o assembly_info.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o assembly_buildcontigs.o assembly_buildcontigs.C assembly_buildcontigs.C:80: 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;} } | g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o assembly_io.o assembly_io.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-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 assembly_misc.C: In member function ‘void Assembly::priv_phahelper(const string&, const string&, uint32, bool, int32, std::string, std::string, std::string)’: assembly_misc.C:376:3: warning: use of an operand of type ‘bool’ in ‘operator++’ is deprecated [-Wdeprecated] 376 | countedthisseq++; | ^~~~~~~~~~~~~~ assembly_misc.C: In instantiation of ‘void Assembly::priv_phahelper(const string&, const string&, uint32, bool, int32, std::string, std::string, std::string) [with TVHASH_T = long unsigned int; std::string = std::__cxx11::basic_string; uint32 = unsigned int; int32 = int]’: assembly_misc.C:471:118: required from here assembly_misc.C:376:3: warning: use of an operand of type ‘bool’ in ‘operator++’ is deprecated [-Wdeprecated] assembly_misc.C: In instantiation of ‘void Assembly::priv_phahelper(const string&, const string&, uint32, bool, int32, std::string, std::string, std::string) [with TVHASH_T = VLuint<128>; std::string = std::__cxx11::basic_string; uint32 = unsigned int; int32 = int]’: assembly_misc.C:473:119: required from here assembly_misc.C:376:3: warning: use of an operand of type ‘bool’ in ‘operator++’ is deprecated [-Wdeprecated] assembly_misc.C: In instantiation of ‘void Assembly::priv_phahelper(const string&, const string&, uint32, bool, int32, std::string, std::string, std::string) [with TVHASH_T = VLuint<256>; std::string = std::__cxx11::basic_string; uint32 = unsigned int; int32 = int]’: assembly_misc.C:475:119: required from here assembly_misc.C:376:3: warning: use of an operand of type ‘bool’ in ‘operator++’ is deprecated [-Wdeprecated] assembly_misc.C: In instantiation of ‘void Assembly::priv_phahelper(const string&, const string&, uint32, bool, int32, std::string, std::string, std::string) [with TVHASH_T = VLuint<512>; std::string = std::__cxx11::basic_string; uint32 = unsigned int; int32 = int]’: assembly_misc.C:477:119: required from here assembly_misc.C:376:3: warning: use of an operand of type ‘bool’ in ‘operator++’ is deprecated [-Wdeprecated] g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o assembly_pbcorrect.o assembly_pbcorrect.C assembly_pbcorrect.C:59: 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) | g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o assembly_reduceskimhits.o assembly_reduceskimhits.C assembly_reduceskimhits.C:1111: warning: "CEBUG" redefined 1111 | #define CEBUG(bla) {cout << bla; cout.flush();} | assembly_reduceskimhits.C:878: note: this is the location of the previous definition 878 | #define CEBUG(bla) | assembly_reduceskimhits.C:1151: warning: "CEBUG" redefined 1151 | #define CEBUG(bla) | assembly_reduceskimhits.C:1111: note: this is the location of the previous definition 1111 | #define CEBUG(bla) {cout << bla; cout.flush();} | assembly_reduceskimhits.C:2742: warning: "CEBUG" redefined 2742 | #define CEBUG(bla) {cout << bla; cout.flush();} | assembly_reduceskimhits.C:1151: note: this is the location of the previous definition 1151 | #define CEBUG(bla) | assembly_reduceskimhits.C:2760: warning: "CEBUG" redefined 2760 | #define CEBUG(bla) | assembly_reduceskimhits.C:2742: note: this is the location of the previous definition 2742 | #define CEBUG(bla) {cout << bla; cout.flush();} | assembly_reduceskimhits.C:2764: warning: "CEBUG" redefined 2764 | #define CEBUG(bla) {cout << bla; cout.flush();} | assembly_reduceskimhits.C:2760: note: this is the location of the previous definition 2760 | #define CEBUG(bla) | assembly_reduceskimhits.C:2803: warning: "CEBUG" redefined 2803 | #define CEBUG(bla) | assembly_reduceskimhits.C:2764: note: this is the location of the previous definition 2764 | #define CEBUG(bla) {cout << bla; cout.flush();} | assembly_reduceskimhits.C:2808: warning: "CEBUG" redefined 2808 | #define CEBUG(bla) {cout << bla; cout.flush();} | assembly_reduceskimhits.C:2803: note: this is the location of the previous definition 2803 | #define CEBUG(bla) | assembly_reduceskimhits.C:2887: warning: "CEBUG" redefined 2887 | #define CEBUG(bla) | assembly_reduceskimhits.C:2808: note: this is the location of the previous definition 2808 | #define CEBUG(bla) {cout << bla; cout.flush();} | g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o assembly_swalign.o assembly_swalign.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o contig_consensus.o contig_consensus.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o contig_edit.o contig_edit.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o contig_output.o contig_output.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-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();} | g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o dataprocessing.o dataprocessing.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o dynamic.o dynamic.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o gbf_parse.o gbf_parse.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o gff_parse.o gff_parse.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o gff_save.o gff_save.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o maf_parse.o maf_parse.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o manifest.o manifest.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-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 g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o pcrcontainer.o pcrcontainer.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o preventinitfiasco.o preventinitfiasco.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o readlotstat.o readlotstat.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o readpool.o readpool.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o sam_collect.o sam_collect.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-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(); } | g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o seqtohash.o seqtohash.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o simplebloomfilter.o simplebloomfilter.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o skim_lowbph.o skim_lowbph.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o warnings.o warnings.C rm -f libmiraestass.a ar cru libmiraestass.a estassembly.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libmiraestass.a g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-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 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 '/<>/src/mira' make[5]: Leaving directory '/<>/src/mira' Making all in caf make[5]: Entering directory '/<>/src/caf' g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-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 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 '/<>/src/caf' Making all in memorc make[5]: Entering directory '/<>/src/memorc' g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o memorc.o memorc.C memorc.C: In static member function ‘static void MemORC::statistics()’: memorc.C:153:39: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64’ {aka ‘long unsigned int’} [-Wformat=] 153 | printf("Current alloc counter : %llu\n", MOC_alloccounter); | ~~~^ ~~~~~~~~~~~~~~~~ | | | | | uint64 {aka long unsigned int} | long long unsigned int | %lu memorc.C:154:39: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64’ {aka ‘long unsigned int’} [-Wformat=] 154 | printf("Total checks performed : %llu\n", MOC_checksperformed); | ~~~^ ~~~~~~~~~~~~~~~~~~~ | | | | | uint64 {aka long unsigned int} | long long unsigned int | %lu memorc.C:155:39: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘std::map::size_type’ {aka ‘long unsigned int’} [-Wformat=] 155 | printf("Num. memory blocks : %llu\n", MOC_memblocks.size()); | ~~~^ ~~~~~~~~~~~~~~~~~~~~ | | | | long long unsigned int std::map::size_type {aka long unsigned int} | %lu memorc.C:156:39: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘std::map::size_type’ {aka ‘long unsigned int’} [-Wformat=] 156 | printf("Num. active hot blocks : %llu\n", MOC_hotblocks.size()); | ~~~^ ~~~~~~~~~~~~~~~~~~~~ | | | | long long unsigned int std::map::size_type {aka long unsigned int} | %lu memorc.C:157:39: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wformat=] 157 | printf("Num. pending hot blocks: %llu\n", MOC_hotaidsrequested.size()); | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long long unsigned int std::vector::size_type {aka long unsigned int} | %lu memorc.C:158:39: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 158 | printf("Total mem reqested : %llu\n", MOC_reqmemalloc); | ~~~^ ~~~~~~~~~~~~~~~ | | | | | size_t {aka long unsigned int} | long long unsigned int | %lu memorc.C:159:39: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 159 | printf("Total mem allocated : %llu (including pads and fences)\n", MOC_totalmemalloc); | ~~~^ ~~~~~~~~~~~~~~~~~ | | | | long long unsigned int size_t {aka long unsigned int} | %lu memorc.C: In static member function ‘static void* MemORC::newMemBlock(size_t)’: memorc.C:225:51: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 225 | printf("Used malloc()\nTried to allocate %llu byte.\nSorry, memory allocation failed. Bailing out.\n", totaln); | ~~~^ ~~~~~~ | | | | long long unsigned int size_t {aka long unsigned int} | %lu memorc.C: In static member function ‘static void MemORC::deleteMemBlock(void*)’: memorc.C:311:35: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘uint64’ {aka ‘long unsigned int’} [-Wformat=] 311 | printf("Nearest memblock above (%d):\t",reinterpret_cast(mbI->first)-reinterpret_cast(usraddr)); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int uint64 {aka long unsigned int} | %ld memorc.C:318:36: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘uint64’ {aka ‘long unsigned int’} [-Wformat=] 318 | printf("Nearest memblock below (-%d):\t",reinterpret_cast(usraddr)-reinterpret_cast(mbI->first)); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int uint64 {aka long unsigned int} | %ld memorc.C: In static member function ‘static bool MemORC::checkMemBlock(std::map::iterator)’: memorc.C:430:56: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=] 430 | printf("check: lower fence .0 destroyed at position: %d\tExpected: %x\tGot: %x\n", i*sizeof(int32),MOC_clowfencemagic[0], *fencecptr); | ~^ ~~~~~~~~~~~~~~~ | | | | int long unsigned int | %ld memorc.C:433:56: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=] 433 | printf("check: lower fence .1 destroyed at position: %d\tExpected: %x\tGot: %x\n", i*sizeof(int32)+1,MOC_clowfencemagic[1], *fencecptr); | ~^ ~~~~~~~~~~~~~~~~~ | | | | int long unsigned int | %ld memorc.C:436:56: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=] 436 | printf("check: lower fence .2 destroyed at position: %d\tExpected: %x\tGot: %x\n", i*sizeof(int32)+2,MOC_clowfencemagic[2], *fencecptr); | ~^ ~~~~~~~~~~~~~~~~~ | | | | int long unsigned int | %ld memorc.C:439:56: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=] 439 | printf("check: lower fence .3 destroyed at position: %d\tExpected: %x\tGot: %x\n", i*sizeof(int32)+3,MOC_clowfencemagic[3], *fencecptr); | ~^ ~~~~~~~~~~~~~~~~~ | | | | int long unsigned int | %ld memorc.C:500:22: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 500 | printf("Size: %llu\n", mbI->second.size); | ~~~^ ~~~~~~~~~~~~~~~~ | | | | | size_t {aka long unsigned int} | long long unsigned int | %lu memorc.C:501:25: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64’ {aka ‘long unsigned int’} [-Wformat=] 501 | printf("AllocID: %llu\n", mbI->second.allocid); | ~~~^ ~~~~~~~~~~~~~~~~~~~ | | | | | uint64 {aka long unsigned int} | long long unsigned int | %lu memorc.C: In static member function ‘static void MemORC::printMemBlockInfo(std::map::iterator)’: memorc.C:558:18: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 558 | printf("%p\t%llu\t",mbI->first,mbI->second.size); | ~~~^ ~~~~~~~~~~~~~~~~ | | | | long long unsigned int size_t {aka long unsigned int} | %lu memorc.C:564:16: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64’ {aka ‘long unsigned int’} [-Wformat=] 564 | printf("\t%llu\n",mbI->second.allocid); | ~~~^ ~~~~~~~~~~~~~~~~~~~ | | | | | uint64 {aka long unsigned int} | long long unsigned int | %lu g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -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/x86_64-linux-gnu -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib -o main main.o -lmiraerrorhandling -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt -lexpat -lm -lz -lbz2 libtool: link: g++ -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -Wl,-Bsymbolic-functions -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/x86_64-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 '/<>/src/memorc' Making all in modules make[5]: Entering directory '/<>/src/modules' g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o mod_sigconex.o mod_sigconex.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o mod_scaffold.o mod_scaffold.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o mod_bait.o mod_bait.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o mod_dbgreplay.o mod_dbgreplay.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o mod_diff.o mod_diff.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o mod_mer.o mod_mer.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o mod_convert.o mod_convert.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-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 mod_mira.C: In function ‘void miraMain_extractContigs(int, char**)’: mod_mira.C:414:10: warning: ignoring return value of ‘int chdir(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 414 | chdir("../.."); | ~~~~~^~~~~~~~~ mod_mira.C:439:10: warning: ignoring return value of ‘int chdir(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 439 | chdir("../.."); | ~~~~~^~~~~~~~~ g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-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 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 '/<>/src/modules' Making all in support make[5]: Entering directory '/<>/src/support' make[5]: Nothing to be done for 'all'. make[5]: Leaving directory '/<>/src/support' Making all in scripts make[5]: Entering directory '/<>/src/scripts' make[5]: Nothing to be done for 'all'. make[5]: Leaving directory '/<>/src/scripts' Making all in version make[5]: Entering directory '/<>/src/version' make all-am make[6]: Entering directory '/<>/src/version' g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-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 '/<>/src/version' make[5]: Leaving directory '/<>/src/version' Making all in progs make[5]: Entering directory '/<>/src/progs' Making .C out of .xxd compileinfo.itxt make all-am make[6]: Entering directory '/<>/src/progs' g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o mira.o mira.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o quirks.o quirks.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o miratest.o miratest.C Making .C out of .xxd compileinfo.itxt g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -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/x86_64-linux-gnu -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib -o mira mira.o quirks.o compileinfo.itxt.xxd.o -lmiraversion -lmiramodules -lmiradebuggersupport -lmira -lmiraestass -lmiracaf -lmirautil -lmiradptools -lmirafio -lmiraerrorhandling -lmiradebuggersupport -lmirafmttext -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt -lexpat -lm -lz -lbz2 libtool: link: g++ -pthread -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -Wl,-Bsymbolic-functions -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/x86_64-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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -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/x86_64-linux-gnu -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib -o miratest miratest.o compileinfo.itxt.xxd.o -lmiraversion -lmiramodules -lmiradebuggersupport -lmira -lmiraestass -lmiracaf -lmirautil -lmiradptools -lmirafio -lmiraerrorhandling -lmiradebuggersupport -lmirafmttext -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt -lexpat -lm -lz -lbz2 libtool: link: g++ -pthread -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -Wl,-Bsymbolic-functions -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/x86_64-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 '/<>/src/progs' make[5]: Leaving directory '/<>/src/progs' Making all in other make[5]: Entering directory '/<>/src/other' Making all in sls make[6]: Entering directory '/<>/src/other/sls' Making all in mira-createsls make[7]: Entering directory '/<>/src/other/sls/mira-createsls' Making all in bin make[8]: Entering directory '/<>/src/other/sls/mira-createsls/bin' make[8]: Nothing to be done for 'all'. make[8]: Leaving directory '/<>/src/other/sls/mira-createsls/bin' make[8]: Entering directory '/<>/src/other/sls/mira-createsls' make[8]: Nothing to be done for 'all-am'. make[8]: Leaving directory '/<>/src/other/sls/mira-createsls' make[7]: Leaving directory '/<>/src/other/sls/mira-createsls' make[7]: Entering directory '/<>/src/other/sls' make[7]: Nothing to be done for 'all-am'. make[7]: Leaving directory '/<>/src/other/sls' make[6]: Leaving directory '/<>/src/other/sls' make[6]: Entering directory '/<>/src/other' make[6]: Nothing to be done for 'all-am'. make[6]: Leaving directory '/<>/src/other' make[5]: Leaving directory '/<>/src/other' make[5]: Entering directory '/<>/src' make[5]: Nothing to be done for 'all-am'. make[5]: Leaving directory '/<>/src' make[4]: Leaving directory '/<>/src' make[4]: Entering directory '/<>' make[4]: Nothing to be done for 'all-am'. make[4]: Leaving directory '/<>' make[3]: Leaving directory '/<>' make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' rm -f debian/mira-assembler.debhelper.log debian/rules override_dh_auto_build-indep make[1]: Entering directory '/<>' dh_auto_build --sourcedir=doc cd doc && make -j4 "INSTALL=install --strip-program=true" make[2]: Entering directory '/<>/doc' Making all in docbook make[3]: Entering directory '/<>/doc/docbook' Making versionfile 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 ERROR: xref linking to chap_dataprep has no generated link text. Error: no ID for constraint linkend: "chap_dataprep". ERROR: xref linking to chap_denovo has no generated link text. Error: no ID for constraint linkend: "chap_denovo". ERROR: xref linking to chap_results has no generated link text. Error: no ID for constraint linkend: "chap_results". ERROR: xref linking to sect_res_looking_at_results has no generated link text. Error: no ID for constraint linkend: "sect_res_looking_at_results". ERROR: xref linking to sect_res_first_look:the_assembly_info has no generated link text. Error: no ID for constraint linkend: "sect_res_first_look:the_assembly_info". ERROR: xref linking to sect_res_converting_results has no generated link text. Error: no ID for constraint linkend: "sect_res_converting_results". ERROR: xref linking to sect_res_filtering_of_results has no generated link text. Error: no ID for constraint linkend: "sect_res_filtering_of_results". ERROR: xref linking to sect_res_places_of_importance_in_a_de_novo_assembly has no generated link text. Error: no ID for constraint linkend: "sect_res_places_of_importance_in_a_de_novo_assembly". ERROR: xref linking to chap_reference has no generated link text. Error: no ID for constraint linkend: "chap_reference". ERROR: xref linking to sect_ref_manifest_basics has no generated link text. Error: no ID for constraint linkend: "sect_ref_manifest_basics". ERROR: xref linking to sect_ref_manifest_readgroups has no generated link text. Error: no ID for constraint linkend: "sect_ref_manifest_readgroups". ERROR: xref linking to sect_ref_manifest_parameters has no generated link text. Error: no ID for constraint linkend: "sect_ref_manifest_parameters". Making .html out of _part.xml chap_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 Element emph in namespace '' encountered in note, but no template matches. Making .html out of _part.xml chap_sra_part.html Making .html out of _part.xml chap_seqadvice_part.html Making .html out of _part.xml chap_bonus_part.html Making .html out of _part.xml chap_preface_part.html 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 Build the book set list... Build the book set list... Build the listings... XSLT stylesheets DocBook - LaTeX 2e (0.3.11py3) =================================================== No template matches copyright in chapterinfo. No template matches year in copyright. No template matches holder in copyright. Build book_3rdparty.pdf '3rdparty_MIRA.pdf' successfully built Element emph in namespace '' encountered in note, but no template matches. Build the listings... XSLT stylesheets DocBook - LaTeX 2e (0.3.11py3) =================================================== 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 '/<>/doc/docbook' make[3]: Entering directory '/<>/doc' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/<>/doc' make[2]: Leaving directory '/<>/doc' make[1]: Leaving directory '/<>' 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 '/<>' make check make[2]: Entering directory '/<>' make check-recursive make[3]: Entering directory '/<>' Making check in man make[4]: Entering directory '/<>/man' make[4]: Nothing to be done for 'check'. make[4]: Leaving directory '/<>/man' Making check in src make[4]: Entering directory '/<>/src' Making check in debuggersupport make[5]: Entering directory '/<>/src/debuggersupport' make[5]: Nothing to be done for 'check'. make[5]: Leaving directory '/<>/src/debuggersupport' Making check in io make[5]: Entering directory '/<>/src/io' make check-am make[6]: Entering directory '/<>/src/io' make[6]: Nothing to be done for 'check-am'. make[6]: Leaving directory '/<>/src/io' make[5]: Leaving directory '/<>/src/io' Making check in stdinc make[5]: Entering directory '/<>/src/stdinc' make[5]: Nothing to be done for 'check'. make[5]: Leaving directory '/<>/src/stdinc' Making check in errorhandling make[5]: Entering directory '/<>/src/errorhandling' make[5]: Nothing to be done for 'check'. make[5]: Leaving directory '/<>/src/errorhandling' Making check in util make[5]: Entering directory '/<>/src/util' make[5]: Nothing to be done for 'check'. make[5]: Leaving directory '/<>/src/util' Making check in mira make[5]: Entering directory '/<>/src/mira' make check-am make[6]: Entering directory '/<>/src/mira' make[6]: Nothing to be done for 'check-am'. make[6]: Leaving directory '/<>/src/mira' make[5]: Leaving directory '/<>/src/mira' Making check in caf make[5]: Entering directory '/<>/src/caf' make[5]: Nothing to be done for 'check'. make[5]: Leaving directory '/<>/src/caf' Making check in memorc make[5]: Entering directory '/<>/src/memorc' make[5]: Nothing to be done for 'check'. make[5]: Leaving directory '/<>/src/memorc' Making check in modules make[5]: Entering directory '/<>/src/modules' make[5]: Nothing to be done for 'check'. make[5]: Leaving directory '/<>/src/modules' Making check in support make[5]: Entering directory '/<>/src/support' make[5]: Nothing to be done for 'check'. make[5]: Leaving directory '/<>/src/support' Making check in scripts make[5]: Entering directory '/<>/src/scripts' make[5]: Nothing to be done for 'check'. make[5]: Leaving directory '/<>/src/scripts' Making check in version make[5]: Entering directory '/<>/src/version' make check-am make[6]: Entering directory '/<>/src/version' make[6]: Leaving directory '/<>/src/version' make[5]: Leaving directory '/<>/src/version' Making check in progs make[5]: Entering directory '/<>/src/progs' Making .C out of .xxd compileinfo.itxt make check-am make[6]: Entering directory '/<>/src/progs' Making .C out of .xxd compileinfo.itxt g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -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/x86_64-linux-gnu -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib -o mira mira.o quirks.o compileinfo.itxt.xxd.o -lmiraversion -lmiramodules -lmiradebuggersupport -lmira -lmiraestass -lmiracaf -lmirautil -lmiradptools -lmirafio -lmiraerrorhandling -lmiradebuggersupport -lmirafmttext -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt -lexpat -lm -lz -lbz2 libtool: link: g++ -pthread -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -Wl,-Bsymbolic-functions -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/x86_64-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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -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/x86_64-linux-gnu -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib -o miratest miratest.o compileinfo.itxt.xxd.o -lmiraversion -lmiramodules -lmiradebuggersupport -lmira -lmiraestass -lmiracaf -lmirautil -lmiradptools -lmirafio -lmiraerrorhandling -lmiradebuggersupport -lmirafmttext -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt -lexpat -lm -lz -lbz2 libtool: link: g++ -pthread -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -Wl,-Bsymbolic-functions -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/x86_64-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 '/<>/src/progs' make[5]: Leaving directory '/<>/src/progs' Making check in other make[5]: Entering directory '/<>/src/other' Making check in sls make[6]: Entering directory '/<>/src/other/sls' Making check in mira-createsls make[7]: Entering directory '/<>/src/other/sls/mira-createsls' Making check in bin make[8]: Entering directory '/<>/src/other/sls/mira-createsls/bin' make[8]: Nothing to be done for 'check'. make[8]: Leaving directory '/<>/src/other/sls/mira-createsls/bin' make[8]: Entering directory '/<>/src/other/sls/mira-createsls' make[8]: Nothing to be done for 'check-am'. make[8]: Leaving directory '/<>/src/other/sls/mira-createsls' make[7]: Leaving directory '/<>/src/other/sls/mira-createsls' make[7]: Entering directory '/<>/src/other/sls' make[7]: Nothing to be done for 'check-am'. make[7]: Leaving directory '/<>/src/other/sls' make[6]: Leaving directory '/<>/src/other/sls' make[6]: Entering directory '/<>/src/other' make[6]: Nothing to be done for 'check-am'. make[6]: Leaving directory '/<>/src/other' make[5]: Leaving directory '/<>/src/other' make[5]: Entering directory '/<>/src' make[5]: Nothing to be done for 'check-am'. make[5]: Leaving directory '/<>/src' make[4]: Leaving directory '/<>/src' make[4]: Entering directory '/<>' make[4]: Nothing to be done for 'check-am'. make[4]: Leaving directory '/<>' make[3]: Leaving directory '/<>' make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot 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/ dh_installdirs install -d debian/mira-assembler/usr/bin debian/rules override_dh_auto_install-arch make[1]: Entering directory '/<>' make install DESTDIR=/<>/debian/mira-assembler make[2]: Entering directory '/<>' make install-recursive make[3]: Entering directory '/<>' Making install in man make[4]: Entering directory '/<>/man' make[5]: Entering directory '/<>/man' make[5]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/<>/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 '/<>/debian/mira-assembler/usr/share/man/man1' make[5]: Leaving directory '/<>/man' make[4]: Leaving directory '/<>/man' Making install in src make[4]: Entering directory '/<>/src' Making install in debuggersupport make[5]: Entering directory '/<>/src/debuggersupport' make[6]: Entering directory '/<>/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 '/<>/src/debuggersupport' make[5]: Leaving directory '/<>/src/debuggersupport' Making install in io make[5]: Entering directory '/<>/src/io' make install-am make[6]: Entering directory '/<>/src/io' make[7]: Entering directory '/<>/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 '/<>/src/io' make[6]: Leaving directory '/<>/src/io' make[5]: Leaving directory '/<>/src/io' Making install in stdinc make[5]: Entering directory '/<>/src/stdinc' make[6]: Entering directory '/<>/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 '/<>/src/stdinc' make[5]: Leaving directory '/<>/src/stdinc' Making install in errorhandling make[5]: Entering directory '/<>/src/errorhandling' make[6]: Entering directory '/<>/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 '/<>/src/errorhandling' make[5]: Leaving directory '/<>/src/errorhandling' Making install in util make[5]: Entering directory '/<>/src/util' make[6]: Entering directory '/<>/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 '/<>/src/util' make[5]: Leaving directory '/<>/src/util' Making install in mira make[5]: Entering directory '/<>/src/mira' make install-am make[6]: Entering directory '/<>/src/mira' make[7]: Entering directory '/<>/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 '/<>/src/mira' make[6]: Leaving directory '/<>/src/mira' make[5]: Leaving directory '/<>/src/mira' Making install in caf make[5]: Entering directory '/<>/src/caf' make[6]: Entering directory '/<>/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 '/<>/src/caf' make[5]: Leaving directory '/<>/src/caf' Making install in memorc make[5]: Entering directory '/<>/src/memorc' make[6]: Entering directory '/<>/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 '/<>/src/memorc' make[5]: Leaving directory '/<>/src/memorc' Making install in modules make[5]: Entering directory '/<>/src/modules' make[6]: Entering directory '/<>/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 '/<>/src/modules' make[5]: Leaving directory '/<>/src/modules' Making install in support make[5]: Entering directory '/<>/src/support' make[6]: Entering directory '/<>/src/support' make[6]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/<>/debian/mira-assembler/usr/share/mira/support_3rdparty_tools' /usr/bin/install -c -m 644 consedrc.13.0 consedtaglib.txt GTAGDB README '/<>/debian/mira-assembler/usr/share/mira/support_3rdparty_tools' make[6]: Leaving directory '/<>/src/support' make[5]: Leaving directory '/<>/src/support' Making install in scripts make[5]: Entering directory '/<>/src/scripts' make[6]: Entering directory '/<>/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 '/<>/src/scripts' make[5]: Leaving directory '/<>/src/scripts' Making install in version make[5]: Entering directory '/<>/src/version' make install-am make[6]: Entering directory '/<>/src/version' make[7]: Entering directory '/<>/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 '/<>/src/version' make[6]: Leaving directory '/<>/src/version' make[5]: Leaving directory '/<>/src/version' Making install in progs make[5]: Entering directory '/<>/src/progs' Making .C out of .xxd compileinfo.itxt make install-am make[6]: Entering directory '/<>/src/progs' Making .C out of .xxd compileinfo.itxt g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -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/x86_64-linux-gnu -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib -o mira mira.o quirks.o compileinfo.itxt.xxd.o -lmiraversion -lmiramodules -lmiradebuggersupport -lmira -lmiraestass -lmiracaf -lmirautil -lmiradptools -lmirafio -lmiraerrorhandling -lmiradebuggersupport -lmirafmttext -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt -lexpat -lm -lz -lbz2 libtool: link: g++ -pthread -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -Wl,-Bsymbolic-functions -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/x86_64-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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -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/x86_64-linux-gnu -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib -o miratest miratest.o compileinfo.itxt.xxd.o -lmiraversion -lmiramodules -lmiradebuggersupport -lmira -lmiraestass -lmiracaf -lmirautil -lmiradptools -lmirafio -lmiraerrorhandling -lmiradebuggersupport -lmirafmttext -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt -lexpat -lm -lz -lbz2 libtool: link: g++ -pthread -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -Wl,-Bsymbolic-functions -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/x86_64-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 '/<>/src/progs' Making .C out of .xxd compileinfo.itxt /bin/mkdir -p '/<>/debian/mira-assembler/usr/bin' /bin/bash ../../libtool --mode=install /usr/bin/install -c mira '/<>/debian/mira-assembler/usr/bin' libtool: install: /usr/bin/install -c mira /<>/debian/mira-assembler/usr/bin/mira make install-exec-hook make[8]: Entering directory '/<>/src/progs' cd /<>/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 '/<>/src/progs' make[7]: Nothing to be done for 'install-data-am'. make[7]: Leaving directory '/<>/src/progs' make[6]: Leaving directory '/<>/src/progs' make[5]: Leaving directory '/<>/src/progs' Making install in other make[5]: Entering directory '/<>/src/other' Making install in sls make[6]: Entering directory '/<>/src/other/sls' Making install in mira-createsls make[7]: Entering directory '/<>/src/other/sls/mira-createsls' Making install in bin make[8]: Entering directory '/<>/src/other/sls/mira-createsls/bin' make[9]: Entering directory '/<>/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 '/<>/src/other/sls/mira-createsls/bin' make[8]: Leaving directory '/<>/src/other/sls/mira-createsls/bin' make[8]: Entering directory '/<>/src/other/sls/mira-createsls' make[9]: Entering directory '/<>/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 '/<>/src/other/sls/mira-createsls' make[8]: Leaving directory '/<>/src/other/sls/mira-createsls' make[7]: Leaving directory '/<>/src/other/sls/mira-createsls' make[7]: Entering directory '/<>/src/other/sls' make[8]: Entering directory '/<>/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 '/<>/src/other/sls' make[7]: Leaving directory '/<>/src/other/sls' make[6]: Leaving directory '/<>/src/other/sls' make[6]: Entering directory '/<>/src/other' make[7]: Entering directory '/<>/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 '/<>/src/other' make[6]: Leaving directory '/<>/src/other' make[5]: Leaving directory '/<>/src/other' make[5]: Entering directory '/<>/src' make[6]: Entering directory '/<>/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 '/<>/src' make[5]: Leaving directory '/<>/src' make[4]: Leaving directory '/<>/src' make[4]: Entering directory '/<>' make[5]: Entering directory '/<>' make[5]: Nothing to be done for 'install-exec-am'. make[5]: Nothing to be done for 'install-data-am'. make[5]: Leaving directory '/<>' make[4]: Leaving directory '/<>' make[3]: Leaving directory '/<>' make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' debian/rules override_dh_auto_install-indep make[1]: Entering directory '/<>' #There is no installation target for the docs mkdir -p /<>/debian/tmp/usr/share/doc/mira-assembler cp -r -t /<>/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 '/<>' dh_install install -d debian/.debhelper/generated/mira-assembler install -d debian/mira-rfam-12s-rrna/usr/share/mira/ cp --reflink=auto -a ./src/other/sls/mira-install-sls-rrna.sh ./src/other/sls/rfam_rrna-21-12.sls.gz debian/mira-rfam-12s-rrna/usr/share/mira// install -d debian/.debhelper/generated/mira-rfam-12s-rrna install -d debian/mira-doc//usr/share cp --reflink=auto -a debian/tmp/usr/share/doc/ debian/mira-doc//usr/share/ install -d debian/.debhelper/generated/mira-doc dh_installdocs install -d debian/mira-assembler/usr/share/doc/mira-assembler cp --reflink=auto -a ./NEWS debian/mira-assembler/usr/share/doc/mira-assembler cp --reflink=auto -a ./README debian/mira-assembler/usr/share/doc/mira-assembler cp --reflink=auto -a ./THANKS debian/mira-assembler/usr/share/doc/mira-assembler cp --reflink=auto -a ./HELP_WANTED debian/mira-assembler/usr/share/doc/mira-assembler cp --reflink=auto -a ./debian/README.test debian/mira-assembler/usr/share/doc/mira-assembler cp --reflink=auto -a ./debian/tests/run-unit-test debian/mira-assembler/usr/share/doc/mira-assembler cp --reflink=auto -a ./debian/tests/est_assembly.conf debian/mira-assembler/usr/share/doc/mira-assembler cp --reflink=auto -a ./debian/tests/solexa1.conf debian/mira-assembler/usr/share/doc/mira-assembler cp --reflink=auto -a ./debian/tests/solexa2.conf debian/mira-assembler/usr/share/doc/mira-assembler cd './debian/tests/test_data//..' && find 'test_data' \( -type f -or -type l \) -and ! -empty -print0 | LC_ALL=C sort -z | xargs -0 -I {} cp --reflink=auto --parents -dp {} /<>/debian/mira-assembler/usr/share/doc/mira-assembler chown -R 0:0 debian/mira-assembler/usr/share/doc chmod -R u\+rw,go=rX debian/mira-assembler/usr/share/doc install -p -m0644 debian/copyright debian/mira-assembler/usr/share/doc/mira-assembler/copyright install -d debian/mira-rfam-12s-rrna/usr/share/doc/mira-rfam-12s-rrna install -p -m0644 debian/copyright debian/mira-rfam-12s-rrna/usr/share/doc/mira-rfam-12s-rrna/copyright install -d debian/mira-doc/usr/share/doc/mira-doc install -p -m0644 debian/mira-doc.README.Debian debian/mira-doc/usr/share/doc/mira-doc/README.Debian install -p -m0644 debian/copyright debian/mira-doc/usr/share/doc/mira-doc/copyright install -d debian/mira-doc/usr/share/doc-base/ install -p -m0644 debian/mira-doc.doc-base debian/mira-doc/usr/share/doc-base/mira-manual debian/rules override_dh_installchangelogs make[1]: Entering directory '/<>' dh_installchangelogs src/mira/CHANGES.txt install -p -m0644 debian/changelog debian/mira-assembler/usr/share/doc/mira-assembler/changelog.Debian install -p -m0644 src/mira/CHANGES.txt debian/mira-assembler/usr/share/doc/mira-assembler/changelog install -p -m0644 debian/changelog debian/mira-rfam-12s-rrna/usr/share/doc/mira-rfam-12s-rrna/changelog.Debian install -p -m0644 src/mira/CHANGES.txt debian/mira-rfam-12s-rrna/usr/share/doc/mira-rfam-12s-rrna/changelog install -p -m0644 debian/changelog debian/mira-doc/usr/share/doc/mira-doc/changelog.Debian install -p -m0644 src/mira/CHANGES.txt debian/mira-doc/usr/share/doc/mira-doc/changelog make[1]: Leaving directory '/<>' dh_installman man-recode --to-code UTF-8 --suffix .dh-new debian/mira-assembler/usr/share/man/man1/mira.1 debian/mira-assembler/usr/share/man/man1/mirabait.1 man-recode --to-code UTF-8 --suffix .dh-new debian/mira-assembler/usr/share/man/man1/miraconvert.1 debian/mira-assembler/usr/share/man/man1/miradiff.1 man-recode --to-code UTF-8 --suffix .dh-new debian/mira-assembler/usr/share/man/man1/miramem.1 debian/mira-assembler/usr/share/man/man1/miramer.1 mv debian/mira-assembler/usr/share/man/man1/miraconvert.1.dh-new debian/mira-assembler/usr/share/man/man1/miraconvert.1 mv debian/mira-assembler/usr/share/man/man1/miradiff.1.dh-new debian/mira-assembler/usr/share/man/man1/miradiff.1 chmod 0644 -- debian/mira-assembler/usr/share/man/man1/miraconvert.1 debian/mira-assembler/usr/share/man/man1/miradiff.1 mv debian/mira-assembler/usr/share/man/man1/miramem.1.dh-new debian/mira-assembler/usr/share/man/man1/miramem.1 mv debian/mira-assembler/usr/share/man/man1/miramer.1.dh-new debian/mira-assembler/usr/share/man/man1/miramer.1 chmod 0644 -- debian/mira-assembler/usr/share/man/man1/miramem.1 debian/mira-assembler/usr/share/man/man1/miramer.1 mv debian/mira-assembler/usr/share/man/man1/mira.1.dh-new debian/mira-assembler/usr/share/man/man1/mira.1 mv debian/mira-assembler/usr/share/man/man1/mirabait.1.dh-new debian/mira-assembler/usr/share/man/man1/mirabait.1 chmod 0644 -- debian/mira-assembler/usr/share/man/man1/mira.1 debian/mira-assembler/usr/share/man/man1/mirabait.1 dh_lintian install -d debian/mira-assembler/usr/share/lintian/overrides install -p -m0644 debian/mira-assembler.lintian-overrides debian/mira-assembler/usr/share/lintian/overrides/mira-assembler dh_perl dh_link rm -f debian/mira-assembler/usr/bin/mirabait ln -s mira debian/mira-assembler/usr/bin/mirabait rm -f debian/mira-assembler/usr/bin/miramem ln -s mira debian/mira-assembler/usr/bin/miramem rm -f debian/mira-assembler/usr/bin/miramer ln -s mira debian/mira-assembler/usr/bin/miramer rm -f debian/mira-assembler/usr/bin/miraconvert ln -s mira debian/mira-assembler/usr/bin/miraconvert dh_strip_nondeterminism Using 1595964063 as canonical time Normalizing debian/mira-rfam-12s-rrna/usr/share/mira/rfam_rrna-21-12.sls.gz using File::StripNondeterminism::handlers::gzip Using 1595964063 as canonical time 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/sxa_unsc_ggcxg2_lenski.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/454_autoedit2.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/454sxa_stms_hybdenovo.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/454sxa_hybdenovo.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/images/warning.png using File::StripNondeterminism::handlers::png Normalizing debian/mira-doc/usr/share/doc/mira-assembler/images/note.png using File::StripNondeterminism::handlers::png Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/haf_danger_join_notok.png using File::StripNondeterminism::handlers::png Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/srmc_in_454sxahyb_lastpass2.png using File::StripNondeterminism::handlers::png Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/haf5_haf2_contigcoverage_ovals.png using File::StripNondeterminism::handlers::png Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/haf2_haf5_clearshortrepeat.png using File::StripNondeterminism::handlers::png Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/sxa_sroc_lenski1.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/haf2_end_nomoredata.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/sxa_unsc_ggc1_lenski.png using File::StripNondeterminism::handlers::png Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/sxa_mcvc_lenski.png using File::StripNondeterminism::handlers::png Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/pb_elasticdarkinserts01.png using File::StripNondeterminism::handlers::png Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/haf_danger_join_ok.png using File::StripNondeterminism::handlers::png Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/454_stacks_join.png using File::StripNondeterminism::handlers::png Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/ion_dh10bdirdepindel.png using File::StripNondeterminism::handlers::png Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/pb_elasticdarkinserts04.png using File::StripNondeterminism::handlers::png Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/454_autoedit1.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/san_autoedit1.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_wrmcsrmc_hiding_lenski1.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/sxa_gcbias_bias2009.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/pb_c227-11-clcr_res.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/sxa_xmastree_lenski2.png using File::StripNondeterminism::handlers::png Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/srmc_in_454sxahyb_1stpass.png using File::StripNondeterminism::handlers::png Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/sxa_unsc_ggc4_lenski.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/sxa_cer_reads2.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/haf5_haf2_contigcoverage.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/san_autoedit2.png using File::StripNondeterminism::handlers::png Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/haf5_repend_rrna.png using File::StripNondeterminism::handlers::png Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/pb_elasticdarkinserts02.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 gzip -9nf usr/share/doc/mira-doc/changelog usr/share/doc/mira-doc/changelog.Debian gzip -9nf usr/share/doc/mira-rfam-12s-rrna/changelog usr/share/doc/mira-rfam-12s-rrna/changelog.Debian 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 cd '/<>' cd '/<>' 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 '/<>' dh_fixperms find debian/mira-assembler -true -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0 find debian/mira-rfam-12s-rrna -true -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0 find debian/mira-doc -true -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0 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-assembler ! -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-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 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 -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/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 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-doc/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/mira-assembler/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x 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 dh_missing dh_strip install -d debian/.debhelper/mira-assembler/dbgsym-root/usr/lib/debug/.build-id/5b objcopy --only-keep-debug --compress-debug-sections debian/mira-assembler/usr/bin/mira debian/.debhelper/mira-assembler/dbgsym-root/usr/lib/debug/.build-id/5b/44d220088348e2319e196db0a4af0baf31f521.debug chmod 0644 -- debian/.debhelper/mira-assembler/dbgsym-root/usr/lib/debug/.build-id/5b/44d220088348e2319e196db0a4af0baf31f521.debug chown 0:0 -- debian/.debhelper/mira-assembler/dbgsym-root/usr/lib/debug/.build-id/5b/44d220088348e2319e196db0a4af0baf31f521.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/5b/44d220088348e2319e196db0a4af0baf31f521.debug debian/mira-assembler/usr/bin/mira install -d debian/.debhelper/mira-assembler/dbgsym-root/usr/share/doc ln -s mira-assembler debian/.debhelper/mira-assembler/dbgsym-root/usr/share/doc/mira-assembler-dbgsym dh_makeshlibs rm -f debian/mira-assembler/DEBIAN/shlibs rm -f debian/mira-rfam-12s-rrna/DEBIAN/shlibs rm -f debian/mira-doc/DEBIAN/shlibs dh_shlibdeps install -d debian/mira-assembler/DEBIAN dpkg-shlibdeps -Tdebian/mira-assembler.substvars debian/mira-assembler/usr/bin/mira dh_installdeb install -d debian/mira-rfam-12s-rrna/DEBIAN cp -f debian/mira-rfam-12s-rrna.postinst debian/mira-rfam-12s-rrna/DEBIAN/postinst [META] Replace #TOKEN#s in "debian/mira-rfam-12s-rrna/DEBIAN/postinst" chmod 0755 -- debian/mira-rfam-12s-rrna/DEBIAN/postinst chown 0:0 -- 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 chown 0:0 -- debian/mira-rfam-12s-rrna/DEBIAN/postrm install -d debian/mira-doc/DEBIAN dh_gencontrol echo misc:Depends= >> debian/mira-rfam-12s-rrna.substvars echo misc:Pre-Depends= >> debian/mira-rfam-12s-rrna.substvars dpkg-gencontrol -pmira-rfam-12s-rrna -ldebian/changelog -Tdebian/mira-rfam-12s-rrna.substvars -Pdebian/mira-rfam-12s-rrna echo misc:Depends= >> debian/mira-doc.substvars echo misc:Pre-Depends= >> debian/mira-doc.substvars dpkg-gencontrol -pmira-doc -ldebian/changelog -Tdebian/mira-doc.substvars -Pdebian/mira-doc echo misc:Depends= >> debian/mira-assembler.substvars echo misc:Pre-Depends= >> debian/mira-assembler.substvars install -d debian/.debhelper/mira-assembler/dbgsym-root/DEBIAN dpkg-gencontrol -pmira-assembler -ldebian/changelog -Tdebian/mira-assembler.substvars -Pdebian/.debhelper/mira-assembler/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -UBuilt-Using -DAuto-Built-Package=debug-symbols -DPackage=mira-assembler-dbgsym "-DDepends=mira-assembler (= \${binary:Version})" "-DDescription=debug symbols for mira-assembler" -DBuild-Ids=5b44d220088348e2319e196db0a4af0baf31f521 -DSection=debug -DPackage-Type=ddeb -UMulti-Arch -UReplaces -UBreaks chmod 0644 -- debian/mira-doc/DEBIAN/control chown 0:0 -- debian/mira-doc/DEBIAN/control chmod 0644 -- debian/mira-rfam-12s-rrna/DEBIAN/control chown 0:0 -- debian/mira-rfam-12s-rrna/DEBIAN/control chmod 0644 -- debian/.debhelper/mira-assembler/dbgsym-root/DEBIAN/control chown 0:0 -- 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 chown 0:0 -- debian/mira-assembler/DEBIAN/control dh_md5sums cd debian/mira-assembler >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/mira-doc >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums 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 chown 0:0 -- debian/mira-doc/DEBIAN/md5sums chmod 0644 -- debian/mira-assembler/DEBIAN/md5sums chown 0:0 -- debian/mira-assembler/DEBIAN/md5sums cd debian/.debhelper/mira-assembler/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/mira-rfam-12s-rrna/DEBIAN/md5sums chown 0:0 -- debian/mira-rfam-12s-rrna/DEBIAN/md5sums chmod 0644 -- debian/.debhelper/mira-assembler/dbgsym-root/DEBIAN/md5sums chown 0:0 -- debian/.debhelper/mira-assembler/dbgsym-root/DEBIAN/md5sums rm -f debian/mira-assembler.debhelper.log debian/mira-doc.debhelper.log debian/mira-rfam-12s-rrna.debhelper.log debian/rules override_dh_builddeb make[1]: Entering directory '/<>' dh_builddeb -- -Z xz dpkg-deb -Z xz --build debian/mira-assembler .. dpkg-deb -Z xz --build debian/mira-rfam-12s-rrna .. dpkg-deb -Z xz --build debian/mira-doc .. install -d debian/.debhelper/scratch-space/build-mira-assembler dpkg-deb -Z xz --build debian/.debhelper/mira-assembler/dbgsym-root debian/.debhelper/scratch-space/build-mira-assembler INFO: pkgstriptranslations version 146 INFO: pkgstriptranslations version 146 INFO: pkgstriptranslations version 146 INFO: pkgstriptranslations version 146 pkgstriptranslations: processing mira-rfam-12s-rrna (in debian/mira-rfam-12s-rrna); do_strip: , oemstrip: pkgstriptranslations: processing mira-assembler (in debian/mira-assembler); do_strip: , oemstrip: pkgstriptranslations: processing mira-doc (in debian/mira-doc); do_strip: , oemstrip: pkgstriptranslations: processing mira-assembler-dbgsym (in debian/.debhelper/mira-assembler/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgstripfiles: processing control file: debian/mira-rfam-12s-rrna/DEBIAN/control, package mira-rfam-12s-rrna, directory debian/mira-rfam-12s-rrna .. removing usr/share/doc/mira-rfam-12s-rrna/changelog.gz pkgstripfiles: processing control file: debian/mira-assembler/DEBIAN/control, package mira-assembler, directory debian/mira-assembler INFO: pkgstripfiles: waiting for lock (mira-rfam-12s-rrna) ... .. removing usr/share/doc/mira-assembler/changelog.gz pkgstripfiles: Truncating usr/share/doc/mira-assembler/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package mira-assembler ... pkgstripfiles: No PNG files. pkgstripfiles: processing control file: debian/.debhelper/mira-assembler/dbgsym-root/DEBIAN/control, package mira-assembler-dbgsym, directory debian/.debhelper/mira-assembler/dbgsym-root dpkg-deb: building package 'mira-assembler-dbgsym' in 'debian/.debhelper/scratch-space/build-mira-assembler/mira-assembler-dbgsym_4.9.6-4build7_amd64.deb'. dpkg-deb: building package 'mira-assembler' in '../mira-assembler_4.9.6-4build7_amd64.deb'. pkgstripfiles: Truncating usr/share/doc/mira-rfam-12s-rrna/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package mira-rfam-12s-rrna ... pkgstripfiles: No PNG files. dpkg-deb: building package 'mira-rfam-12s-rrna' in '../mira-rfam-12s-rrna_4.9.6-4build7_all.deb'. pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgstripfiles: processing control file: debian/mira-doc/DEBIAN/control, package mira-doc, directory debian/mira-doc .. removing usr/share/doc/mira-doc/changelog.gz pkgstripfiles: Truncating usr/share/doc/mira-doc/changelog.Debian.gz to topmost ten records pkgstripfiles: Disabled PNG optimization for -doc package mira-doc (to save build time) dpkg-deb: building package 'mira-doc' in '../mira-doc_4.9.6-4build7_all.deb'. Renaming mira-assembler-dbgsym_4.9.6-4build7_amd64.deb to mira-assembler-dbgsym_4.9.6-4build7_amd64.ddeb mv debian/.debhelper/scratch-space/build-mira-assembler/mira-assembler-dbgsym_4.9.6-4build7_amd64.deb ../mira-assembler-dbgsym_4.9.6-4build7_amd64.ddeb make[1]: Leaving directory '/<>' dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary -mLaunchpad Build Daemon >../mira_4.9.6-4build7_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 20200728-1932 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ mira_4.9.6-4build7_amd64.changes: --------------------------------- Format: 1.8 Date: Tue, 28 Jul 2020 19:21:03 +0000 Source: mira Binary: mira-assembler mira-doc mira-rfam-12s-rrna Architecture: amd64 all Version: 4.9.6-4build7 Distribution: groovy-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Steve Langasek 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 Changes: mira (4.9.6-4build7) groovy; urgency=medium . * No-change rebuild against libboost-regex1.71.0-icu67 Checksums-Sha1: fe1806d82a876d6a85ce891c1472bdf9c4dde8af 38104072 mira-assembler-dbgsym_4.9.6-4build7_amd64.ddeb 92984a1c7c540f3f39a83e99adf0aff44f4ac916 2435260 mira-assembler_4.9.6-4build7_amd64.deb 4d1f3d9d0d18f509872b4b516b36d657de65ea42 2785080 mira-doc_4.9.6-4build7_all.deb 51e9e1b1717a314aceb41e4afdcbcbc951d03fe6 10427216 mira-rfam-12s-rrna_4.9.6-4build7_all.deb e72f2de9c4c47c3526fb753a4df5f8bf4676a2e5 10665 mira_4.9.6-4build7_amd64.buildinfo Checksums-Sha256: 2afed83576929685058a44f76eb62b51c576fd3f5f0ea5f103dd039f0a830ebc 38104072 mira-assembler-dbgsym_4.9.6-4build7_amd64.ddeb 34835b7461afb1970941c25bf8bff62cfed073dfb434ca284ed085733769f102 2435260 mira-assembler_4.9.6-4build7_amd64.deb f28371141f5d60e1a9b35bd9e40f9cc43480218d4168b92849d3d97dd0d43de2 2785080 mira-doc_4.9.6-4build7_all.deb c2f92bfdb5d384284b6a53260de76392275dc1c3054eb1da9c17702fc859147a 10427216 mira-rfam-12s-rrna_4.9.6-4build7_all.deb 1f0cdf0e55590c4dd1641e42397b5c9510c2a709d614f37af0f6fb8289fd7d74 10665 mira_4.9.6-4build7_amd64.buildinfo Files: 57b4473ab04ff1eb8658b8c005e8aa5f 38104072 debug optional mira-assembler-dbgsym_4.9.6-4build7_amd64.ddeb 6407011ddfec2be10fa4bd0cfd80d9f6 2435260 science optional mira-assembler_4.9.6-4build7_amd64.deb 8f377e6d464ccdc0980566ef077e2403 2785080 doc optional mira-doc_4.9.6-4build7_all.deb 258e94e9b2b3ae2ad3d03841ff2d7c1a 10427216 science optional mira-rfam-12s-rrna_4.9.6-4build7_all.deb 81439b8db92e0c647f6ee547f2ee16b8 10665 science optional mira_4.9.6-4build7_amd64.buildinfo Original-Maintainer: Debian Med Packaging Team +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ mira-assembler_4.9.6-4build7_amd64.deb -------------------------------------- new debian package, version 2.0. size 2435260 bytes: control archive=2100 bytes. 1700 bytes, 33 lines control 2357 bytes, 29 lines md5sums Package: mira-assembler Source: mira Version: 4.9.6-4build7 Architecture: amd64 Maintainer: Ubuntu Developers Installed-Size: 7618 Depends: libboost-filesystem1.71.0, libboost-regex1.71.0-icu67, libboost-thread1.71.0, libc6 (>= 2.29), libexpat1 (>= 2.0.1), libgcc-s1 (>= 3.0), libgomp1 (>= 4.9), libstdc++6 (>= 9), zlib1g (>= 1:1.2.6) Recommends: mira-rfam-12s-rrna Suggests: mira-doc Section: science Priority: optional Homepage: http://chevreux.org/projects_mira.html Description: Whole Genome Shotgun and EST Sequence Assembler The mira genome fragment assembler is a specialised assembler for sequencing projects classified as 'hard' due to high number of similar repeats. For expressed sequence tags (ESTs) transcripts, miraEST is specialised on reconstructing pristine mRNA transcripts while detecting and classifying single nucleotide polymorphisms (SNP) occurring in different variations thereof. . The assembler is routinely used for such various tasks as mutation detection in different cell types, similarity analysis of transcripts between organisms, and pristine assembly of sequences from various sources for oligo design in clinical microarray experiments. . The package provides the following executables: Binaries provided: * mira: for assembly of genome sequences * miramem: estimating memory needed to assemble projects. * mirabait: a "grep" like tool to select reads with kmers up to 256 bases. * miraconvert: is a tool to convert, extract and sometimes recalculate all kinds of data related to sequence assembly files. Original-Maintainer: Debian Med Packaging Team drwxr-xr-x root/root 0 2020-07-28 19:21 ./ drwxr-xr-x root/root 0 2020-07-28 19:21 ./usr/ drwxr-xr-x root/root 0 2020-07-28 19:21 ./usr/bin/ -rwxr-xr-x root/root 7655040 2020-07-28 19:21 ./usr/bin/mira lrwxrwxrwx root/root 0 2020-07-28 19:21 ./usr/bin/mirabait -> mira lrwxrwxrwx root/root 0 2020-07-28 19:21 ./usr/bin/miraconvert -> mira lrwxrwxrwx root/root 0 2020-07-28 19:21 ./usr/bin/miramem -> mira lrwxrwxrwx root/root 0 2020-07-28 19:21 ./usr/bin/miramer -> mira drwxr-xr-x root/root 0 2020-07-28 19:21 ./usr/share/ drwxr-xr-x root/root 0 2020-07-28 19:21 ./usr/share/doc/ drwxr-xr-x root/root 0 2020-07-28 19:21 ./usr/share/doc/mira-assembler/ -rw-r--r-- root/root 1384 2016-05-01 15:18 ./usr/share/doc/mira-assembler/HELP_WANTED -rw-r--r-- root/root 263 2016-05-01 15:18 ./usr/share/doc/mira-assembler/NEWS.gz -rw-r--r-- root/root 2691 2016-05-01 15:18 ./usr/share/doc/mira-assembler/README -rw-r--r-- root/root 180 2018-09-19 20:13 ./usr/share/doc/mira-assembler/README.test -rw-r--r-- root/root 3929 2016-05-01 15:18 ./usr/share/doc/mira-assembler/THANKS -rw-r--r-- root/root 828 2020-07-28 19:21 ./usr/share/doc/mira-assembler/changelog.Debian.gz -rw-r--r-- root/root 2400 2018-09-19 20:13 ./usr/share/doc/mira-assembler/copyright -rw-r--r-- root/root 135 2018-09-19 20:13 ./usr/share/doc/mira-assembler/est_assembly.conf -rw-r--r-- root/root 415 2018-09-19 20:13 ./usr/share/doc/mira-assembler/run-unit-test -rw-r--r-- root/root 1533 2018-09-19 20:13 ./usr/share/doc/mira-assembler/solexa1.conf -rw-r--r-- root/root 219 2018-09-19 20:13 ./usr/share/doc/mira-assembler/solexa2.conf drwxr-xr-x root/root 0 2018-09-19 20:13 ./usr/share/doc/mira-assembler/test_data/ drwxr-xr-x root/root 0 2020-07-28 19:21 ./usr/share/doc/mira-assembler/test_data/fasta_estset1/ -rw-r--r-- root/root 1159 2018-09-19 20:13 ./usr/share/doc/mira-assembler/test_data/fasta_estset1/tvc_mini.fasta.gz -rw-r--r-- root/root 3572 2018-09-19 20:13 ./usr/share/doc/mira-assembler/test_data/fasta_estset1/tvc_mini.fasta.qual.gz drwxr-xr-x root/root 0 2020-07-28 19:21 ./usr/share/doc/mira-assembler/test_data/solexa_eco_art/ -rw-r--r-- root/root 4982 2018-09-19 20:13 ./usr/share/doc/mira-assembler/test_data/solexa_eco_art/ecoli_backbone_in.gbf.gz -rw-r--r-- root/root 29260 2018-09-19 20:13 ./usr/share/doc/mira-assembler/test_data/solexa_eco_art/ecoli_in.solexa.fasta.gz -rw-r--r-- root/root 14391 2018-09-19 20:13 ./usr/share/doc/mira-assembler/test_data/solexa_eco_art/ecoli_in.solexa.fasta.qual.gz -rw-r--r-- root/root 11879 2018-09-19 20:13 ./usr/share/doc/mira-assembler/test_data/solexa_eco_art/ecoli_straindata_in.txt.gz drwxr-xr-x root/root 0 2020-07-28 19:21 ./usr/share/lintian/ drwxr-xr-x root/root 0 2020-07-28 19:21 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 147 2018-09-19 20:13 ./usr/share/lintian/overrides/mira-assembler drwxr-xr-x root/root 0 2020-07-28 19:21 ./usr/share/man/ drwxr-xr-x root/root 0 2020-07-28 19:21 ./usr/share/man/man1/ -rw-r--r-- root/root 1140 2020-07-28 19:21 ./usr/share/man/man1/mira.1.gz -rw-r--r-- root/root 2649 2020-07-28 19:21 ./usr/share/man/man1/mirabait.1.gz -rw-r--r-- root/root 3577 2020-07-28 19:21 ./usr/share/man/man1/miraconvert.1.gz -rw-r--r-- root/root 568 2020-07-28 19:21 ./usr/share/man/man1/miradiff.1.gz -rw-r--r-- root/root 761 2020-07-28 19:21 ./usr/share/man/man1/miramem.1.gz -rw-r--r-- root/root 566 2020-07-28 19:21 ./usr/share/man/man1/miramer.1.gz drwxr-xr-x root/root 0 2020-07-28 19:21 ./usr/share/mira/ drwxr-xr-x root/root 0 2020-07-28 19:21 ./usr/share/mira/support_3rdparty_tools/ -rw-r--r-- root/root 2571 2020-07-28 19:21 ./usr/share/mira/support_3rdparty_tools/GTAGDB -rw-r--r-- root/root 735 2020-07-28 19:21 ./usr/share/mira/support_3rdparty_tools/README -rw-r--r-- root/root 58 2020-07-28 19:21 ./usr/share/mira/support_3rdparty_tools/consedrc.13.0 -rw-r--r-- root/root 762 2020-07-28 19:21 ./usr/share/mira/support_3rdparty_tools/consedtaglib.txt mira-doc_4.9.6-4build7_all.deb ------------------------------ new debian package, version 2.0. size 2785080 bytes: control archive=2300 bytes. 622 bytes, 17 lines control 5377 bytes, 56 lines md5sums Package: mira-doc Source: mira Version: 4.9.6-4build7 Architecture: all Maintainer: Ubuntu Developers Installed-Size: 3831 Suggests: mira-assembler Section: doc Priority: optional Homepage: http://chevreux.org/projects_mira.html Description: documentation for the mira assembler The mira genome fragment assembler is a specialised assembler for sequencing projects classified as 'hard' due to high number of similar repeats. . This package contains an HTML book introducing to mira. Original-Maintainer: Debian Med Packaging Team drwxr-xr-x root/root 0 2020-07-28 19:21 ./ drwxr-xr-x root/root 0 2020-07-28 19:21 ./usr/ drwxr-xr-x root/root 0 2020-07-28 19:21 ./usr/share/ drwxr-xr-x root/root 0 2020-07-28 19:21 ./usr/share/doc-base/ -rw-r--r-- root/root 320 2018-09-19 20:13 ./usr/share/doc-base/mira-manual drwxr-xr-x root/root 0 2020-07-28 19:21 ./usr/share/doc/ drwxr-xr-x root/root 0 2020-07-28 19:21 ./usr/share/doc/mira-assembler/ -rw-r--r-- root/root 867721 2020-07-28 19:21 ./usr/share/doc/mira-assembler/DefinitiveGuideToMIRA.html drwxr-xr-x root/root 0 2020-07-28 19:21 ./usr/share/doc/mira-assembler/bookfigures/ -rw-r--r-- root/root 50839 2020-07-28 19:21 ./usr/share/doc/mira-assembler/bookfigures/454_autoedit1.png -rw-r--r-- root/root 47236 2020-07-28 19:21 ./usr/share/doc/mira-assembler/bookfigures/454_autoedit2.png -rw-r--r-- root/root 44224 2020-07-28 19:21 ./usr/share/doc/mira-assembler/bookfigures/454_stacks_join.png -rw-r--r-- root/root 148931 2020-07-28 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2020-07-28 19:21 ./usr/share/doc/mira-assembler/doccss/miradocstyle.css drwxr-xr-x root/root 0 2020-07-28 19:21 ./usr/share/doc/mira-assembler/images/ -rw-r--r-- root/root 427 2020-07-28 19:21 ./usr/share/doc/mira-assembler/images/README.txt -rw-r--r-- root/root 4144 2020-07-28 19:21 ./usr/share/doc/mira-assembler/images/note.png -rw-r--r-- root/root 3452 2020-07-28 19:21 ./usr/share/doc/mira-assembler/images/warning.png drwxr-xr-x root/root 0 2020-07-28 19:21 ./usr/share/doc/mira-doc/ -rw-r--r-- root/root 186 2018-09-19 20:13 ./usr/share/doc/mira-doc/README.Debian -rw-r--r-- root/root 827 2020-07-28 19:21 ./usr/share/doc/mira-doc/changelog.Debian.gz -rw-r--r-- root/root 2400 2018-09-19 20:13 ./usr/share/doc/mira-doc/copyright mira-rfam-12s-rrna_4.9.6-4build7_all.deb ---------------------------------------- new debian package, version 2.0. size 10427216 bytes: control archive=1004 bytes. 740 bytes, 19 lines control 310 bytes, 4 lines md5sums 214 bytes, 10 lines * postinst #!/bin/bash 50 bytes, 7 lines * postrm #!/bin/bash Package: mira-rfam-12s-rrna Source: mira Version: 4.9.6-4build7 Architecture: all Maintainer: Ubuntu Developers Installed-Size: 10209 Pre-Depends: mira-assembler Suggests: mira-doc Section: science Priority: optional Homepage: http://chevreux.org/projects_mira.html Description: extract of RFAM 12 rRNA database The mira genome fragment assembler is a specialised assembler for sequencing projects classified as 'hard' due to high number of similar repeats. . This package contains data to enable MIRA and MIRABAIT to search for rRNA and rDNA. This data set contains an excerpt of the RFAM database. Original-Maintainer: Debian Med Packaging Team drwxr-xr-x root/root 0 2020-07-28 19:21 ./ drwxr-xr-x root/root 0 2020-07-28 19:21 ./usr/ drwxr-xr-x root/root 0 2020-07-28 19:21 ./usr/share/ drwxr-xr-x root/root 0 2020-07-28 19:21 ./usr/share/doc/ drwxr-xr-x root/root 0 2020-07-28 19:21 ./usr/share/doc/mira-rfam-12s-rrna/ -rw-r--r-- root/root 833 2020-07-28 19:21 ./usr/share/doc/mira-rfam-12s-rrna/changelog.Debian.gz -rw-r--r-- root/root 2400 2018-09-19 20:13 ./usr/share/doc/mira-rfam-12s-rrna/copyright drwxr-xr-x root/root 0 2020-07-28 19:21 ./usr/share/mira/ -rwxr-xr-x root/root 2548 2016-05-01 15:18 ./usr/share/mira/mira-install-sls-rrna.sh -rw-r--r-- root/root 10421035 2020-07-28 19:21 ./usr/share/mira/rfam_rrna-21-12.sls.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build-Space: 1175188 Build-Time: 311 Distribution: groovy-proposed Host Architecture: amd64 Install-Time: 79 Job: mira_4.9.6-4build7.dsc Machine Architecture: amd64 Package: mira Package-Time: 392 Source-Version: 4.9.6-4build7 Space: 1175188 Status: successful Version: 4.9.6-4build7 -------------------------------------------------------------------------------- Finished at 20200728-1932 Build needed 00:06:32, 1175188k disc space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=groovy --arch=amd64 PACKAGEBUILD-19742897 Scanning for processes to kill in build PACKAGEBUILD-19742897