sbuild (Debian sbuild) 0.73.0 (23 Dec 2016) on gcc131.bak.milne.osuosl.org +==============================================================================+ | velvet 1.2.10+dfsg1-5 (mips64el) Fri, 10 May 2019 05:11:35 +0000 | +==============================================================================+ Package: velvet Version: 1.2.10+dfsg1-5 Source Version: 1.2.10+dfsg1-5 Distribution: unstable Machine Architecture: amd64 Host Architecture: mips64el Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any I: NOTICE: Log filtering will replace 'var/run/schroot/mount/unstable-amd64-sbuild-bc1b8b87-8af5-4d41-9a1d-447a48fecd9f' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 http://debian.oregonstate.edu/debian unstable InRelease [247 kB] Get:2 http://debian.oregonstate.edu/debian unstable/main Sources.diff/Index [27.9 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 Packages.diff/Index [27.9 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main Sources 2019-05-09-0810.37.pdiff [35 B] Get:5 http://debian.oregonstate.edu/debian unstable/main Sources 2019-05-09-1407.29.pdiff [2058 B] Get:6 http://debian.oregonstate.edu/debian unstable/main Sources 2019-05-09-2009.23.pdiff [2110 B] Get:7 http://debian.oregonstate.edu/debian unstable/main Sources 2019-05-10-0209.45.pdiff [860 B] Get:7 http://debian.oregonstate.edu/debian unstable/main Sources 2019-05-10-0209.45.pdiff [860 B] Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2019-05-09-1407.29.pdiff [2410 B] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2019-05-09-2009.23.pdiff [2356 B] Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2019-05-10-0209.45.pdiff [538 B] Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2019-05-10-0209.45.pdiff [538 B] Get:11 http://debian.oregonstate.edu/debian unstable/main mips64el Packages [8026 kB] Fetched 8339 kB in 2s (3816 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Check APT --------- Checking available source versions... Download source files with APT ------------------------------ Reading package lists... NOTICE: 'velvet' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/velvet.git Please use: git clone https://salsa.debian.org/med-team/velvet.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 13.6 MB of source archives. Get:1 http://debian.oregonstate.edu/debian unstable/main velvet 1.2.10+dfsg1-5 (dsc) [2268 B] Get:2 http://debian.oregonstate.edu/debian unstable/main velvet 1.2.10+dfsg1-5 (tar) [13.6 MB] Get:3 http://debian.oregonstate.edu/debian unstable/main velvet 1.2.10+dfsg1-5 (diff) [14.2 kB] Fetched 13.6 MB in 0s (52.6 MB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/velvet-dIf4fJ/velvet-1.2.10+dfsg1' with '<>' I: NOTICE: Log filtering will replace 'build/velvet-dIf4fJ' with '<>' +------------------------------------------------------------------------------+ | Install crossbuild-essential | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: build-essential:amd64, fakeroot:amd64, crossbuild-essential-mips64el:amd64 Filtered Build-Depends: build-essential:amd64, fakeroot:amd64, crossbuild-essential-mips64el:amd64 dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-URaN8F/apt_archive/sbuild-build-depends-core-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy dpkg-scanpackages: info: Wrote 1 entries to output Packages file. Ign:1 copy:/<>/resolver-URaN8F/apt_archive ./ InRelease Get:2 copy:/<>/resolver-URaN8F/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-URaN8F/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-URaN8F/apt_archive ./ Sources [364 B] Get:5 copy:/<>/resolver-URaN8F/apt_archive ./ Packages [453 B] Fetched 1774 B in 0s (96.8 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 additional packages will be installed: binutils-mips64el-linux-gnuabi64 cpp-8-mips64el-linux-gnuabi64 cpp-mips64el-linux-gnuabi64 cross-config crossbuild-essential-mips64el dpkg-cross file g++-8-mips64el-linux-gnuabi64 g++-mips64el-linux-gnuabi64 gcc-8-cross-base gcc-8-mips64el-linux-gnuabi64 gcc-8-mips64el-linux-gnuabi64-base gcc-mips64el-linux-gnuabi64 libatomic1-mips64el-cross libc6-dev-mips64el-cross libc6-mips64el-cross libconfig-auto-perl libconfig-inifiles-perl libdebian-dpkgcross-perl libfile-homedir-perl libfile-which-perl libgcc-8-dev-mips64el-cross libgcc1-mips64el-cross libgomp1-mips64el-cross libicu63 libio-string-perl liblocale-gettext-perl libmagic-mgc libmagic1 libstdc++-8-dev-mips64el-cross libstdc++6-mips64el-cross libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev-mips64el-cross sensible-utils ucf Suggested packages: binutils-doc gcc-8-locales cpp-doc binutils-multiarch g++-8-multilib-mips64el-linux-gnuabi64 gcc-8-doc libstdc++6-8-dbg-mips64el-cross gcc-8-multilib-mips64el-linux-gnuabi64 libgcc1-dbg-mips64el-cross libgomp1-dbg-mips64el-cross libitm1-dbg-mips64el-cross libatomic1-dbg-mips64el-cross libasan5-dbg-mips64el-cross liblsan0-dbg-mips64el-cross libtsan0-dbg-mips64el-cross libubsan1-dbg-mips64el-cross libmpx2-dbg-mips64el-cross libquadmath0-dbg-mips64el-cross manpages-dev autoconf automake libtool flex bison gdb-mips64el-linux-gnuabi64 gcc-doc libyaml-shell-perl Recommended packages: libwww-perl libxml-sax-expat-perl libyaml-libyaml-perl | libyaml-syck-perl The following NEW packages will be installed: binutils-mips64el-linux-gnuabi64 cpp-8-mips64el-linux-gnuabi64 cpp-mips64el-linux-gnuabi64 cross-config crossbuild-essential-mips64el dpkg-cross file g++-8-mips64el-linux-gnuabi64 g++-mips64el-linux-gnuabi64 gcc-8-cross-base gcc-8-mips64el-linux-gnuabi64 gcc-8-mips64el-linux-gnuabi64-base gcc-mips64el-linux-gnuabi64 libatomic1-mips64el-cross libc6-dev-mips64el-cross libc6-mips64el-cross libconfig-auto-perl libconfig-inifiles-perl libdebian-dpkgcross-perl libfile-homedir-perl libfile-which-perl libgcc-8-dev-mips64el-cross libgcc1-mips64el-cross libgomp1-mips64el-cross libicu63 libio-string-perl liblocale-gettext-perl libmagic-mgc libmagic1 libstdc++-8-dev-mips64el-cross libstdc++6-mips64el-cross libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev-mips64el-cross sbuild-build-depends-core-dummy:mips64el sensible-utils ucf 0 upgraded, 42 newly installed, 0 to remove and 0 not upgraded. Need to get 40.4 MB of archives. After this operation, 151 MB of additional disk space will be used. Get:1 copy:/<>/resolver-URaN8F/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [876 B] Get:2 http://debian.oregonstate.edu/debian unstable/main amd64 liblocale-gettext-perl amd64 1.07-3+b4 [18.9 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 sensible-utils all 0.0.12 [15.8 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic-mgc amd64 1:5.35-4 [242 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic1 amd64 1:5.35-4 [117 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 file amd64 1:5.35-4 [66.3 kB] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 ucf all 3.0038+nmu1 [69.0 kB] Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 binutils-mips64el-linux-gnuabi64 amd64 2.31.1-16 [2489 kB] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-8-mips64el-linux-gnuabi64-base amd64 8.3.0-7cross1 [191 kB] Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-8-mips64el-linux-gnuabi64 amd64 8.3.0-7cross1 [6277 kB] Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-mips64el-linux-gnuabi64 amd64 4:8.3.0-1 [16.5 kB] Get:12 http://debian.oregonstate.edu/debian unstable/main amd64 cross-config all 2.6.15-2 [39.7 kB] Get:13 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-8-cross-base all 8.3.0-7cross1 [186 kB] Get:14 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-mips64el-cross all 2.28-10cross2 [1355 kB] Get:15 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc1-mips64el-cross all 1:8.3.0-7cross1 [68.8 kB] Get:16 http://debian.oregonstate.edu/debian unstable/main amd64 libgomp1-mips64el-cross all 8.3.0-7cross1 [66.0 kB] Get:17 http://debian.oregonstate.edu/debian unstable/main amd64 libatomic1-mips64el-cross all 8.3.0-7cross1 [7384 B] Get:18 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc-8-dev-mips64el-cross all 8.3.0-7cross1 [235 kB] Get:19 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-8-mips64el-linux-gnuabi64 amd64 8.3.0-7cross1 [6691 kB] Get:20 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-mips64el-linux-gnuabi64 amd64 4:8.3.0-1 [1472 B] Get:21 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++6-mips64el-cross all 8.3.0-7cross1 [310 kB] Get:22 http://debian.oregonstate.edu/debian unstable/main amd64 linux-libc-dev-mips64el-cross all 4.19.28-2cross2 [1240 kB] Get:23 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-dev-mips64el-cross all 2.28-10cross2 [2512 kB] Get:24 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++-8-dev-mips64el-cross all 8.3.0-7cross1 [1559 kB] Get:25 http://debian.oregonstate.edu/debian unstable/main amd64 g++-8-mips64el-linux-gnuabi64 amd64 8.3.0-7cross1 [6850 kB] Get:26 http://debian.oregonstate.edu/debian unstable/main amd64 g++-mips64el-linux-gnuabi64 amd64 4:8.3.0-1 [1192 B] Get:27 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-inifiles-perl all 3.000001-1 [51.9 kB] Get:28 http://debian.oregonstate.edu/debian unstable/main amd64 libio-string-perl all 1.08-3 [12.3 kB] Get:29 http://debian.oregonstate.edu/debian unstable/main amd64 libicu63 amd64 63.1-6 [8292 kB] Get:30 http://debian.oregonstate.edu/debian unstable/main amd64 libxml2 amd64 2.9.4+dfsg1-7+b3 [687 kB] Get:31 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-namespacesupport-perl all 1.12-1 [14.8 kB] Get:32 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-base-perl all 1.09-1 [20.4 kB] Get:33 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-perl all 1.00+dfsg-1 [58.6 kB] Get:34 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-libxml-perl amd64 2.0134+dfsg-1 [344 kB] Get:35 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-simple-perl all 2.25-1 [72.0 kB] Get:36 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-perl all 1.27-1 [66.8 kB] Get:37 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-auto-perl all 0.44-1 [19.5 kB] Get:38 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-which-perl all 1.23-1 [16.6 kB] Get:39 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-homedir-perl all 1.004-1 [42.7 kB] Get:40 http://debian.oregonstate.edu/debian unstable/main amd64 libdebian-dpkgcross-perl all 2.6.15-2 [38.5 kB] Get:41 http://debian.oregonstate.edu/debian unstable/main amd64 dpkg-cross all 2.6.15-2 [49.3 kB] Get:42 http://debian.oregonstate.edu/debian unstable/main amd64 crossbuild-essential-mips64el all 12.6 [6584 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 40.4 MB in 1s (64.2 MB/s) Selecting previously unselected package liblocale-gettext-perl. (Reading database ... 11942 files and directories currently installed.) Preparing to unpack .../00-liblocale-gettext-perl_1.07-3+b4_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-3+b4) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.35-4_amd64.deb ... Unpacking libmagic-mgc (1:5.35-4) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../03-libmagic1_1%3a5.35-4_amd64.deb ... Unpacking libmagic1:amd64 (1:5.35-4) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.35-4_amd64.deb ... Unpacking file (1:5.35-4) ... Selecting previously unselected package ucf. Preparing to unpack .../05-ucf_3.0038+nmu1_all.deb ... Moving old data out of the way Unpacking ucf (3.0038+nmu1) ... 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Setting up libconfig-inifiles-perl (3.000001-1) ... Setting up libfile-which-perl (1.23-1) ... Setting up libmagic-mgc (1:5.35-4) ... Setting up gcc-8-cross-base (8.3.0-7cross1) ... Setting up libmagic1:amd64 (1:5.35-4) ... Setting up libc6-mips64el-cross (2.28-10cross2) ... Setting up libxml-namespacesupport-perl (1.12-1) ... Setting up file (1:5.35-4) ... Setting up libyaml-perl (1.27-1) ... Setting up binutils-mips64el-linux-gnuabi64 (2.31.1-16) ... Setting up libicu63:amd64 (63.1-6) ... Setting up libxml-sax-base-perl (1.09-1) ... Setting up libio-string-perl (1.08-3) ... Setting up cross-config (2.6.15-2) ... Setting up gcc-8-mips64el-linux-gnuabi64-base:amd64 (8.3.0-7cross1) ... Setting up sensible-utils (0.0.12) ... Setting up linux-libc-dev-mips64el-cross (4.19.28-2cross2) ... Setting up libfile-homedir-perl (1.004-1) ... Setting up libgomp1-mips64el-cross (8.3.0-7cross1) ... Setting up libxml2:amd64 (2.9.4+dfsg1-7+b3) ... Setting up liblocale-gettext-perl (1.07-3+b4) ... Setting up cpp-8-mips64el-linux-gnuabi64 (8.3.0-7cross1) ... Setting up libatomic1-mips64el-cross (8.3.0-7cross1) ... Setting up libgcc1-mips64el-cross (1:8.3.0-7cross1) ... Setting up libc6-dev-mips64el-cross (2.28-10cross2) ... Setting up ucf (3.0038+nmu1) ... Setting up libstdc++6-mips64el-cross (8.3.0-7cross1) ... Setting up cpp-mips64el-linux-gnuabi64 (4:8.3.0-1) ... Setting up libgcc-8-dev-mips64el-cross (8.3.0-7cross1) ... Setting up libxml-sax-perl (1.00+dfsg-1) ... update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::PurePerl with priority 10... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Creating config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up libxml-libxml-perl (2.0134+dfsg-1) ... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX::Parser with priority 50... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX with priority 50... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up libstdc++-8-dev-mips64el-cross (8.3.0-7cross1) ... Setting up gcc-8-mips64el-linux-gnuabi64 (8.3.0-7cross1) ... Setting up g++-8-mips64el-linux-gnuabi64 (8.3.0-7cross1) ... Setting up libxml-simple-perl (2.25-1) ... Setting up gcc-mips64el-linux-gnuabi64 (4:8.3.0-1) ... Setting up g++-mips64el-linux-gnuabi64 (4:8.3.0-1) ... Setting up libconfig-auto-perl (0.44-1) ... Setting up libdebian-dpkgcross-perl (2.6.15-2) ... Setting up dpkg-cross (2.6.15-2) ... Setting up crossbuild-essential-mips64el (12.6) ... Setting up sbuild-build-depends-core-dummy:mips64el (0.invalid.0) ... Processing triggers for libc-bin (2.28-10) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (mips64el included in any all) Setup apt archive ----------------- dpkg-deb: building package 'sbuild-build-depends-essential-dummy' in '/<>/resolver-URaN8F/apt_archive/sbuild-build-depends-essential-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-essential-dummy dpkg-scanpackages: info: Wrote 2 entries to output Packages file. Ign:1 copy:/<>/resolver-URaN8F/apt_archive ./ InRelease Get:2 copy:/<>/resolver-URaN8F/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-URaN8F/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-URaN8F/apt_archive ./ Sources [484 B] Get:5 copy:/<>/resolver-URaN8F/apt_archive ./ Packages [572 B] Fetched 2019 B in 0s (137 kB/s) Reading package lists... Reading package lists... Install essential 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-essential-dummy:mips64el 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 844 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-URaN8F/apt_archive ./ sbuild-build-depends-essential-dummy 0.invalid.0 [844 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 844 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-essential-dummy:mips64el. (Reading database ... 15114 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-essential-dummy_0.invalid.0_mips64el.deb ... Unpacking sbuild-build-depends-essential-dummy:mips64el (0.invalid.0) ... Setting up sbuild-build-depends-essential-dummy:mips64el (0.invalid.0) ... +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: libc-dev, libstdc++-dev, debhelper (>= 11~), zlib1g-dev, texlive-latex-base, texlive-latex-recommended Filtered Build-Depends: libc-dev, libstdc++-dev, debhelper (>= 11~), zlib1g-dev, texlive-latex-base, texlive-latex-recommended dpkg-deb: building package 'sbuild-build-depends-velvet-dummy' in '/<>/resolver-URaN8F/apt_archive/sbuild-build-depends-velvet-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-essential-dummy sbuild-build-depends-velvet-dummy dpkg-scanpackages: info: Wrote 3 entries to output Packages file. Ign:1 copy:/<>/resolver-URaN8F/apt_archive ./ InRelease Get:2 copy:/<>/resolver-URaN8F/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-URaN8F/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-URaN8F/apt_archive ./ Sources [662 B] Get:5 copy:/<>/resolver-URaN8F/apt_archive ./ Packages [748 B] Fetched 2373 B in 0s (128 kB/s) Reading package lists... Reading package lists... Install velvet 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 automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism dwz fontconfig-config fonts-dejavu-core fonts-lmodern gcc-8-base:mips64el gettext gettext-base groff-base intltool-debian libarchive-zip-perl libatomic1:mips64el libavahi-client3 libavahi-common-data libavahi-common3 libbrotli1 libbsd0 libc6:mips64el libc6-dev:mips64el libcairo2 libcroco3 libcups2 libcupsimage2 libdbus-1-3 libelf1 libexpat1 libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libgcc-8-dev:mips64el libgcc1:mips64el libglib2.0-0 libgomp1:mips64el libgraphite2-3 libgs9 libgs9-common libgssapi-krb5-2 libharfbuzz-icu0 libharfbuzz0b libice6 libidn11 libijs-0.35 libjbig0 libjbig2dec0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkpathsea6 libkrb5-3 libkrb5support0 liblcms2-2 libncurses6 libopenjp2-7 libpaper-utils libpaper1 libpipeline1 libpixman-1-0 libpng16-16 libpotrace0 libptexenc1 libsigsegv2 libsm6 libssl1.1 libstdc++-8-dev:mips64el libstdc++6:mips64el libsynctex2 libteckit0 libtexlua52 libtexlua53 libtexluajit2 libtiff5 libtool libuchardet0 libwebp6 libwoff1 libx11-6 libx11-data libxau6 libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxi6 libxmu6 libxpm4 libxrender1 libxt6 libxxhash0 libzzip-0-13 linux-libc-dev:mips64el lsb-base m4 man-db po-debconf poppler-data t1utils tex-common texlive-base texlive-binaries texlive-latex-base texlive-latex-recommended x11-common xdg-utils zlib1g:mips64el zlib1g-dev:mips64el Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff glibc-doc:mips64el libc-l10n:mips64el locales:mips64el manpages-dev:mips64el cups-common krb5-doc krb5-user liblcms2-utils libstdc++-8-doc:mips64el libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl poppler-utils ghostscript fonts-japanese-mincho | fonts-ipafont-mincho fonts-japanese-gothic | fonts-ipafont-gothic fonts-arphic-ukai fonts-arphic-uming fonts-nanum gv | postscript-viewer perl-tk xpdf-reader | pdf-viewer texlive-latex-base-doc texlive-latex-recommended-doc texlive-pstricks Recommended packages: curl | wget | lynx libidn2-0:mips64el libcupsfilters1 dbus libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs fonts-droid-fallback krb5-locales libgpm2 libltdl-dev libmail-sendmail-perl lmodern libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism dwz fontconfig-config fonts-dejavu-core fonts-lmodern gcc-8-base:mips64el gettext gettext-base groff-base intltool-debian libarchive-zip-perl libatomic1:mips64el libavahi-client3 libavahi-common-data libavahi-common3 libbrotli1 libbsd0 libc6:mips64el libc6-dev:mips64el libcairo2 libcroco3 libcups2 libcupsimage2 libdbus-1-3 libelf1 libexpat1 libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libgcc-8-dev:mips64el libgcc1:mips64el libglib2.0-0 libgomp1:mips64el libgraphite2-3 libgs9 libgs9-common libgssapi-krb5-2 libharfbuzz-icu0 libharfbuzz0b libice6 libidn11 libijs-0.35 libjbig0 libjbig2dec0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkpathsea6 libkrb5-3 libkrb5support0 liblcms2-2 libncurses6 libopenjp2-7 libpaper-utils libpaper1 libpipeline1 libpixman-1-0 libpng16-16 libpotrace0 libptexenc1 libsigsegv2 libsm6 libssl1.1 libstdc++-8-dev:mips64el libstdc++6:mips64el libsynctex2 libteckit0 libtexlua52 libtexlua53 libtexluajit2 libtiff5 libtool libuchardet0 libwebp6 libwoff1 libx11-6 libx11-data libxau6 libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxi6 libxmu6 libxpm4 libxrender1 libxt6 libxxhash0 libzzip-0-13 linux-libc-dev:mips64el lsb-base m4 man-db po-debconf poppler-data sbuild-build-depends-velvet-dummy:mips64el t1utils tex-common texlive-base texlive-binaries texlive-latex-base texlive-latex-recommended x11-common xdg-utils zlib1g:mips64el zlib1g-dev:mips64el 0 upgraded, 115 newly installed, 0 to remove and 0 not upgraded. Need to get 93.7 MB of archives. After this operation, 327 MB of additional disk space will be used. Get:1 copy:/<>/resolver-URaN8F/apt_archive ./ sbuild-build-depends-velvet-dummy 0.invalid.0 [908 B] Get:2 http://debian.oregonstate.edu/debian unstable/main amd64 libbsd0 amd64 0.9.1-2 [99.5 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 bsdmainutils amd64 11.1.2+b1 [191 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 groff-base amd64 1.22.4-3 [916 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 libpipeline1 amd64 1.5.1-2 [31.2 kB] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 man-db amd64 2.8.5-2 [1274 kB] Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 poppler-data all 0.4.9-2 [1473 kB] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 tex-common all 6.11 [53.1 kB] Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 gettext-base amd64 0.19.8.1-9 [123 kB] Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get:12 http://debian.oregonstate.edu/debian unstable/main amd64 m4 amd64 1.4.18-2 [203 kB] Get:13 http://debian.oregonstate.edu/debian unstable/main amd64 autoconf all 2.69-11 [341 kB] Get:14 http://debian.oregonstate.edu/debian unstable/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get:15 http://debian.oregonstate.edu/debian unstable/main amd64 automake all 1:1.16.1-4 [771 kB] Get:16 http://debian.oregonstate.edu/debian unstable/main amd64 autopoint all 0.19.8.1-9 [434 kB] Get:17 http://debian.oregonstate.edu/debian unstable/main amd64 libtool all 2.4.6-10 [547 kB] Get:18 http://debian.oregonstate.edu/debian unstable/main amd64 dh-autoreconf all 19 [16.9 kB] Get:19 http://debian.oregonstate.edu/debian unstable/main amd64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get:20 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get:21 http://debian.oregonstate.edu/debian unstable/main amd64 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get:22 http://debian.oregonstate.edu/debian unstable/main amd64 libelf1 amd64 0.176-1 [160 kB] Get:23 http://debian.oregonstate.edu/debian unstable/main amd64 dwz amd64 0.12-3 [78.0 kB] Get:24 http://debian.oregonstate.edu/debian unstable/main amd64 libglib2.0-0 amd64 2.58.3-1 [1258 kB] Get:25 http://debian.oregonstate.edu/debian unstable/main amd64 libcroco3 amd64 0.6.12-3 [145 kB] Get:26 http://debian.oregonstate.edu/debian unstable/main amd64 libncurses6 amd64 6.1+20181013-2 [102 kB] Get:27 http://debian.oregonstate.edu/debian unstable/main amd64 gettext amd64 0.19.8.1-9 [1303 kB] Get:28 http://debian.oregonstate.edu/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get:29 http://debian.oregonstate.edu/debian unstable/main amd64 po-debconf all 1.0.21 [248 kB] Get:30 http://debian.oregonstate.edu/debian unstable/main amd64 debhelper all 12.1.1 [1016 kB] Get:31 http://debian.oregonstate.edu/debian unstable/main amd64 fonts-dejavu-core all 2.37-1 [1068 kB] Get:32 http://debian.oregonstate.edu/debian unstable/main amd64 fontconfig-config all 2.13.1-2 [280 kB] Get:33 http://debian.oregonstate.edu/debian unstable/main amd64 fonts-lmodern all 2.004.5-6 [4539 kB] Get:34 http://debian.oregonstate.edu/debian unstable/main mips64el gcc-8-base mips64el 8.3.0-7 [191 kB] Get:35 http://debian.oregonstate.edu/debian unstable/main mips64el libgcc1 mips64el 1:8.3.0-7 [68.5 kB] Get:36 http://debian.oregonstate.edu/debian unstable/main mips64el libc6 mips64el 2.28-10 [2562 kB] Get:37 http://debian.oregonstate.edu/debian unstable/main mips64el libatomic1 mips64el 8.3.0-7 [7432 B] Get:38 http://debian.oregonstate.edu/debian unstable/main amd64 libavahi-common-data amd64 0.7-4+b1 [122 kB] Get:39 http://debian.oregonstate.edu/debian unstable/main amd64 libavahi-common3 amd64 0.7-4+b1 [54.6 kB] Get:40 http://debian.oregonstate.edu/debian unstable/main amd64 libdbus-1-3 amd64 1.12.12-1 [212 kB] Get:41 http://debian.oregonstate.edu/debian unstable/main amd64 libavahi-client3 amd64 0.7-4+b1 [58.1 kB] Get:42 http://debian.oregonstate.edu/debian unstable/main amd64 libbrotli1 amd64 1.0.7-2 [270 kB] Get:43 http://debian.oregonstate.edu/debian unstable/main mips64el linux-libc-dev mips64el 4.19.37-1 [1178 kB] Get:44 http://debian.oregonstate.edu/debian unstable/main mips64el libc6-dev mips64el 2.28-10 [2513 kB] Get:45 http://debian.oregonstate.edu/debian unstable/main amd64 libexpat1 amd64 2.2.6-1 [105 kB] Get:46 http://debian.oregonstate.edu/debian unstable/main amd64 libpng16-16 amd64 1.6.36-6 [292 kB] Get:47 http://debian.oregonstate.edu/debian unstable/main amd64 libfreetype6 amd64 2.9.1-3 [379 kB] Get:48 http://debian.oregonstate.edu/debian unstable/main amd64 libfontconfig1 amd64 2.13.1-2 [346 kB] Get:49 http://debian.oregonstate.edu/debian unstable/main amd64 libpixman-1-0 amd64 0.36.0-1 [537 kB] Get:50 http://debian.oregonstate.edu/debian unstable/main amd64 libxau6 amd64 1:1.0.8-1+b2 [19.9 kB] Get:51 http://debian.oregonstate.edu/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get:52 http://debian.oregonstate.edu/debian unstable/main amd64 libxcb1 amd64 1.13.1-2 [137 kB] Get:53 http://debian.oregonstate.edu/debian unstable/main amd64 libx11-data all 2:1.6.7-1 [298 kB] Get:54 http://debian.oregonstate.edu/debian unstable/main amd64 libx11-6 amd64 2:1.6.7-1 [754 kB] Get:55 http://debian.oregonstate.edu/debian unstable/main amd64 libxcb-render0 amd64 1.13.1-2 [109 kB] Get:56 http://debian.oregonstate.edu/debian unstable/main amd64 libxcb-shm0 amd64 1.13.1-2 [99.2 kB] Get:57 http://debian.oregonstate.edu/debian unstable/main amd64 libxext6 amd64 2:1.3.3-1+b2 [52.5 kB] Get:58 http://debian.oregonstate.edu/debian unstable/main amd64 libxrender1 amd64 1:0.9.10-1 [33.0 kB] Get:59 http://debian.oregonstate.edu/debian unstable/main amd64 libcairo2 amd64 1.16.0-4 [689 kB] Get:60 http://debian.oregonstate.edu/debian unstable/main amd64 libkeyutils1 amd64 1.6-6 [15.0 kB] Get:61 http://debian.oregonstate.edu/debian unstable/main amd64 libkrb5support0 amd64 1.17-2 [65.6 kB] Get:62 http://debian.oregonstate.edu/debian unstable/main amd64 libk5crypto3 amd64 1.17-2 [121 kB] Get:63 http://debian.oregonstate.edu/debian unstable/main amd64 libssl1.1 amd64 1.1.1b-2 [1530 kB] Get:64 http://debian.oregonstate.edu/debian unstable/main amd64 libkrb5-3 amd64 1.17-2 [368 kB] Get:65 http://debian.oregonstate.edu/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.17-2 [158 kB] Get:66 http://debian.oregonstate.edu/debian unstable/main amd64 libcups2 amd64 2.2.10-6 [324 kB] Get:67 http://debian.oregonstate.edu/debian unstable/main amd64 libcupsimage2 amd64 2.2.10-6 [132 kB] Get:68 http://debian.oregonstate.edu/debian unstable/main mips64el libgomp1 mips64el 8.3.0-7 [67.3 kB] Get:69 http://debian.oregonstate.edu/debian unstable/main mips64el libgcc-8-dev mips64el 8.3.0-7 [234 kB] Get:70 http://debian.oregonstate.edu/debian unstable/main amd64 libgraphite2-3 amd64 1.3.13-7 [80.7 kB] Get:71 http://debian.oregonstate.edu/debian unstable/main amd64 libgs9-common all 9.27~dfsg-2 [5135 kB] Get:72 http://debian.oregonstate.edu/debian unstable/main amd64 libidn11 amd64 1.33-2.2 [116 kB] Get:73 http://debian.oregonstate.edu/debian unstable/main amd64 libijs-0.35 amd64 0.35-13 [18.5 kB] Get:74 http://debian.oregonstate.edu/debian unstable/main amd64 libjbig2dec0 amd64 0.16-1 [62.0 kB] Get:75 http://debian.oregonstate.edu/debian unstable/main amd64 libjpeg62-turbo amd64 1:1.5.2-2+b1 [134 kB] Get:76 http://debian.oregonstate.edu/debian unstable/main amd64 liblcms2-2 amd64 2.9-3 [145 kB] Get:77 http://debian.oregonstate.edu/debian unstable/main amd64 libopenjp2-7 amd64 2.3.0-2 [158 kB] Get:78 http://debian.oregonstate.edu/debian unstable/main amd64 libpaper1 amd64 1.1.26 [20.8 kB] Get:79 http://debian.oregonstate.edu/debian unstable/main amd64 libjbig0 amd64 2.1-3.1+b2 [31.0 kB] Get:80 http://debian.oregonstate.edu/debian unstable/main amd64 libwebp6 amd64 0.6.1-2 [263 kB] Get:81 http://debian.oregonstate.edu/debian unstable/main amd64 libtiff5 amd64 4.0.10-4 [257 kB] Get:82 http://debian.oregonstate.edu/debian unstable/main amd64 libgs9 amd64 9.27~dfsg-2 [2195 kB] Get:83 http://debian.oregonstate.edu/debian unstable/main amd64 libharfbuzz0b amd64 2.3.1-1 [1187 kB] Get:84 http://debian.oregonstate.edu/debian unstable/main amd64 libharfbuzz-icu0 amd64 2.3.1-1 [834 kB] Get:85 http://debian.oregonstate.edu/debian unstable/main amd64 lsb-base all 10.2019031300 [28.3 kB] Get:86 http://debian.oregonstate.edu/debian unstable/main amd64 x11-common all 1:7.7+19 [251 kB] Get:87 http://debian.oregonstate.edu/debian unstable/main amd64 libice6 amd64 2:1.0.9-2 [58.7 kB] Get:88 http://debian.oregonstate.edu/debian unstable/main amd64 libkpathsea6 amd64 2018.20181218.49446-2 [167 kB] Get:89 http://debian.oregonstate.edu/debian unstable/main amd64 libpaper-utils amd64 1.1.26 [17.9 kB] Get:90 http://debian.oregonstate.edu/debian unstable/main amd64 libpotrace0 amd64 1.15-1 [26.3 kB] Get:91 http://debian.oregonstate.edu/debian unstable/main amd64 libptexenc1 amd64 2018.20181218.49446-2 [61.2 kB] Get:92 http://debian.oregonstate.edu/debian unstable/main amd64 libsm6 amd64 2:1.2.3-1 [35.1 kB] Get:93 http://debian.oregonstate.edu/debian unstable/main mips64el libstdc++6 mips64el 8.3.0-7 [348 kB] Get:94 http://debian.oregonstate.edu/debian unstable/main mips64el libstdc++-8-dev mips64el 8.3.0-7 [1573 kB] Get:95 http://debian.oregonstate.edu/debian unstable/main amd64 libsynctex2 amd64 2018.20181218.49446-2 [80.7 kB] Get:96 http://debian.oregonstate.edu/debian unstable/main amd64 libteckit0 amd64 2.5.8+ds2-5 [318 kB] Get:97 http://debian.oregonstate.edu/debian unstable/main amd64 libtexlua52 amd64 2018.20181218.49446-2 [113 kB] Get:98 http://debian.oregonstate.edu/debian unstable/main amd64 libtexlua53 amd64 2018.20181218.49446-2 [126 kB] Get:99 http://debian.oregonstate.edu/debian unstable/main amd64 libtexluajit2 amd64 2018.20181218.49446-2 [256 kB] Get:100 http://debian.oregonstate.edu/debian unstable/main amd64 libwoff1 amd64 1.0.2-1 [43.2 kB] Get:101 http://debian.oregonstate.edu/debian unstable/main amd64 libxt6 amd64 1:1.1.5-1+b3 [190 kB] Get:102 http://debian.oregonstate.edu/debian unstable/main amd64 libxmu6 amd64 2:1.1.2-2+b3 [60.8 kB] Get:103 http://debian.oregonstate.edu/debian unstable/main amd64 libxpm4 amd64 1:3.5.12-1 [49.1 kB] Get:104 http://debian.oregonstate.edu/debian unstable/main amd64 libxaw7 amd64 2:1.0.13-1+b2 [201 kB] Get:105 http://debian.oregonstate.edu/debian unstable/main amd64 libxi6 amd64 2:1.7.9-1 [82.6 kB] Get:106 http://debian.oregonstate.edu/debian unstable/main amd64 libxxhash0 amd64 0.6.5-3 [7188 B] Get:107 http://debian.oregonstate.edu/debian unstable/main amd64 libzzip-0-13 amd64 0.13.62-3.2 [55.4 kB] Get:108 http://debian.oregonstate.edu/debian unstable/main amd64 t1utils amd64 1.41-3 [62.3 kB] Get:109 http://debian.oregonstate.edu/debian unstable/main amd64 texlive-binaries amd64 2018.20181218.49446-2 [11.4 MB] Get:110 http://debian.oregonstate.edu/debian unstable/main amd64 xdg-utils all 1.1.3-1 [73.3 kB] Get:111 http://debian.oregonstate.edu/debian unstable/main amd64 texlive-base all 2018.20190227-2 [19.7 MB] Get:112 http://debian.oregonstate.edu/debian unstable/main amd64 texlive-latex-base all 2018.20190227-2 [984 kB] Get:113 http://debian.oregonstate.edu/debian unstable/main amd64 texlive-latex-recommended all 2018.20190227-2 [15.2 MB] Get:114 http://debian.oregonstate.edu/debian unstable/main mips64el zlib1g mips64el 1:1.2.11.dfsg-1 [91.1 kB] Get:115 http://debian.oregonstate.edu/debian unstable/main mips64el zlib1g-dev mips64el 1:1.2.11.dfsg-1 [215 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 93.7 MB in 1s (63.8 MB/s) Selecting previously unselected package libbsd0:amd64. 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Setting up libarchive-zip-perl (1.64-1) ... Setting up libglib2.0-0:amd64 (2.58.3-1) ... No schema files found: doing nothing. Setting up libssl1.1:amd64 (1.1.1b-2) ... Setting up libijs-0.35:amd64 (0.35-13) ... Setting up libtexluajit2:amd64 (2018.20181218.49446-2) ... Setting up libbrotli1:amd64 (1.0.7-2) ... Setting up x11-common (1:7.7+19) ... update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults invoke-rc.d: could not determine current runlevel All runlevel operations denied by policy invoke-rc.d: policy-rc.d denied execution of start. Setting up linux-libc-dev:mips64el (4.19.37-1) ... Setting up gettext-base (0.19.8.1-9) ... Setting up libzzip-0-13:amd64 (0.13.62-3.2) ... Setting up libpaper-utils (1.1.26) ... Setting up libjbig0:amd64 (2.1-3.1+b2) ... Setting up poppler-data (0.4.9-2) ... Setting up libkrb5support0:amd64 (1.17-2) ... Setting up tex-common (6.11) ... update-language: texlive-base not installed and configured, doing nothing! Setting up autotools-dev (20180224.1) ... Setting up libjpeg62-turbo:amd64 (1:1.5.2-2+b1) ... Setting up libx11-data (2:1.6.7-1) ... Setting up libjbig2dec0:amd64 (0.16-1) ... Setting up libidn11:amd64 (1.33-2.2) ... Setting up libteckit0:amd64 (2.5.8+ds2-5) ... Setting up libavahi-common-data:amd64 (0.7-4+b1) ... Setting up libncurses6:amd64 (6.1+20181013-2) ... Setting up libdbus-1-3:amd64 (1.12.12-1) ... Setting up libsigsegv2:amd64 (2.12-2) ... Setting up t1utils (1.41-3) ... Setting up libpng16-16:amd64 (1.6.36-6) ... Setting up gcc-8-base:mips64el (8.3.0-7) ... Setting up autopoint (0.19.8.1-9) ... Setting up libwebp6:amd64 (0.6.1-2) ... Setting up libcroco3:amd64 (0.6.12-3) ... Setting up fonts-dejavu-core (2.37-1) ... Setting up libk5crypto3:amd64 (1.17-2) ... Setting up libkpathsea6:amd64 (2018.20181218.49446-2) ... Setting up libxxhash0:amd64 (0.6.5-3) ... Setting up libuchardet0:amd64 (0.0.6-3) ... Setting up fonts-lmodern (2.004.5-6) ... Setting up libopenjp2-7:amd64 (2.3.0-2) ... Setting up libkrb5-3:amd64 (1.17-2) ... Setting up libtiff5:amd64 (4.0.10-4) ... Setting up libbsd0:amd64 (0.9.1-2) ... Setting up libelf1:amd64 (0.176-1) ... Setting up xdg-utils (1.1.3-1) ... Setting up libsynctex2:amd64 (2018.20181218.49446-2) ... Setting up libpotrace0:amd64 (1.15-1) ... Setting up libfile-stripnondeterminism-perl (1.1.2-1) ... Setting up libice6:amd64 (2:1.0.9-2) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up libxcb1:amd64 (1.13.1-2) ... Setting up gettext (0.19.8.1-9) ... Setting up libwoff1:amd64 (1.0.2-1) ... Setting up libtool (2.4.6-10) ... Setting up libxcb-render0:amd64 (1.13.1-2) ... Setting up fontconfig-config (2.13.1-2) ... Setting up libavahi-common3:amd64 (0.7-4+b1) ... Setting up m4 (1.4.18-2) ... Setting up libxcb-shm0:amd64 (1.13.1-2) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libptexenc1:amd64 (2018.20181218.49446-2) ... Setting up libfreetype6:amd64 (2.9.1-3) ... Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libgssapi-krb5-2:amd64 (1.17-2) ... Setting up autoconf (2.69-11) ... Setting up dwz (0.12-3) ... Setting up groff-base (1.22.4-3) ... Setting up libx11-6:amd64 (2:1.6.7-1) ... Setting up libharfbuzz0b:amd64 (2.3.1-1) ... Setting up libfontconfig1:amd64 (2.13.1-2) ... Setting up libsm6:amd64 (2:1.2.3-1) ... Setting up libavahi-client3:amd64 (0.7-4+b1) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libharfbuzz-icu0:amd64 (2.3.1-1) ... Setting up libxpm4:amd64 (1:3.5.12-1) ... Setting up libxrender1:amd64 (1:0.9.10-1) ... Setting up po-debconf (1.0.21) ... Setting up libxext6:amd64 (2:1.3.3-1+b2) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:amd64 (1.16.0-4) ... Setting up libxt6:amd64 (1:1.1.5-1+b3) ... Setting up libcups2:amd64 (2.2.10-6) ... Setting up libxmu6:amd64 (2:1.1.2-2+b3) ... Setting up libxi6:amd64 (2:1.7.9-1) ... Setting up libxaw7:amd64 (2:1.0.13-1+b2) ... Setting up libcupsimage2:amd64 (2.2.10-6) ... Setting up libgs9:amd64 (9.27~dfsg-2) ... Setting up texlive-binaries (2018.20181218.49446-2) ... update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode Setting up texlive-base (2018.20190227-2) ... tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/config/pdftexconfig.tex tl-paper: setting paper size for dvipdfmx to letter: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg tl-paper: setting paper size for dvips to letter: /var/lib/texmf/dvips/config/config-paper.ps tl-paper: setting paper size for pdftex to letter: /var/lib/texmf/tex/generic/config/pdftexconfig.tex tl-paper: setting paper size for xdvi to letter: /var/lib/texmf/xdvi/XDvi-paper Setting up texlive-latex-base (2018.20190227-2) ... Setting up texlive-latex-recommended (2018.20190227-2) ... Setting up libc6:mips64el (2.28-10) ... Setting up libc6-dev:mips64el (2.28-10) ... Setting up libgcc1:mips64el (1:8.3.0-7) ... Setting up zlib1g:mips64el (1:1.2.11.dfsg-1) ... Setting up libgomp1:mips64el (8.3.0-7) ... Setting up dh-autoreconf (19) ... Setting up libatomic1:mips64el (8.3.0-7) ... Setting up libgcc-8-dev:mips64el (8.3.0-7) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Setting up zlib1g-dev:mips64el (1:1.2.11.dfsg-1) ... Setting up libstdc++6:mips64el (8.3.0-7) ... Setting up libstdc++-8-dev:mips64el (8.3.0-7) ... Setting up debhelper (12.1.1) ... Setting up sbuild-build-depends-velvet-dummy:mips64el (0.invalid.0) ... Processing triggers for libc-bin (2.28-10) ... Processing triggers for tex-common (6.11) ... Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Building format(s) --all. This may take some time... done. +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.9.0-8-amd64 amd64 (x86_64) Toolchain package versions: binutils_2.31.1-16 dpkg-dev_1.19.6 g++-8_8.3.0-7 gcc-8_8.3.0-7 libc6-dev_2.28-10 libstdc++-8-dev_8.3.0-7 libstdc++-8-dev-mips64el-cross_8.3.0-7cross1 libstdc++6_8.3.0-7 libstdc++6-mips64el-cross_8.3.0-7cross1 linux-libc-dev_4.19.37-1 Package versions: adduser_3.118 apt_1.8.1 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_10.2 base-passwd_3.5.46 bash_5.0-4 binutils_2.31.1-16 binutils-common_2.31.1-16 binutils-mips64el-linux-gnuabi64_2.31.1-16 binutils-x86-64-linux-gnu_2.31.1-16 bsdmainutils_11.1.2+b1 bsdutils_1:2.33.1-0.1 build-essential_12.6 bzip2_1.0.6-9 coreutils_8.30-3 cpp_4:8.3.0-1 cpp-8_8.3.0-7 cpp-8-mips64el-linux-gnuabi64_8.3.0-7cross1 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libtexlua52_2018.20181218.49446-2 libtexlua53_2018.20181218.49446-2 libtexluajit2_2018.20181218.49446-2 libtiff5_4.0.10-4 libtinfo6_6.1+20181013-2 libtool_2.4.6-10 libtsan0_8.3.0-7 libubsan1_8.3.0-7 libuchardet0_0.0.6-3 libudev1_241-3 libunistring2_0.9.10-1 libuuid1_2.33.1-0.1 libwebp6_0.6.1-2 libwoff1_1.0.2-1 libx11-6_2:1.6.7-1 libx11-data_2:1.6.7-1 libxau6_1:1.0.8-1+b2 libxaw7_2:1.0.13-1+b2 libxcb-render0_1.13.1-2 libxcb-shm0_1.13.1-2 libxcb1_1.13.1-2 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.3-1+b2 libxi6_2:1.7.9-1 libxml-libxml-perl_2.0134+dfsg-1 libxml-namespacesupport-perl_1.12-1 libxml-sax-base-perl_1.09-1 libxml-sax-perl_1.00+dfsg-1 libxml-simple-perl_2.25-1 libxml2_2.9.4+dfsg1-7+b3 libxmu6_2:1.1.2-2+b3 libxpm4_1:3.5.12-1 libxrender1_1:0.9.10-1 libxt6_1:1.1.5-1+b3 libxxhash0_0.6.5-3 libyaml-perl_1.27-1 libzstd1_1.3.8+dfsg-3 libzzip-0-13_0.13.62-3.2 linux-libc-dev_4.19.37-1 linux-libc-dev-mips64el-cross_4.19.28-2cross2 login_1:4.5-1.1 lsb-base_10.2019031300 m4_1.4.18-2 make_4.2.1-1.2 man-db_2.8.5-2 mawk_1.3.3-17+b3 mount_2.33.1-0.1 ncurses-base_6.1+20181013-2 ncurses-bin_6.1+20181013-2 passwd_1:4.5-1.1 patch_2.7.6-3 perl_5.28.1-6 perl-base_5.28.1-6 perl-modules-5.28_5.28.1-6 po-debconf_1.0.21 poppler-data_0.4.9-2 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-essential-dummy_0.invalid.0 sbuild-build-depends-velvet-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12 sysvinit-utils_2.93-8 t1utils_1.41-3 tar_1.30+dfsg-6 tex-common_6.11 texlive-base_2018.20190227-2 texlive-binaries_2018.20181218.49446-2 texlive-latex-base_2018.20190227-2 texlive-latex-recommended_2018.20190227-2 tzdata_2019a-1 ucf_3.0038+nmu1 util-linux_2.33.1-0.1 x11-common_1:7.7+19 xdg-utils_1.1.3-1 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-1 zlib1g-dev_1:1.2.11.dfsg-1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Thu Jul 5 08:47:28 2018 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./velvet_1.2.10+dfsg1-5.dsc dpkg-source: info: extracting velvet in /<>/velvet-1.2.10+dfsg1 dpkg-source: info: unpacking velvet_1.2.10+dfsg1.orig.tar.xz dpkg-source: info: unpacking velvet_1.2.10+dfsg1-5.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying include_debians_zlib.patch dpkg-source: info: applying shuffleSequences_fasta.patch dpkg-source: info: applying fix-perl-path.patch dpkg-source: info: applying 0001-isCreateBinary-should-not-be-inline.patch dpkg-source: info: applying hardening.patch dpkg-source: info: applying spelling.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf CONFIG_SITE=/etc/dpkg-cross/cross-config.mips64el DEB_BUILD_OPTIONS=nocheck HOME=/sbuild-nonexistent LANG=en_US.UTF-8 LC_ALL=POSIX LOGNAME=helmut PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=unstable-amd64-sbuild SCHROOT_CHROOT_NAME=unstable-amd64-sbuild SCHROOT_COMMAND=env SCHROOT_GID=1003 SCHROOT_GROUP=helmut SCHROOT_SESSION_ID=unstable-amd64-sbuild-bc1b8b87-8af5-4d41-9a1d-447a48fecd9f SCHROOT_UID=1003 SCHROOT_USER=helmut SHELL=/bin/sh USER=helmut dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package velvet dpkg-buildpackage: info: source version 1.2.10+dfsg1-5 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-architecture: warning: specified GNU system type mips64el-linux-gnuabi64 does not match CC system type x86_64-linux-gnu, try setting a correct CC environment variable dpkg-source --before-build . dpkg-buildpackage: info: host architecture mips64el fakeroot debian/rules clean dh clean --no-parallel debian/rules override_dh_auto_clean make[1]: Entering directory '/<>/velvet-1.2.10+dfsg1' # If tarball was not pre-cleaned this will do it. dh_auto_clean make -j1 clean make[2]: Entering directory '/<>/velvet-1.2.10+dfsg1' rm obj/*.o obj/dbg/*.o ./velvet* rm: cannot remove 'obj/*.o': No such file or directory rm: cannot remove 'obj/dbg/*.o': No such file or directory rm: cannot remove './velvet*': No such file or directory make[2]: [Makefile:45: clean] Error 1 (ignored) rm -f doc/manual_src/Manual.toc doc/manual_src/Manual.aux doc/manual_src/Manual.out doc/manual_src/Manual.log rm -f doc/manual_src/Columbus_manual.aux doc/manual_src/Columbus_manual.out doc/manual_src/Columbus_manual.log make[2]: Leaving directory '/<>/velvet-1.2.10+dfsg1' rm -rf zlib rm -rf third-party rm -rf debian.upstream rm -f *.pdf find -name '._*' -delete rm -rf contrib/MetaVelvet* rm -rf contrib/VelvetOptimiser* make[1]: Leaving directory '/<>/velvet-1.2.10+dfsg1' dh_clean debian/rules build-arch dh build-arch --no-parallel dh_update_autotools_config -a dh_autoreconf -a dh_auto_configure -a debian/rules override_dh_auto_build make[1]: Entering directory '/<>/velvet-1.2.10+dfsg1' touch zlib #Make _long version dh_auto_build -- LONGSEQUENCES=Y OPENMP=Y velveth velvetg OPENMP=1 CPPFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2" CFLAGS="-g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security" LDFLAGS="-Wl,-z,relro" make -j1 "INSTALL=install --strip-program=true" PKG_CONFIG=mips64el-linux-gnuabi64-pkg-config CXX=mips64el-linux-gnuabi64-g\+\+ CC=mips64el-linux-gnuabi64-gcc LONGSEQUENCES=Y OPENMP=Y velveth velvetg OPENMP=1 "CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2" "CFLAGS=-g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security" LDFLAGS=-Wl,-z,relro make[2]: Entering directory '/<>/velvet-1.2.10+dfsg1' rm obj/*.o obj/dbg/*.o rm: cannot remove 'obj/*.o': No such file or directory rm: cannot remove 'obj/dbg/*.o': No such file or directory make[2]: [Makefile:50: cleanobj] Error 1 (ignored) mkdir -p obj mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/tightString.c -o obj/tightString.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/run.c -o obj/run.o In file included from src/run.h:34, from src/run.c:31: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/splay.c -o obj/splay.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/splayTable.c -o obj/splayTable.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/graph.c -o obj/graph.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/run2.c -o obj/run2.o In file included from src/run.h:34, from src/run2.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/fibHeap.c -o obj/fibHeap.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/fib.c -o obj/fib.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/concatenatedGraph.c -o obj/concatenatedGraph.o In file included from src/concatenatedGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/passageMarker.c -o obj/passageMarker.o In file included from src/passageMarker.c:29: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/graphStats.c -o obj/graphStats.o In file included from src/graphStats.c:28: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/correctedGraph.c -o obj/correctedGraph.o In file included from src/correctedGraph.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/dfib.c -o obj/dfib.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/dfibHeap.c -o obj/dfibHeap.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/recycleBin.c -o obj/recycleBin.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/readSet.c -o obj/readSet.o src/readSet.c: In function 'readFastXFile': src/readSet.c:641:21: warning: assignment to 'gzFile' {aka 'struct gzFile_s *'} from incompatible pointer type 'AutoFile *' {aka 'struct *'} [-Wincompatible-pointer-types] file.gzFile = file.autoFile = NULL; ^ src/readSet.c: In function 'readFastXPair': src/readSet.c:680:22: warning: assignment to 'gzFile' {aka 'struct gzFile_s *'} from incompatible pointer type 'AutoFile *' {aka 'struct *'} [-Wincompatible-pointer-types] file1.gzFile = file1.autoFile = NULL; ^ src/readSet.c:681:22: warning: assignment to 'gzFile' {aka 'struct gzFile_s *'} from incompatible pointer type 'AutoFile *' {aka 'struct *'} [-Wincompatible-pointer-types] file2.gzFile = file2.autoFile = NULL; ^ src/readSet.c: In function 'importReadSet': src/readSet.c:1613:4: warning: 'strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(sequence + bpCount, line, lineLength); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/readSet.c:1612:17: note: length computed here lineLength = strlen(line) - 1; ^~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/binarySequences.c -o obj/binarySequences.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/shortReadPairs.c -o obj/shortReadPairs.o In file included from src/shortReadPairs.c:27: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/locallyCorrectedGraph.c -o obj/locallyCorrectedGraph.o In file included from src/locallyCorrectedGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/graphReConstruction.c -o obj/graphReConstruction.o In file included from src/graphReConstruction.c:33: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/roadMap.c -o obj/roadMap.o In file included from src/roadMap.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/preGraph.c -o obj/preGraph.o In file included from src/run.h:34, from src/preGraph.c:35: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/preGraphConstruction.c -o obj/preGraphConstruction.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/readCoherentGraph.c -o obj/readCoherentGraph.o In file included from src/readCoherentGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/utility.c -o obj/utility.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/kmer.c -o obj/kmer.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/scaffold.c -o obj/scaffold.o In file included from src/scaffold.c:32: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/kmerOccurenceTable.c -o obj/kmerOccurenceTable.o In file included from src/kmerOccurenceTable.c:27: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/allocArray.c -o obj/allocArray.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/autoOpen.c -o obj/autoOpen.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -Wl,-z,relro -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/binarySequences.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/autoOpen.o -lz -lm mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -Wl,-z,relro -o velvetg obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/binarySequences.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o obj/autoOpen.o -lz -lm make[2]: Leaving directory '/<>/velvet-1.2.10+dfsg1' mv velveth velveth_long ; mv velvetg velvetg_long #Make _63 kmer version dh_auto_build -- MAXKMERLENGTH=63 velveth velvetg OPENMP=1 CPPFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2" CFLAGS="-g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security" LDFLAGS="-Wl,-z,relro" make -j1 "INSTALL=install --strip-program=true" PKG_CONFIG=mips64el-linux-gnuabi64-pkg-config CXX=mips64el-linux-gnuabi64-g\+\+ CC=mips64el-linux-gnuabi64-gcc MAXKMERLENGTH=63 velveth velvetg OPENMP=1 "CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2" "CFLAGS=-g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security" LDFLAGS=-Wl,-z,relro make[2]: Entering directory '/<>/velvet-1.2.10+dfsg1' rm obj/*.o obj/dbg/*.o rm: cannot remove 'obj/dbg/*.o': No such file or directory make[2]: [Makefile:50: cleanobj] Error 1 (ignored) mkdir -p obj mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/tightString.c -o obj/tightString.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/run.c -o obj/run.o In file included from src/run.h:34, from src/run.c:31: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/splay.c -o obj/splay.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/splayTable.c -o obj/splayTable.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/graph.c -o obj/graph.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/run2.c -o obj/run2.o In file included from src/run.h:34, from src/run2.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/fibHeap.c -o obj/fibHeap.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/fib.c -o obj/fib.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/concatenatedGraph.c -o obj/concatenatedGraph.o In file included from src/concatenatedGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/passageMarker.c -o obj/passageMarker.o In file included from src/passageMarker.c:29: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/graphStats.c -o obj/graphStats.o In file included from src/graphStats.c:28: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/correctedGraph.c -o obj/correctedGraph.o In file included from src/correctedGraph.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/dfib.c -o obj/dfib.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/dfibHeap.c -o obj/dfibHeap.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/recycleBin.c -o obj/recycleBin.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/readSet.c -o obj/readSet.o src/readSet.c: In function 'readFastXFile': src/readSet.c:641:21: warning: assignment to 'gzFile' {aka 'struct gzFile_s *'} from incompatible pointer type 'AutoFile *' {aka 'struct *'} [-Wincompatible-pointer-types] file.gzFile = file.autoFile = NULL; ^ src/readSet.c: In function 'readFastXPair': src/readSet.c:680:22: warning: assignment to 'gzFile' {aka 'struct gzFile_s *'} from incompatible pointer type 'AutoFile *' {aka 'struct *'} [-Wincompatible-pointer-types] file1.gzFile = file1.autoFile = NULL; ^ src/readSet.c:681:22: warning: assignment to 'gzFile' {aka 'struct gzFile_s *'} from incompatible pointer type 'AutoFile *' {aka 'struct *'} [-Wincompatible-pointer-types] file2.gzFile = file2.autoFile = NULL; ^ src/readSet.c: In function 'importReadSet': src/readSet.c:1613:4: warning: 'strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(sequence + bpCount, line, lineLength); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/readSet.c:1612:17: note: length computed here lineLength = strlen(line) - 1; ^~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/binarySequences.c -o obj/binarySequences.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/shortReadPairs.c -o obj/shortReadPairs.o In file included from src/shortReadPairs.c:27: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/locallyCorrectedGraph.c -o obj/locallyCorrectedGraph.o In file included from src/locallyCorrectedGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/graphReConstruction.c -o obj/graphReConstruction.o In file included from src/graphReConstruction.c:33: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/roadMap.c -o obj/roadMap.o In file included from src/roadMap.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/preGraph.c -o obj/preGraph.o In file included from src/run.h:34, from src/preGraph.c:35: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/preGraphConstruction.c -o obj/preGraphConstruction.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/readCoherentGraph.c -o obj/readCoherentGraph.o In file included from src/readCoherentGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/utility.c -o obj/utility.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/kmer.c -o obj/kmer.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/scaffold.c -o obj/scaffold.o In file included from src/scaffold.c:32: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/kmerOccurenceTable.c -o obj/kmerOccurenceTable.o In file included from src/kmerOccurenceTable.c:27: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/allocArray.c -o obj/allocArray.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -c src/autoOpen.c -o obj/autoOpen.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -Wl,-z,relro -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/binarySequences.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/autoOpen.o -lz -lm mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -Wl,-z,relro -o velvetg obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/binarySequences.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o obj/autoOpen.o -lz -lm make[2]: Leaving directory '/<>/velvet-1.2.10+dfsg1' mv velveth velveth_63 ; mv velvetg velvetg_63 #And also one with both options dh_auto_build -- MAXKMERLENGTH=63 LONGSEQUENCES=Y OPENMP=Y velveth velvetg OPENMP=1 CPPFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2" CFLAGS="-g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security" LDFLAGS="-Wl,-z,relro" make -j1 "INSTALL=install --strip-program=true" PKG_CONFIG=mips64el-linux-gnuabi64-pkg-config CXX=mips64el-linux-gnuabi64-g\+\+ CC=mips64el-linux-gnuabi64-gcc MAXKMERLENGTH=63 LONGSEQUENCES=Y OPENMP=Y velveth velvetg OPENMP=1 "CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2" "CFLAGS=-g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security" LDFLAGS=-Wl,-z,relro make[2]: Entering directory '/<>/velvet-1.2.10+dfsg1' rm obj/*.o obj/dbg/*.o rm: cannot remove 'obj/dbg/*.o': No such file or directory make[2]: [Makefile:50: cleanobj] Error 1 (ignored) mkdir -p obj mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/tightString.c -o obj/tightString.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/run.c -o obj/run.o In file included from src/run.h:34, from src/run.c:31: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/splay.c -o obj/splay.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/splayTable.c -o obj/splayTable.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/graph.c -o obj/graph.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/run2.c -o obj/run2.o In file included from src/run.h:34, from src/run2.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/fibHeap.c -o obj/fibHeap.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/fib.c -o obj/fib.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/concatenatedGraph.c -o obj/concatenatedGraph.o In file included from src/concatenatedGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/passageMarker.c -o obj/passageMarker.o In file included from src/passageMarker.c:29: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/graphStats.c -o obj/graphStats.o In file included from src/graphStats.c:28: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/correctedGraph.c -o obj/correctedGraph.o In file included from src/correctedGraph.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/dfib.c -o obj/dfib.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/dfibHeap.c -o obj/dfibHeap.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/recycleBin.c -o obj/recycleBin.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/readSet.c -o obj/readSet.o src/readSet.c: In function 'readFastXFile': src/readSet.c:641:21: warning: assignment to 'gzFile' {aka 'struct gzFile_s *'} from incompatible pointer type 'AutoFile *' {aka 'struct *'} [-Wincompatible-pointer-types] file.gzFile = file.autoFile = NULL; ^ src/readSet.c: In function 'readFastXPair': src/readSet.c:680:22: warning: assignment to 'gzFile' {aka 'struct gzFile_s *'} from incompatible pointer type 'AutoFile *' {aka 'struct *'} [-Wincompatible-pointer-types] file1.gzFile = file1.autoFile = NULL; ^ src/readSet.c:681:22: warning: assignment to 'gzFile' {aka 'struct gzFile_s *'} from incompatible pointer type 'AutoFile *' {aka 'struct *'} [-Wincompatible-pointer-types] file2.gzFile = file2.autoFile = NULL; ^ src/readSet.c: In function 'importReadSet': src/readSet.c:1613:4: warning: 'strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(sequence + bpCount, line, lineLength); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/readSet.c:1612:17: note: length computed here lineLength = strlen(line) - 1; ^~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/binarySequences.c -o obj/binarySequences.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/shortReadPairs.c -o obj/shortReadPairs.o In file included from src/shortReadPairs.c:27: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/locallyCorrectedGraph.c -o obj/locallyCorrectedGraph.o In file included from src/locallyCorrectedGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/graphReConstruction.c -o obj/graphReConstruction.o In file included from src/graphReConstruction.c:33: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/roadMap.c -o obj/roadMap.o In file included from src/roadMap.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/preGraph.c -o obj/preGraph.o In file included from src/run.h:34, from src/preGraph.c:35: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/preGraphConstruction.c -o obj/preGraphConstruction.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/readCoherentGraph.c -o obj/readCoherentGraph.o In file included from src/readCoherentGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/utility.c -o obj/utility.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/kmer.c -o obj/kmer.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/scaffold.c -o obj/scaffold.o In file included from src/scaffold.c:32: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/kmerOccurenceTable.c -o obj/kmerOccurenceTable.o In file included from src/kmerOccurenceTable.c:27: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/allocArray.c -o obj/allocArray.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=63 -D CATEGORIES=2 -D LONGSEQUENCES -c src/autoOpen.c -o obj/autoOpen.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -Wl,-z,relro -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/binarySequences.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/autoOpen.o -lz -lm mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -Wl,-z,relro -o velvetg obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/binarySequences.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o obj/autoOpen.o -lz -lm make[2]: Leaving directory '/<>/velvet-1.2.10+dfsg1' mv velveth velveth_63_long ; mv velvetg velvetg_63_long #Make _127 kmer version dh_auto_build -- MAXKMERLENGTH=127 velveth velvetg OPENMP=1 CPPFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2" CFLAGS="-g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security" LDFLAGS="-Wl,-z,relro" make -j1 "INSTALL=install --strip-program=true" PKG_CONFIG=mips64el-linux-gnuabi64-pkg-config CXX=mips64el-linux-gnuabi64-g\+\+ CC=mips64el-linux-gnuabi64-gcc MAXKMERLENGTH=127 velveth velvetg OPENMP=1 "CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2" "CFLAGS=-g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security" LDFLAGS=-Wl,-z,relro make[2]: Entering directory '/<>/velvet-1.2.10+dfsg1' rm obj/*.o obj/dbg/*.o rm: cannot remove 'obj/dbg/*.o': No such file or directory make[2]: [Makefile:50: cleanobj] Error 1 (ignored) mkdir -p obj mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/tightString.c -o obj/tightString.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/run.c -o obj/run.o In file included from src/run.h:34, from src/run.c:31: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/splay.c -o obj/splay.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/splayTable.c -o obj/splayTable.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/graph.c -o obj/graph.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/run2.c -o obj/run2.o In file included from src/run.h:34, from src/run2.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/fibHeap.c -o obj/fibHeap.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/fib.c -o obj/fib.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/concatenatedGraph.c -o obj/concatenatedGraph.o In file included from src/concatenatedGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/passageMarker.c -o obj/passageMarker.o In file included from src/passageMarker.c:29: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/graphStats.c -o obj/graphStats.o In file included from src/graphStats.c:28: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/correctedGraph.c -o obj/correctedGraph.o In file included from src/correctedGraph.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/dfib.c -o obj/dfib.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/dfibHeap.c -o obj/dfibHeap.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/recycleBin.c -o obj/recycleBin.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/readSet.c -o obj/readSet.o src/readSet.c: In function 'readFastXFile': src/readSet.c:641:21: warning: assignment to 'gzFile' {aka 'struct gzFile_s *'} from incompatible pointer type 'AutoFile *' {aka 'struct *'} [-Wincompatible-pointer-types] file.gzFile = file.autoFile = NULL; ^ src/readSet.c: In function 'readFastXPair': src/readSet.c:680:22: warning: assignment to 'gzFile' {aka 'struct gzFile_s *'} from incompatible pointer type 'AutoFile *' {aka 'struct *'} [-Wincompatible-pointer-types] file1.gzFile = file1.autoFile = NULL; ^ src/readSet.c:681:22: warning: assignment to 'gzFile' {aka 'struct gzFile_s *'} from incompatible pointer type 'AutoFile *' {aka 'struct *'} [-Wincompatible-pointer-types] file2.gzFile = file2.autoFile = NULL; ^ src/readSet.c: In function 'importReadSet': src/readSet.c:1613:4: warning: 'strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(sequence + bpCount, line, lineLength); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/readSet.c:1612:17: note: length computed here lineLength = strlen(line) - 1; ^~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/binarySequences.c -o obj/binarySequences.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/shortReadPairs.c -o obj/shortReadPairs.o In file included from src/shortReadPairs.c:27: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/locallyCorrectedGraph.c -o obj/locallyCorrectedGraph.o In file included from src/locallyCorrectedGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/graphReConstruction.c -o obj/graphReConstruction.o In file included from src/graphReConstruction.c:33: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/roadMap.c -o obj/roadMap.o In file included from src/roadMap.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/preGraph.c -o obj/preGraph.o In file included from src/run.h:34, from src/preGraph.c:35: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/preGraphConstruction.c -o obj/preGraphConstruction.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/readCoherentGraph.c -o obj/readCoherentGraph.o In file included from src/readCoherentGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/utility.c -o obj/utility.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/kmer.c -o obj/kmer.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/scaffold.c -o obj/scaffold.o In file included from src/scaffold.c:32: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/kmerOccurenceTable.c -o obj/kmerOccurenceTable.o In file included from src/kmerOccurenceTable.c:27: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/allocArray.c -o obj/allocArray.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -c src/autoOpen.c -o obj/autoOpen.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -Wl,-z,relro -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/binarySequences.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/autoOpen.o -lz -lm mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -Wl,-z,relro -o velvetg obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/binarySequences.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o obj/autoOpen.o -lz -lm make[2]: Leaving directory '/<>/velvet-1.2.10+dfsg1' mv velveth velveth_127 ; mv velvetg velvetg_127 #And also one with both options dh_auto_build -- MAXKMERLENGTH=127 LONGSEQUENCES=Y OPENMP=Y velveth velvetg OPENMP=1 CPPFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2" CFLAGS="-g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security" LDFLAGS="-Wl,-z,relro" make -j1 "INSTALL=install --strip-program=true" PKG_CONFIG=mips64el-linux-gnuabi64-pkg-config CXX=mips64el-linux-gnuabi64-g\+\+ CC=mips64el-linux-gnuabi64-gcc MAXKMERLENGTH=127 LONGSEQUENCES=Y OPENMP=Y velveth velvetg OPENMP=1 "CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2" "CFLAGS=-g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security" LDFLAGS=-Wl,-z,relro make[2]: Entering directory '/<>/velvet-1.2.10+dfsg1' rm obj/*.o obj/dbg/*.o rm: cannot remove 'obj/dbg/*.o': No such file or directory make[2]: [Makefile:50: cleanobj] Error 1 (ignored) mkdir -p obj mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/tightString.c -o obj/tightString.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/run.c -o obj/run.o In file included from src/run.h:34, from src/run.c:31: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/splay.c -o obj/splay.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/splayTable.c -o obj/splayTable.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/graph.c -o obj/graph.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/run2.c -o obj/run2.o In file included from src/run.h:34, from src/run2.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/fibHeap.c -o obj/fibHeap.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/fib.c -o obj/fib.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/concatenatedGraph.c -o obj/concatenatedGraph.o In file included from src/concatenatedGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/passageMarker.c -o obj/passageMarker.o In file included from src/passageMarker.c:29: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/graphStats.c -o obj/graphStats.o In file included from src/graphStats.c:28: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/correctedGraph.c -o obj/correctedGraph.o In file included from src/correctedGraph.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/dfib.c -o obj/dfib.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/dfibHeap.c -o obj/dfibHeap.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/recycleBin.c -o obj/recycleBin.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/readSet.c -o obj/readSet.o src/readSet.c: In function 'readFastXFile': src/readSet.c:641:21: warning: assignment to 'gzFile' {aka 'struct gzFile_s *'} from incompatible pointer type 'AutoFile *' {aka 'struct *'} [-Wincompatible-pointer-types] file.gzFile = file.autoFile = NULL; ^ src/readSet.c: In function 'readFastXPair': src/readSet.c:680:22: warning: assignment to 'gzFile' {aka 'struct gzFile_s *'} from incompatible pointer type 'AutoFile *' {aka 'struct *'} [-Wincompatible-pointer-types] file1.gzFile = file1.autoFile = NULL; ^ src/readSet.c:681:22: warning: assignment to 'gzFile' {aka 'struct gzFile_s *'} from incompatible pointer type 'AutoFile *' {aka 'struct *'} [-Wincompatible-pointer-types] file2.gzFile = file2.autoFile = NULL; ^ src/readSet.c: In function 'importReadSet': src/readSet.c:1613:4: warning: 'strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(sequence + bpCount, line, lineLength); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/readSet.c:1612:17: note: length computed here lineLength = strlen(line) - 1; ^~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/binarySequences.c -o obj/binarySequences.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/shortReadPairs.c -o obj/shortReadPairs.o In file included from src/shortReadPairs.c:27: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/locallyCorrectedGraph.c -o obj/locallyCorrectedGraph.o In file included from src/locallyCorrectedGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/graphReConstruction.c -o obj/graphReConstruction.o In file included from src/graphReConstruction.c:33: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/roadMap.c -o obj/roadMap.o In file included from src/roadMap.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/preGraph.c -o obj/preGraph.o In file included from src/run.h:34, from src/preGraph.c:35: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/preGraphConstruction.c -o obj/preGraphConstruction.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/readCoherentGraph.c -o obj/readCoherentGraph.o In file included from src/readCoherentGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/utility.c -o obj/utility.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/kmer.c -o obj/kmer.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/scaffold.c -o obj/scaffold.o In file included from src/scaffold.c:32: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/kmerOccurenceTable.c -o obj/kmerOccurenceTable.o In file included from src/kmerOccurenceTable.c:27: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/allocArray.c -o obj/allocArray.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=127 -D CATEGORIES=2 -D LONGSEQUENCES -c src/autoOpen.c -o obj/autoOpen.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -Wl,-z,relro -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/binarySequences.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/autoOpen.o -lz -lm mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -Wl,-z,relro -o velvetg obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/binarySequences.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o obj/autoOpen.o -lz -lm make[2]: Leaving directory '/<>/velvet-1.2.10+dfsg1' mv velveth velveth_127_long ; mv velvetg velvetg_127_long touch zlib # prevents the zlib in the ‘third-party’ folder to be built. dh_auto_build -- OPENMP=1 CPPFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2" CFLAGS="-g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security" LDFLAGS="-Wl,-z,relro" make -j1 "INSTALL=install --strip-program=true" PKG_CONFIG=mips64el-linux-gnuabi64-pkg-config CXX=mips64el-linux-gnuabi64-g\+\+ CC=mips64el-linux-gnuabi64-gcc OPENMP=1 "CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2" "CFLAGS=-g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security" LDFLAGS=-Wl,-z,relro make[2]: Entering directory '/<>/velvet-1.2.10+dfsg1' rm obj/*.o obj/dbg/*.o rm: cannot remove 'obj/dbg/*.o': No such file or directory make[2]: [Makefile:50: cleanobj] Error 1 (ignored) mkdir -p obj mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/tightString.c -o obj/tightString.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/run.c -o obj/run.o In file included from src/run.h:34, from src/run.c:31: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/splay.c -o obj/splay.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/splayTable.c -o obj/splayTable.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/graph.c -o obj/graph.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/run2.c -o obj/run2.o In file included from src/run.h:34, from src/run2.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/fibHeap.c -o obj/fibHeap.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/fib.c -o obj/fib.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/concatenatedGraph.c -o obj/concatenatedGraph.o In file included from src/concatenatedGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/passageMarker.c -o obj/passageMarker.o In file included from src/passageMarker.c:29: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/graphStats.c -o obj/graphStats.o In file included from src/graphStats.c:28: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/correctedGraph.c -o obj/correctedGraph.o In file included from src/correctedGraph.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/dfib.c -o obj/dfib.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/dfibHeap.c -o obj/dfibHeap.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/recycleBin.c -o obj/recycleBin.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/readSet.c -o obj/readSet.o src/readSet.c: In function 'readFastXFile': src/readSet.c:641:21: warning: assignment to 'gzFile' {aka 'struct gzFile_s *'} from incompatible pointer type 'AutoFile *' {aka 'struct *'} [-Wincompatible-pointer-types] file.gzFile = file.autoFile = NULL; ^ src/readSet.c: In function 'readFastXPair': src/readSet.c:680:22: warning: assignment to 'gzFile' {aka 'struct gzFile_s *'} from incompatible pointer type 'AutoFile *' {aka 'struct *'} [-Wincompatible-pointer-types] file1.gzFile = file1.autoFile = NULL; ^ src/readSet.c:681:22: warning: assignment to 'gzFile' {aka 'struct gzFile_s *'} from incompatible pointer type 'AutoFile *' {aka 'struct *'} [-Wincompatible-pointer-types] file2.gzFile = file2.autoFile = NULL; ^ src/readSet.c: In function 'importReadSet': src/readSet.c:1613:4: warning: 'strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(sequence + bpCount, line, lineLength); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/readSet.c:1612:17: note: length computed here lineLength = strlen(line) - 1; ^~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/binarySequences.c -o obj/binarySequences.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/shortReadPairs.c -o obj/shortReadPairs.o In file included from src/shortReadPairs.c:27: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/locallyCorrectedGraph.c -o obj/locallyCorrectedGraph.o In file included from src/locallyCorrectedGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/graphReConstruction.c -o obj/graphReConstruction.o In file included from src/graphReConstruction.c:33: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/roadMap.c -o obj/roadMap.o In file included from src/roadMap.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/preGraph.c -o obj/preGraph.o In file included from src/run.h:34, from src/preGraph.c:35: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/preGraphConstruction.c -o obj/preGraphConstruction.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/readCoherentGraph.c -o obj/readCoherentGraph.o In file included from src/readCoherentGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/utility.c -o obj/utility.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/kmer.c -o obj/kmer.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/scaffold.c -o obj/scaffold.o In file included from src/scaffold.c:32: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/kmerOccurenceTable.c -o obj/kmerOccurenceTable.o In file included from src/kmerOccurenceTable.c:27: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/allocArray.c -o obj/allocArray.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/autoOpen.c -o obj/autoOpen.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -Wl,-z,relro -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/binarySequences.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/autoOpen.o -lz -lm mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -Wl,-z,relro -o velvetg obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/binarySequences.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o obj/autoOpen.o -lz -lm cd doc/manual_src; pdflatex Manual.tex; pdflatex Manual.tex; mv Manual.pdf ../..; pdflatex Columbus_manual.tex; mv Columbus_manual.pdf ../.. This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2019/dev/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./Manual.tex LaTeX2e <2018-12-01> (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2018/09/03 v1.4i Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))) No file Manual.aux. (/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty)) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] Overfull \hbox (11.99689pt too wide) in paragraph at lines 59--59 []\OT1/cmtt/m/n/10 (Final graph has 16 nodes and n50 of 24184, max 44966, total 100080,[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 59--59 []\OT1/cmtt/m/n/10 > ./velvetg sillyDirectory -cov_cutoff 5 -read_trkg yes -amo s_file yes[] Overfull \hbox (1.49698pt too wide) in paragraph at lines 59--59 []\OT1/cmtt/m/n/10 (Final graph has 1 nodes and n50 of 99975, max 99975, total 99975,[] Overfull \hbox (1.49698pt too wide) in paragraph at lines 59--59 []\OT1/cmtt/m/n/10 (Final graph has 1 nodes and n50 of 99975, max 99975, total 99975,[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 59--59 []\OT1/cmtt/m/n/10 (Final graph has 12 nodes and n50 of 99975, max 99975, total 100165,[] Overfull \hbox (1.49698pt too wide) in paragraph at lines 59--59 []\OT1/cmtt/m/n/10 (Final graph has 1 nodes and n50 of 99975, max 99975, total 99975,[] Overfull \hbox (69.74638pt too wide) in paragraph at lines 59--59 []\OT1/cmtt/m/n/10 > ./velveth sillyDirectory 21 -short data/test_reads.fa -lon g data/test_long.fa[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 59--59 []\OT1/cmtt/m/n/10 (Final graph has 10 nodes and n50 of 80927, max 80927, total 100122,[] Overfull \hbox (1.49698pt too wide) in paragraph at lines 59--59 []\OT1/cmtt/m/n/10 (Final graph has 1 nodes and n50 of 99975, max 99975, total 99975,[] [2] LaTeX Warning: Reference `sec:kmercov' on page 3 undefined on input line 115. [3] Overfull \hbox (9.77472pt too wide) in paragraph at lines 159--161 \OT1/cmr/m/n/10 ma-chine. You might have to set the en-vi-ron-ment vari-ables O MP[]NUM[]THREADS Overfull \hbox (11.18709pt too wide) in paragraph at lines 159--161 \OT1/cmr/m/n/10 and OMP[]THREAD[]LIMIT. Vel-vet will the use up to $\OML/cmm/m/ it/10 OMP[]NUM[]THREADS \OT1/cmr/m/n/10 + Overfull \hbox (16.93419pt too wide) in paragraph at lines 159--161 [][]\OT1/cmr/m/n/10 http://www.ats.ucla.edu/clusters/common/computing/parallel/ using[]openmp.htm[][] [4] LaTeX Warning: Reference `sec:kmercov' on page 5 undefined on input line 192. [5] Overfull \hbox (101.24611pt too wide) in paragraph at lines 223--223 []\OT1/cmtt/m/n/10 > ./velveth output_directory/ 21 -fasta -short solexa1.fa so lexa2.fa solexa3.fa -long[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 241--241 []\OT1/cmtt/m/n/10 > velveth directory 21 -fastq other_reads.fastq -fasta selec ted_reads[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 248--248 []\OT1/cmtt/m/n/10 > myprogram | velveth directory 21 -fastq other_reads.fastq -fasta -[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 256--256 []\OT1/cmtt/m/n/10 > ./velveth output_directory/ 21 (...data files...) -strand_ specific[] [6] [7] LaTeX Warning: Reference `sec:covcutoff' on page 8 undefined on input line 331. Overfull \hbox (43.49661pt too wide) in paragraph at lines 341--341 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -max_coverage 300 (... other p arameters ...)[] LaTeX Warning: Reference `sec:hashing' on page 8 undefined on input line 354. LaTeX Warning: Reference `sec:kmercov' on page 8 undefined on input line 358. LaTeX Warning: Reference `sec:expcov' on page 8 undefined on input line 358. Overfull \hbox (11.99689pt too wide) in paragraph at lines 362--362 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -exp_cov 19 (... other paramet ers ...)[] [8] Overfull \hbox (22.4968pt too wide) in paragraph at lines 368--368 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -exp_cov auto (... other param eters ...)[] LaTeX Warning: Reference `sec:hashing' on page 9 undefined on input line 377. LaTeX Warning: Reference `sec:kmercov' on page 9 undefined on input line 379. LaTeX Warning: Reference `sec:pairedformat' on page 9 undefined on input line 3 95. Overfull \hbox (22.4968pt too wide) in paragraph at lines 406--406 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -exp_cov auto (... other param eters ...)[] [9] [10] Overfull \hbox (32.9967pt too wide) in paragraph at lines 451--451 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -read_trkg yes (... other par ameters ...)[] LaTeX Warning: Reference `sec:amos' on page 11 undefined on input line 455. Overfull \hbox (32.9967pt too wide) in paragraph at lines 459--459 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -amos_file yes (... other par ameters ...)[] LaTeX Warning: Reference `sec:hashing' on page 11 undefined on input line 470. Overfull \hbox (48.74657pt too wide) in paragraph at lines 489--489 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -unused_reads yes (... other parameters ...)[] Overfull \hbox (5.18578pt too wide) in paragraph at lines 497--498 []$[]$\OT1/cmr/m/n/10 . If set LaTeX Warning: Reference `sec:paper' on page 11 undefined on input line 499. [11] Overfull \hbox (59.24648pt too wide) in paragraph at lines 514--514 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -max_branch_length 200 (...oth er parameters...)[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 522--522 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -max_divergence 0.33 (...other parameters...)[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 530--530 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -max_gap_count 5 (...other par ameters...)[] [12] Overfull \hbox (38.24666pt too wide) in paragraph at lines 546--546 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -min_pair_count 20 (...other p arameters...)[] Overfull \hbox (38.24666pt too wide) in paragraph at lines 575--575 []\OT1/cmtt/m/n/10 > ./shuffleSequences_fasta.pl forward_reads.fa reverse_reads .fa output.fa[] [13] LaTeX Warning: Reference `sec:kmercov' on page 14 undefined on input line 593. LaTeX Warning: Reference `sec:kmercov' on page 14 undefined on input line 605. Overfull \hbox (8.06886pt too wide) in paragraph at lines 605--606 []\OT1/cmr/m/n/10 The cov-er-ages in columns \OT1/cmr/m/it/10 short1[]cov\OT1/c mr/m/n/10 , \OT1/cmr/m/it/10 short1[]Ocov\OT1/cmr/m/n/10 , \OT1/cmr/m/it/10 sho rt2[]cov\OT1/cmr/m/n/10 , and \OT1/cmr/m/it/10 short2[]Ocov LaTeX Warning: Reference `sec:fasta' on page 14 undefined on input line 615. [14] (/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd) Overfull \hbox (73.7466pt too wide) in paragraph at lines 638--638 []\OT1/cmtt/m/n/10 NODE $NODE_ID $COV_SHORT1 $O_COV_SHORT1 $COV_SHORT 2 $O_COV_SHORT2[] LaTeX Warning: Reference `sec:stats' on page 15 undefined on input line 642. Overfull \hbox (36.99692pt too wide) in paragraph at lines 656--656 []\OT1/cmtt/m/n/10 $NODE_ID $OFFSET_FROM_START $START_COORD $END_COORD $OFFSET _FROM_END[] [15] LaTeX Warning: Reference `sec:maxlength' on page 16 undefined on input line 683 . LaTeX Warning: Reference `sec:paper' on page 16 undefined on input line 695. LaTeX Warning: Reference `sec:kmercov' on page 16 undefined on input line 695. [16] [17 <./Suis_plot_1.pdf>] [18 <./suis_plot.pdf>] Overfull \hbox (16.9262pt too wide) in paragraph at lines 768--769 []\OT1/cmr/m/n/10 by Torsten See-man (torsten.seemann@infotech.monash.edu.au) [19] Overfull \hbox (47.5168pt too wide) in paragraph at lines 786--787 []\OT1/cmr/m/n/10 by Eric Cabot (ecabot@wisc.edu) Pe-ter (pe-ter@maubp.freeserv e.co.uk) [20] [21] (./Manual.aux) Package rerunfilecheck Warning: File `Manual.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information) Output written on Manual.pdf (21 pages, 422893 bytes). Transcript written on Manual.log. This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2019/dev/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./Manual.tex LaTeX2e <2018-12-01> (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2018/09/03 v1.4i Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))) (./Manual.aux) (/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty)) (./Manual.out) (./Manual.out) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) (./Manual.toc [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}]) [2] Overfull \hbox (11.99689pt too wide) in paragraph at lines 59--59 []\OT1/cmtt/m/n/10 (Final graph has 16 nodes and n50 of 24184, max 44966, total 100080,[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 59--59 []\OT1/cmtt/m/n/10 > ./velvetg sillyDirectory -cov_cutoff 5 -read_trkg yes -amo s_file yes[] Overfull \hbox (1.49698pt too wide) in paragraph at lines 59--59 []\OT1/cmtt/m/n/10 (Final graph has 1 nodes and n50 of 99975, max 99975, total 99975,[] Overfull \hbox (1.49698pt too wide) in paragraph at lines 59--59 []\OT1/cmtt/m/n/10 (Final graph has 1 nodes and n50 of 99975, max 99975, total 99975,[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 59--59 []\OT1/cmtt/m/n/10 (Final graph has 12 nodes and n50 of 99975, max 99975, total 100165,[] Overfull \hbox (1.49698pt too wide) in paragraph at lines 59--59 []\OT1/cmtt/m/n/10 (Final graph has 1 nodes and n50 of 99975, max 99975, total 99975,[] Overfull \hbox (69.74638pt too wide) in paragraph at lines 59--59 []\OT1/cmtt/m/n/10 > ./velveth sillyDirectory 21 -short data/test_reads.fa -lon g data/test_long.fa[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 59--59 []\OT1/cmtt/m/n/10 (Final graph has 10 nodes and n50 of 80927, max 80927, total 100122,[] Overfull \hbox (1.49698pt too wide) in paragraph at lines 59--59 []\OT1/cmtt/m/n/10 (Final graph has 1 nodes and n50 of 99975, max 99975, total 99975,[] [3] [4] Overfull \hbox (9.77472pt too wide) in paragraph at lines 159--161 \OT1/cmr/m/n/10 ma-chine. You might have to set the en-vi-ron-ment vari-ables O MP[]NUM[]THREADS Overfull \hbox (11.18709pt too wide) in paragraph at lines 159--161 \OT1/cmr/m/n/10 and OMP[]THREAD[]LIMIT. Vel-vet will the use up to $\OML/cmm/m/ it/10 OMP[]NUM[]THREADS \OT1/cmr/m/n/10 + Overfull \hbox (16.93419pt too wide) in paragraph at lines 159--161 [][]\OT1/cmr/m/n/10 http://www.ats.ucla.edu/clusters/common/computing/parallel/ using[]openmp.htm[][] [5] [6] Overfull \hbox (101.24611pt too wide) in paragraph at lines 223--223 []\OT1/cmtt/m/n/10 > ./velveth output_directory/ 21 -fasta -short solexa1.fa so lexa2.fa solexa3.fa -long[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 241--241 []\OT1/cmtt/m/n/10 > velveth directory 21 -fastq other_reads.fastq -fasta selec ted_reads[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 248--248 []\OT1/cmtt/m/n/10 > myprogram | velveth directory 21 -fastq other_reads.fastq -fasta -[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 256--256 []\OT1/cmtt/m/n/10 > ./velveth output_directory/ 21 (...data files...) -strand_ specific[] [7] [8] Overfull \hbox (43.49661pt too wide) in paragraph at lines 341--341 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -max_coverage 300 (... other p arameters ...)[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 362--362 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -exp_cov 19 (... other paramet ers ...)[] [9] Overfull \hbox (22.4968pt too wide) in paragraph at lines 368--368 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -exp_cov auto (... other param eters ...)[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 406--406 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -exp_cov auto (... other param eters ...)[] [10] [11] Overfull \hbox (32.9967pt too wide) in paragraph at lines 451--451 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -read_trkg yes (... other par ameters ...)[] Overfull \hbox (32.9967pt too wide) in paragraph at lines 459--459 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -amos_file yes (... other par ameters ...)[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 489--489 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -unused_reads yes (... other parameters ...)[] Overfull \hbox (5.18578pt too wide) in paragraph at lines 497--498 []$[]$\OT1/cmr/m/n/10 . If set [12] Overfull \hbox (59.24648pt too wide) in paragraph at lines 514--514 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -max_branch_length 200 (...oth er parameters...)[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 522--522 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -max_divergence 0.33 (...other parameters...)[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 530--530 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -max_gap_count 5 (...other par ameters...)[] [13] Overfull \hbox (38.24666pt too wide) in paragraph at lines 546--546 []\OT1/cmtt/m/n/10 > ./velvetg output_directory/ -min_pair_count 20 (...other p arameters...)[] Overfull \hbox (38.24666pt too wide) in paragraph at lines 575--575 []\OT1/cmtt/m/n/10 > ./shuffleSequences_fasta.pl forward_reads.fa reverse_reads .fa output.fa[] [14] Overfull \hbox (8.06886pt too wide) in paragraph at lines 605--606 []\OT1/cmr/m/n/10 The cov-er-ages in columns \OT1/cmr/m/it/10 short1[]cov\OT1/c mr/m/n/10 , \OT1/cmr/m/it/10 short1[]Ocov\OT1/cmr/m/n/10 , \OT1/cmr/m/it/10 sho rt2[]cov\OT1/cmr/m/n/10 , and \OT1/cmr/m/it/10 short2[]Ocov [15] (/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd) Overfull \hbox (73.7466pt too wide) in paragraph at lines 638--638 []\OT1/cmtt/m/n/10 NODE $NODE_ID $COV_SHORT1 $O_COV_SHORT1 $COV_SHORT 2 $O_COV_SHORT2[] Overfull \hbox (36.99692pt too wide) in paragraph at lines 656--656 []\OT1/cmtt/m/n/10 $NODE_ID $OFFSET_FROM_START $START_COORD $END_COORD $OFFSET _FROM_END[] [16] [17] [18 <./Suis_plot_1.pdf>] [19 <./suis_plot.pdf>] Overfull \hbox (16.9262pt too wide) in paragraph at lines 768--769 []\OT1/cmr/m/n/10 by Torsten See-man (torsten.seemann@infotech.monash.edu.au) [20] Overfull \hbox (47.5168pt too wide) in paragraph at lines 786--787 []\OT1/cmr/m/n/10 by Eric Cabot (ecabot@wisc.edu) Pe-ter (pe-ter@maubp.freeserv e.co.uk) [21] [22] (./Manual.aux) LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information) Output written on Manual.pdf (22 pages, 430447 bytes). Transcript written on Manual.log. This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2019/dev/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./Columbus_manual.tex LaTeX2e <2018-12-01> (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2018/09/03 v1.4i Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size12.clo)) No file Columbus_manual.aux. Overfull \hbox (14.63878pt too wide) in paragraph at lines 36--37 []\OT1/cmr/m/n/12 You se-quenced an in-di-vid-ual genome by WGS, mapped [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd) [3] [4] Overfull \hbox (5.12076pt too wide) in paragraph at lines 132--134 []\OT1/cmr/m/n/12 This scripts adds an ar-bi-trary buffer length (de-fault $100 \OML/cmm/m/it/12 bp$\OT1/cmr/m/n/12 ) Overfull \hbox (36.07521pt too wide) in paragraph at lines 145--145 []\OT1/cmtt/m/n/12 grep exon my_annotation.gtf | enlarge_exons.pl | merge_gtf_e xons.pl \[] Overfull \hbox (23.7252pt too wide) in paragraph at lines 145--145 []\OT1/cmtt/m/n/12 | gff2fasta.pl my_reference_assembly.fa > my_reference_seque nces.fa[] [5] (./Columbus_manual.aux) ) (see the transcript file for additional information) Output written on Columbus_manual.pdf (5 pages, 90140 bytes). Transcript written on Columbus_manual.log. make[2]: Leaving directory '/<>/velvet-1.2.10+dfsg1' dh_auto_build -- color OPENMP=1 CPPFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2" CFLAGS="-g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security" LDFLAGS="-Wl,-z,relro" make -j1 "INSTALL=install --strip-program=true" PKG_CONFIG=mips64el-linux-gnuabi64-pkg-config CXX=mips64el-linux-gnuabi64-g\+\+ CC=mips64el-linux-gnuabi64-gcc color OPENMP=1 "CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2" "CFLAGS=-g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security" LDFLAGS=-Wl,-z,relro make[2]: Entering directory '/<>/velvet-1.2.10+dfsg1' rm obj/*.o obj/dbg/*.o rm: cannot remove 'obj/dbg/*.o': No such file or directory make[2]: [Makefile:50: cleanobj] Error 1 (ignored) mkdir -p obj mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/tightString.c -o obj/tightString.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/run.c -o obj/run.o In file included from src/run.h:34, from src/run.c:31: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/splay.c -o obj/splay.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/splayTable.c -o obj/splayTable.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/graph.c -o obj/graph.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/run2.c -o obj/run2.o In file included from src/run.h:34, from src/run2.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/fibHeap.c -o obj/fibHeap.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/fib.c -o obj/fib.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/concatenatedGraph.c -o obj/concatenatedGraph.o In file included from src/concatenatedGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/passageMarker.c -o obj/passageMarker.o In file included from src/passageMarker.c:29: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/graphStats.c -o obj/graphStats.o In file included from src/graphStats.c:28: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/correctedGraph.c -o obj/correctedGraph.o In file included from src/correctedGraph.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/dfib.c -o obj/dfib.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/dfibHeap.c -o obj/dfibHeap.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/recycleBin.c -o obj/recycleBin.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/readSet.c -o obj/readSet.o src/readSet.c: In function 'readFastXFile': src/readSet.c:641:21: warning: assignment to 'gzFile' {aka 'struct gzFile_s *'} from incompatible pointer type 'AutoFile *' {aka 'struct *'} [-Wincompatible-pointer-types] file.gzFile = file.autoFile = NULL; ^ src/readSet.c: In function 'readFastXPair': src/readSet.c:680:22: warning: assignment to 'gzFile' {aka 'struct gzFile_s *'} from incompatible pointer type 'AutoFile *' {aka 'struct *'} [-Wincompatible-pointer-types] file1.gzFile = file1.autoFile = NULL; ^ src/readSet.c:681:22: warning: assignment to 'gzFile' {aka 'struct gzFile_s *'} from incompatible pointer type 'AutoFile *' {aka 'struct *'} [-Wincompatible-pointer-types] file2.gzFile = file2.autoFile = NULL; ^ src/readSet.c: In function 'importReadSet': src/readSet.c:1613:4: warning: 'strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(sequence + bpCount, line, lineLength); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/readSet.c:1612:17: note: length computed here lineLength = strlen(line) - 1; ^~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/binarySequences.c -o obj/binarySequences.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/shortReadPairs.c -o obj/shortReadPairs.o In file included from src/shortReadPairs.c:27: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/locallyCorrectedGraph.c -o obj/locallyCorrectedGraph.o In file included from src/locallyCorrectedGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/graphReConstruction.c -o obj/graphReConstruction.o In file included from src/graphReConstruction.c:33: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/roadMap.c -o obj/roadMap.o In file included from src/roadMap.c:26: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/preGraph.c -o obj/preGraph.o In file included from src/run.h:34, from src/preGraph.c:35: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/preGraphConstruction.c -o obj/preGraphConstruction.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/readCoherentGraph.c -o obj/readCoherentGraph.o In file included from src/readCoherentGraph.c:25: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/utility.c -o obj/utility.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/kmer.c -o obj/kmer.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/scaffold.c -o obj/scaffold.o In file included from src/scaffold.c:32: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/kmerOccurenceTable.c -o obj/kmerOccurenceTable.o In file included from src/kmerOccurenceTable.c:27: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/allocArray.c -o obj/allocArray.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/autoOpen.c -o obj/autoOpen.o mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -Wl,-z,relro -o velveth_de obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/binarySequences.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o obj/autoOpen.o -lz -lm mips64el-linux-gnuabi64-gcc -g -O2 -fdebug-prefix-map=/<>/velvet-1.2.10+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -Wl,-z,relro -o velvetg_de obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/binarySequences.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o obj/autoOpen.o -lz -lm make[2]: Leaving directory '/<>/velvet-1.2.10+dfsg1' make[1]: Leaving directory '/<>/velvet-1.2.10+dfsg1' dh_auto_test -a create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary-arch dh binary-arch --no-parallel dh_testroot -a dh_prep -a dh_auto_install -a debian/rules override_dh_install make[1]: Entering directory '/<>/velvet-1.2.10+dfsg1' dh_install # remove extra copies of GPL find /<>/velvet-1.2.10+dfsg1/debian -type f -name 'LICENSE*' -delete #MetaVelvet should be scrubbed, and VelvetOptimiser is now separate. Note that these #will not have been installed if this was a binarry-only build. [ ! -e debian/velvet-example/usr ] || \ cp debian/VelvetOptimiser.README debian/velvet-example/usr/share/doc/velvet/contrib/ make[1]: Leaving directory '/<>/velvet-1.2.10+dfsg1' dh_installdocs -a dh_installchangelogs -a dh_installman -a dh_perl -a dh_link -a dh_strip_nondeterminism -a debian/rules override_dh_compress make[1]: Entering directory '/<>/velvet-1.2.10+dfsg1' dh_compress -X.pdf -X.c -X.pl -X.h -X.xz make[1]: Leaving directory '/<>/velvet-1.2.10+dfsg1' dh_fixperms -a dh_missing -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'velvet' in '../velvet_1.2.10+dfsg1-5_mips64el.deb'. dpkg-deb: building package 'velvet-dbgsym' in '../velvet-dbgsym_1.2.10+dfsg1-5_mips64el.deb'. dpkg-deb: building package 'velvet-long' in '../velvet-long_1.2.10+dfsg1-5_mips64el.deb'. dpkg-deb: building package 'velvet-long-dbgsym' in '../velvet-long-dbgsym_1.2.10+dfsg1-5_mips64el.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../velvet_1.2.10+dfsg1-5_mips64el.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2019-05-10T05:14:45Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ lintian ------- Setup apt archive ----------------- Merged Build-Depends: lintian:amd64 Filtered Build-Depends: lintian:amd64 dpkg-deb: building package 'sbuild-build-depends-lintian-dummy' in '/<>/resolver-URaN8F/apt_archive/sbuild-build-depends-lintian-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-essential-dummy sbuild-build-depends-lintian-dummy sbuild-build-depends-velvet-dummy dpkg-scanpackages: info: Wrote 4 entries to output Packages file. Ign:1 copy:/<>/resolver-URaN8F/apt_archive ./ InRelease Get:2 copy:/<>/resolver-URaN8F/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-URaN8F/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-URaN8F/apt_archive ./ Sources [781 B] Get:5 copy:/<>/resolver-URaN8F/apt_archive ./ Packages [860 B] Fetched 2604 B in 0s (134 kB/s) Reading package lists... Reading package lists... Install lintian build dependencies (apt-based resolver) ------------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: diffstat gpg gpgconf libapt-pkg-perl libassuan0 libcapture-tiny-perl libcgi-pm-perl libclass-accessor-perl libclone-perl libdigest-hmac-perl libemail-valid-perl libexporter-tiny-perl libfile-basedir-perl libfuture-perl libhtml-parser-perl libhtml-tagset-perl libio-async-perl libio-pty-perl libio-socket-ssl-perl libipc-run-perl libipc-system-simple-perl liblist-moreutils-perl libmailtools-perl libnet-dns-perl libnet-domain-tld-perl libnet-ip-perl libnet-smtp-ssl-perl libnet-ssleay-perl libparse-debianchangelog-perl libpath-tiny-perl libreadline7 libsqlite3-0 libstruct-dumb-perl libsub-name-perl libtext-levenshtein-perl libtimedate-perl libtry-tiny-perl liburi-perl libyaml-0-2 libyaml-libyaml-perl lintian netbase patchutils perl-openssl-defaults readline-common Suggested packages: libdata-dump-perl ca-certificates libhtml-template-perl libwww-perl binutils-multiarch libtext-template-perl readline-doc Recommended packages: gnupg libcgi-fast-perl libhttp-message-perl libasync-mergepoint-perl libsereal-perl libtest-fatal-perl libtest-refcount-perl libdigest-bubblebabble-perl libnet-dns-sec-perl libnet-libidn-perl libauthen-sasl-perl libunicode-utf8-perl libperlio-gzip-perl The following NEW packages will be installed: diffstat gpg gpgconf libapt-pkg-perl libassuan0 libcapture-tiny-perl libcgi-pm-perl libclass-accessor-perl libclone-perl libdigest-hmac-perl libemail-valid-perl libexporter-tiny-perl libfile-basedir-perl libfuture-perl libhtml-parser-perl libhtml-tagset-perl libio-async-perl libio-pty-perl libio-socket-ssl-perl libipc-run-perl libipc-system-simple-perl liblist-moreutils-perl libmailtools-perl libnet-dns-perl libnet-domain-tld-perl libnet-ip-perl libnet-smtp-ssl-perl libnet-ssleay-perl libparse-debianchangelog-perl libpath-tiny-perl libreadline7 libsqlite3-0 libstruct-dumb-perl libsub-name-perl libtext-levenshtein-perl libtimedate-perl libtry-tiny-perl liburi-perl libyaml-0-2 libyaml-libyaml-perl lintian netbase patchutils perl-openssl-defaults readline-common sbuild-build-depends-lintian-dummy:mips64el 0 upgraded, 46 newly installed, 0 to remove and 0 not upgraded. Need to get 6170 kB of archives. After this operation, 16.2 MB of additional disk space will be used. Get:1 copy:/<>/resolver-URaN8F/apt_archive ./ sbuild-build-depends-lintian-dummy 0.invalid.0 [852 B] Get:2 http://debian.oregonstate.edu/debian unstable/main amd64 netbase all 5.6 [19.4 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 readline-common all 7.0-5 [70.6 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main amd64 diffstat amd64 1.62-1 [33.4 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 libassuan0 amd64 2.5.2-1 [49.4 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 libreadline7 amd64 7.0-5 [151 kB] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 gpgconf amd64 2.2.13-1 [512 kB] Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 libsqlite3-0 amd64 3.27.2-2 [640 kB] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 gpg amd64 2.2.13-1 [867 kB] Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 libapt-pkg-perl amd64 0.1.34+b1 [71.2 kB] Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 libcapture-tiny-perl all 0.48-1 [26.0 kB] Get:12 http://debian.oregonstate.edu/debian unstable/main amd64 libhtml-tagset-perl all 3.20-3 [12.7 kB] Get:13 http://debian.oregonstate.edu/debian unstable/main amd64 liburi-perl all 1.76-1 [89.9 kB] Get:14 http://debian.oregonstate.edu/debian unstable/main amd64 libhtml-parser-perl amd64 3.72-3+b3 [105 kB] Get:15 http://debian.oregonstate.edu/debian unstable/main amd64 libcgi-pm-perl all 4.40-1 [222 kB] Get:16 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-name-perl amd64 0.21-1+b3 [13.6 kB] Get:17 http://debian.oregonstate.edu/debian unstable/main amd64 libclass-accessor-perl all 0.51-1 [23.2 kB] Get:18 http://debian.oregonstate.edu/debian unstable/main amd64 libclone-perl amd64 0.41-1+b1 [14.6 kB] Get:19 http://debian.oregonstate.edu/debian unstable/main amd64 libdigest-hmac-perl all 1.03+dfsg-2 [10.6 kB] Get:20 http://debian.oregonstate.edu/debian unstable/main amd64 libtimedate-perl all 2.3000-2 [42.2 kB] Get:21 http://debian.oregonstate.edu/debian unstable/main amd64 perl-openssl-defaults amd64 3 [6782 B] Get:22 http://debian.oregonstate.edu/debian unstable/main amd64 libnet-ssleay-perl amd64 1.85-2+b1 [308 kB] Get:23 http://debian.oregonstate.edu/debian unstable/main amd64 libio-socket-ssl-perl all 2.060-3 [207 kB] Get:24 http://debian.oregonstate.edu/debian unstable/main amd64 libnet-smtp-ssl-perl all 1.04-1 [6184 B] Get:25 http://debian.oregonstate.edu/debian unstable/main amd64 libmailtools-perl all 2.18-1 [88.5 kB] Get:26 http://debian.oregonstate.edu/debian unstable/main amd64 libnet-ip-perl all 1.26-2 [29.0 kB] Get:27 http://debian.oregonstate.edu/debian unstable/main amd64 libnet-dns-perl all 1.19-1 [372 kB] Get:28 http://debian.oregonstate.edu/debian unstable/main amd64 libnet-domain-tld-perl all 1.75-1 [33.3 kB] Get:29 http://debian.oregonstate.edu/debian unstable/main amd64 libemail-valid-perl all 1.202-1 [23.0 kB] Get:30 http://debian.oregonstate.edu/debian unstable/main amd64 libexporter-tiny-perl all 1.002001-1 [36.9 kB] Get:31 http://debian.oregonstate.edu/debian unstable/main amd64 libipc-system-simple-perl all 1.25-4 [26.5 kB] Get:32 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-basedir-perl all 0.08-1 [17.7 kB] Get:33 http://debian.oregonstate.edu/debian unstable/main amd64 libfuture-perl all 0.39-1 [74.5 kB] Get:34 http://debian.oregonstate.edu/debian unstable/main amd64 libstruct-dumb-perl all 0.09-1 [11.1 kB] Get:35 http://debian.oregonstate.edu/debian unstable/main amd64 libio-async-perl all 0.72-1 [262 kB] Get:36 http://debian.oregonstate.edu/debian unstable/main amd64 libio-pty-perl amd64 1:1.08-1.1+b5 [33.7 kB] Get:37 http://debian.oregonstate.edu/debian unstable/main amd64 libipc-run-perl all 20180523.0-1 [101 kB] Get:38 http://debian.oregonstate.edu/debian unstable/main amd64 liblist-moreutils-perl amd64 0.416-1+b4 [64.2 kB] Get:39 http://debian.oregonstate.edu/debian unstable/main amd64 libparse-debianchangelog-perl all 1.2.0-13 [59.5 kB] Get:40 http://debian.oregonstate.edu/debian unstable/main amd64 libpath-tiny-perl all 0.108-1 [53.3 kB] Get:41 http://debian.oregonstate.edu/debian unstable/main amd64 libtext-levenshtein-perl all 0.13-1 [11.1 kB] Get:42 http://debian.oregonstate.edu/debian unstable/main amd64 libtry-tiny-perl all 0.30-1 [23.3 kB] Get:43 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-0-2 amd64 0.2.1-1 [47.2 kB] Get:44 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-libyaml-perl amd64 0.76+repack-1 [33.1 kB] Get:45 http://debian.oregonstate.edu/debian unstable/main amd64 patchutils amd64 0.3.4-2 [90.4 kB] Get:46 http://debian.oregonstate.edu/debian unstable/main amd64 lintian all 2.13.0 [1175 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 6170 kB in 0s (28.7 MB/s) Selecting previously unselected package netbase. (Reading database ... 25215 files and directories currently installed.) Preparing to unpack .../00-netbase_5.6_all.deb ... Unpacking netbase (5.6) ... Selecting previously unselected package readline-common. Preparing to unpack .../01-readline-common_7.0-5_all.deb ... Unpacking readline-common (7.0-5) ... Selecting previously unselected package diffstat. Preparing to unpack .../02-diffstat_1.62-1_amd64.deb ... Unpacking diffstat (1.62-1) ... Selecting previously unselected package libassuan0:amd64. Preparing to unpack .../03-libassuan0_2.5.2-1_amd64.deb ... Unpacking libassuan0:amd64 (2.5.2-1) ... Selecting previously unselected package libreadline7:amd64. Preparing to unpack .../04-libreadline7_7.0-5_amd64.deb ... Unpacking libreadline7:amd64 (7.0-5) ... Selecting previously unselected package gpgconf. Preparing to unpack .../05-gpgconf_2.2.13-1_amd64.deb ... Unpacking gpgconf (2.2.13-1) ... Selecting previously unselected package libsqlite3-0:amd64. Preparing to unpack .../06-libsqlite3-0_3.27.2-2_amd64.deb ... Unpacking libsqlite3-0:amd64 (3.27.2-2) ... Selecting previously unselected package gpg. Preparing to unpack .../07-gpg_2.2.13-1_amd64.deb ... Unpacking gpg (2.2.13-1) ... Selecting previously unselected package libapt-pkg-perl. Preparing to unpack .../08-libapt-pkg-perl_0.1.34+b1_amd64.deb ... Unpacking libapt-pkg-perl (0.1.34+b1) ... Selecting previously unselected package libcapture-tiny-perl. Preparing to unpack .../09-libcapture-tiny-perl_0.48-1_all.deb ... Unpacking libcapture-tiny-perl (0.48-1) ... Selecting previously unselected package libhtml-tagset-perl. Preparing to unpack .../10-libhtml-tagset-perl_3.20-3_all.deb ... Unpacking libhtml-tagset-perl (3.20-3) ... Selecting previously unselected package liburi-perl. Preparing to unpack .../11-liburi-perl_1.76-1_all.deb ... Unpacking liburi-perl (1.76-1) ... Selecting previously unselected package libhtml-parser-perl. 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Selecting previously unselected package libtimedate-perl. Preparing to unpack .../18-libtimedate-perl_2.3000-2_all.deb ... Unpacking libtimedate-perl (2.3000-2) ... Selecting previously unselected package perl-openssl-defaults:amd64. Preparing to unpack .../19-perl-openssl-defaults_3_amd64.deb ... Unpacking perl-openssl-defaults:amd64 (3) ... Selecting previously unselected package libnet-ssleay-perl. Preparing to unpack .../20-libnet-ssleay-perl_1.85-2+b1_amd64.deb ... Unpacking libnet-ssleay-perl (1.85-2+b1) ... Selecting previously unselected package libio-socket-ssl-perl. Preparing to unpack .../21-libio-socket-ssl-perl_2.060-3_all.deb ... Unpacking libio-socket-ssl-perl (2.060-3) ... Selecting previously unselected package libnet-smtp-ssl-perl. Preparing to unpack .../22-libnet-smtp-ssl-perl_1.04-1_all.deb ... Unpacking libnet-smtp-ssl-perl (1.04-1) ... Selecting previously unselected package libmailtools-perl. Preparing to unpack .../23-libmailtools-perl_2.18-1_all.deb ... Unpacking libmailtools-perl (2.18-1) ... Selecting previously unselected package libnet-ip-perl. Preparing to unpack .../24-libnet-ip-perl_1.26-2_all.deb ... Unpacking libnet-ip-perl (1.26-2) ... Selecting previously unselected package libnet-dns-perl. Preparing to unpack .../25-libnet-dns-perl_1.19-1_all.deb ... Unpacking libnet-dns-perl (1.19-1) ... Selecting previously unselected package libnet-domain-tld-perl. Preparing to unpack .../26-libnet-domain-tld-perl_1.75-1_all.deb ... Unpacking libnet-domain-tld-perl (1.75-1) ... Selecting previously unselected package libemail-valid-perl. Preparing to unpack .../27-libemail-valid-perl_1.202-1_all.deb ... Unpacking libemail-valid-perl (1.202-1) ... Selecting previously unselected package libexporter-tiny-perl. Preparing to unpack .../28-libexporter-tiny-perl_1.002001-1_all.deb ... Unpacking libexporter-tiny-perl (1.002001-1) ... Selecting previously unselected package libipc-system-simple-perl. Preparing to unpack .../29-libipc-system-simple-perl_1.25-4_all.deb ... Unpacking libipc-system-simple-perl (1.25-4) ... Selecting previously unselected package libfile-basedir-perl. Preparing to unpack .../30-libfile-basedir-perl_0.08-1_all.deb ... Unpacking libfile-basedir-perl (0.08-1) ... Selecting previously unselected package libfuture-perl. Preparing to unpack .../31-libfuture-perl_0.39-1_all.deb ... Unpacking libfuture-perl (0.39-1) ... Selecting previously unselected package libstruct-dumb-perl. Preparing to unpack .../32-libstruct-dumb-perl_0.09-1_all.deb ... Unpacking libstruct-dumb-perl (0.09-1) ... Selecting previously unselected package libio-async-perl. Preparing to unpack .../33-libio-async-perl_0.72-1_all.deb ... Unpacking libio-async-perl (0.72-1) ... Selecting previously unselected package libio-pty-perl. Preparing to unpack .../34-libio-pty-perl_1%3a1.08-1.1+b5_amd64.deb ... Unpacking libio-pty-perl (1:1.08-1.1+b5) ... Selecting previously unselected package libipc-run-perl. Preparing to unpack .../35-libipc-run-perl_20180523.0-1_all.deb ... Unpacking libipc-run-perl (20180523.0-1) ... Selecting previously unselected package liblist-moreutils-perl. Preparing to unpack .../36-liblist-moreutils-perl_0.416-1+b4_amd64.deb ... Unpacking liblist-moreutils-perl (0.416-1+b4) ... Selecting previously unselected package libparse-debianchangelog-perl. Preparing to unpack .../37-libparse-debianchangelog-perl_1.2.0-13_all.deb ... Unpacking libparse-debianchangelog-perl (1.2.0-13) ... Selecting previously unselected package libpath-tiny-perl. Preparing to unpack .../38-libpath-tiny-perl_0.108-1_all.deb ... Unpacking libpath-tiny-perl (0.108-1) ... Selecting previously unselected package libtext-levenshtein-perl. Preparing to unpack .../39-libtext-levenshtein-perl_0.13-1_all.deb ... Unpacking libtext-levenshtein-perl (0.13-1) ... Selecting previously unselected package libtry-tiny-perl. Preparing to unpack .../40-libtry-tiny-perl_0.30-1_all.deb ... Unpacking libtry-tiny-perl (0.30-1) ... Selecting previously unselected package libyaml-0-2:amd64. Preparing to unpack .../41-libyaml-0-2_0.2.1-1_amd64.deb ... Unpacking libyaml-0-2:amd64 (0.2.1-1) ... Selecting previously unselected package libyaml-libyaml-perl. Preparing to unpack .../42-libyaml-libyaml-perl_0.76+repack-1_amd64.deb ... Unpacking libyaml-libyaml-perl (0.76+repack-1) ... Selecting previously unselected package patchutils. Preparing to unpack .../43-patchutils_0.3.4-2_amd64.deb ... Unpacking patchutils (0.3.4-2) ... Selecting previously unselected package lintian. Preparing to unpack .../44-lintian_2.13.0_all.deb ... Unpacking lintian (2.13.0) ... Selecting previously unselected package sbuild-build-depends-lintian-dummy:mips64el. Preparing to unpack .../45-sbuild-build-depends-lintian-dummy_0.invalid.0_mips64el.deb ... Unpacking sbuild-build-depends-lintian-dummy:mips64el (0.invalid.0) ... Setting up libapt-pkg-perl (0.1.34+b1) ... Setting up libstruct-dumb-perl (0.09-1) ... Setting up libio-pty-perl (1:1.08-1.1+b5) ... Setting up libclone-perl (0.41-1+b1) ... Setting up libyaml-0-2:amd64 (0.2.1-1) ... Setting up libhtml-tagset-perl (3.20-3) ... Setting up libsqlite3-0:amd64 (3.27.2-2) ... Setting up libfuture-perl (0.39-1) ... Setting up libyaml-libyaml-perl (0.76+repack-1) ... Setting up libtry-tiny-perl (0.30-1) ... Setting up perl-openssl-defaults:amd64 (3) ... Setting up libtext-levenshtein-perl (0.13-1) ... Setting up libassuan0:amd64 (2.5.2-1) ... Setting up libio-async-perl (0.72-1) ... Setting up patchutils (0.3.4-2) ... Setting up libdigest-hmac-perl (1.03+dfsg-2) ... Setting up libipc-system-simple-perl (1.25-4) ... Setting up libnet-domain-tld-perl (1.75-1) ... Setting up diffstat (1.62-1) ... Setting up libipc-run-perl (20180523.0-1) ... Setting up libcapture-tiny-perl (0.48-1) ... Setting up libtimedate-perl (2.3000-2) ... Setting up libsub-name-perl (0.21-1+b3) ... Setting up libpath-tiny-perl (0.108-1) ... Setting up netbase (5.6) ... Setting up libexporter-tiny-perl (1.002001-1) ... Setting up libclass-accessor-perl (0.51-1) ... Setting up libnet-ip-perl (1.26-2) ... Setting up readline-common (7.0-5) ... Setting up liburi-perl (1.76-1) ... Setting up libreadline7:amd64 (7.0-5) ... Setting up libnet-ssleay-perl (1.85-2+b1) ... Setting up libfile-basedir-perl (0.08-1) ... Setting up liblist-moreutils-perl (0.416-1+b4) ... Setting up libnet-dns-perl (1.19-1) ... Setting up libhtml-parser-perl (3.72-3+b3) ... Setting up gpgconf (2.2.13-1) ... Setting up libio-socket-ssl-perl (2.060-3) ... Setting up gpg (2.2.13-1) ... Setting up libcgi-pm-perl (4.40-1) ... Setting up libnet-smtp-ssl-perl (1.04-1) ... Setting up libmailtools-perl (2.18-1) ... Setting up libparse-debianchangelog-perl (1.2.0-13) ... Setting up libemail-valid-perl (1.202-1) ... Setting up lintian (2.13.0) ... Setting up sbuild-build-depends-lintian-dummy:mips64el (0.invalid.0) ... Processing triggers for man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Processing triggers for libc-bin (2.28-10) ... I: Lintian run was successful. +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ velvet_1.2.10+dfsg1-5_mips64el.changes: --------------------------------------- Format: 1.8 Date: Thu, 05 Jul 2018 10:17:41 +0200 Source: velvet Binary: velvet velvet-dbgsym velvet-long velvet-long-dbgsym Built-For-Profiles: cross nocheck Architecture: mips64el Version: 1.2.10+dfsg1-5 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: velvet - Nucleic acid sequence assembler for very short reads velvet-long - Nucleic acid sequence assembler for very short reads, long versio Changes: velvet (1.2.10+dfsg1-5) unstable; urgency=medium . [ Steffen Moeller ] * debian/upstream/metadata: Added references to registries. . [ Andreas Tille ] * drop unneeded get-orig-source target * debhelper 11 (--no-parallel needed) * Point Vcs fields to salsa.debian.org * Standards-Version: 4.1.4 * d/control: Drop unnecessary Testsuite field * Provide manpages for versions with MAXKMERLENGTH = 127 * Try better hardening but failed (hints are welcome) * Fix spelling * Secure URI in watch file * Remove unused lintian override Checksums-Sha1: 832d599cf61b78e4241b55b46480eeef0f0e5a78 1041068 velvet-dbgsym_1.2.10+dfsg1-5_mips64el.deb e12c21f64b8b6481a1f463cb66a191ad0a667c9a 2062644 velvet-long-dbgsym_1.2.10+dfsg1-5_mips64el.deb a212d9274d80632dab70c95e5fe60540b97175cb 205208 velvet-long_1.2.10+dfsg1-5_mips64el.deb 7ddb2db7246546a0c5d9e5466bf2e5c2da97c810 7541 velvet_1.2.10+dfsg1-5_mips64el.buildinfo 8e472a8a4f27b44f52812cfc147e906d906d133a 656304 velvet_1.2.10+dfsg1-5_mips64el.deb Checksums-Sha256: 126b9584f4ee568cbc21bdeaa580b5f124514d4a9ba51e1833f0cf483eaebf99 1041068 velvet-dbgsym_1.2.10+dfsg1-5_mips64el.deb 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bzip2 (= 1.0.6-9), coreutils (= 8.30-3), cpp (= 4:8.3.0-1), cpp-8 (= 8.3.0-7), dash (= 0.5.10.2-5), debconf (= 1.5.72), debhelper (= 12.1.1), debianutils (= 4.8.6.1), dh-autoreconf (= 19), dh-strip-nondeterminism (= 1.1.2-1), diffutils (= 1:3.7-3), dpkg (= 1.19.6), dpkg-dev (= 1.19.6), dwz (= 0.12-3), fdisk (= 2.33.1-0.1), file (= 1:5.35-4), findutils (= 4.6.0+git+20190209-2), fontconfig-config (= 2.13.1-2), fonts-dejavu-core (= 2.37-1), fonts-lmodern (= 2.004.5-6), g++ (= 4:8.3.0-1), g++-8 (= 8.3.0-7), gcc (= 4:8.3.0-1), gcc-8 (= 8.3.0-7), gcc-8-base (= 8.3.0-7), gettext (= 0.19.8.1-9), gettext-base (= 0.19.8.1-9), grep (= 3.3-1), groff-base (= 1.22.4-3), gzip (= 1.9-3), hostname (= 3.21), init-system-helpers (= 1.56+nmu1), intltool-debian (= 0.35.0+20060710.5), libacl1 (= 2.2.53-4), libarchive-zip-perl (= 1.64-1), libasan5 (= 8.3.0-7), libatomic1 (= 8.3.0-7), libattr1 (= 1:2.4.48-4), libaudit-common (= 1:2.8.4-3), libaudit1 (= 1:2.8.4-3), libavahi-client3 (= 0.7-4+b1), libavahi-common-data (= 0.7-4+b1), libavahi-common3 (= 0.7-4+b1), libbinutils (= 2.31.1-16), libblkid1 (= 2.33.1-0.1), libbrotli1 (= 1.0.7-2), libbsd0 (= 0.9.1-2), libbz2-1.0 (= 1.0.6-9), libc-bin (= 2.28-10), libc-dev-bin (= 2.28-10), libc6 (= 2.28-10), libc6-dev (= 2.28-10), libcairo2 (= 1.16.0-4), libcap-ng0 (= 0.7.9-2), libcc1-0 (= 8.3.0-7), libcom-err2 (= 1.45.0-1), libcroco3 (= 0.6.12-3), libcups2 (= 2.2.10-6), libcupsimage2 (= 2.2.10-6), libdb5.3 (= 5.3.28+dfsg1-0.6), libdbus-1-3 (= 1.12.12-1), libdebconfclient0 (= 0.249), libdpkg-perl (= 1.19.6), libelf1 (= 0.176-1), libexpat1 (= 2.2.6-1), libfdisk1 (= 2.33.1-0.1), libffi6 (= 3.2.1-9), libfile-stripnondeterminism-perl (= 1.1.2-1), libfontconfig1 (= 2.13.1-2), libfreetype6 (= 2.9.1-3), libgcc-8-dev (= 8.3.0-7), libgcc1 (= 1:8.3.0-7), libgcrypt20 (= 1.8.4-5), libgdbm-compat4 (= 1.18.1-4), libgdbm6 (= 1.18.1-4), libglib2.0-0 (= 2.58.3-1), libgmp10 (= 2:6.1.2+dfsg-4), libgnutls30 (= 3.6.7-2), libgomp1 (= 8.3.0-7), libgpg-error0 (= 1.35-1), libgraphite2-3 (= 1.3.13-7), libgs9 (= 9.27~dfsg-2), libgs9-common (= 9.27~dfsg-2), libgssapi-krb5-2 (= 1.17-2), libharfbuzz-icu0 (= 2.3.1-1), libharfbuzz0b (= 2.3.1-1), libhogweed4 (= 3.4.1-1), libice6 (= 2:1.0.9-2), libicu63 (= 63.1-6), libidn11 (= 1.33-2.2), libidn2-0 (= 2.0.5-1), libijs-0.35 (= 0.35-13), libisl19 (= 0.20-2), libitm1 (= 8.3.0-7), libjbig0 (= 2.1-3.1+b2), libjbig2dec0 (= 0.16-1), libjpeg62-turbo (= 1:1.5.2-2+b1), libk5crypto3 (= 1.17-2), libkeyutils1 (= 1.6-6), libkpathsea6 (= 2018.20181218.49446-2), libkrb5-3 (= 1.17-2), libkrb5support0 (= 1.17-2), liblcms2-2 (= 2.9-3), liblsan0 (= 8.3.0-7), liblz4-1 (= 1.8.3-1), liblzma5 (= 5.2.4-1), libmagic-mgc (= 1:5.35-4), libmagic1 (= 1:5.35-4), libmount1 (= 2.33.1-0.1), libmpc3 (= 1.1.0-1), libmpfr6 (= 4.0.2-1), libmpx2 (= 8.3.0-7), libncurses6 (= 6.1+20181013-2), libncursesw6 (= 6.1+20181013-2), libnettle6 (= 3.4.1-1), libopenjp2-7 (= 2.3.0-2), libp11-kit0 (= 0.23.15-2), libpam-modules (= 1.3.1-5), libpam-modules-bin (= 1.3.1-5), libpam-runtime (= 1.3.1-5), libpam0g (= 1.3.1-5), libpaper-utils (= 1.1.26), libpaper1 (= 1.1.26), libpcre3 (= 2:8.39-12), libperl5.28 (= 5.28.1-6), libpipeline1 (= 1.5.1-2), libpixman-1-0 (= 0.36.0-1), libpng16-16 (= 1.6.36-6), libpotrace0 (= 1.15-1), libptexenc1 (= 2018.20181218.49446-2), libquadmath0 (= 8.3.0-7), libseccomp2 (= 2.3.3-4), libselinux1 (= 2.8-1+b1), libsigsegv2 (= 2.12-2), libsm6 (= 2:1.2.3-1), libsmartcols1 (= 2.33.1-0.1), libssl1.1 (= 1.1.1b-2), libstdc++-8-dev (= 8.3.0-7), libstdc++6 (= 8.3.0-7), libsynctex2 (= 2018.20181218.49446-2), libsystemd0 (= 241-3), libtasn1-6 (= 4.13-3), libteckit0 (= 2.5.8+ds2-5), libtexlua52 (= 2018.20181218.49446-2), libtexlua53 (= 2018.20181218.49446-2), libtexluajit2 (= 2018.20181218.49446-2), libtiff5 (= 4.0.10-4), libtinfo6 (= 6.1+20181013-2), libtool (= 2.4.6-10), libtsan0 (= 8.3.0-7), libubsan1 (= 8.3.0-7), libuchardet0 (= 0.0.6-3), libudev1 (= 241-3), libunistring2 (= 0.9.10-1), libuuid1 (= 2.33.1-0.1), libwebp6 (= 0.6.1-2), libwoff1 (= 1.0.2-1), libx11-6 (= 2:1.6.7-1), libx11-data (= 2:1.6.7-1), libxau6 (= 1:1.0.8-1+b2), libxaw7 (= 2:1.0.13-1+b2), libxcb-render0 (= 1.13.1-2), libxcb-shm0 (= 1.13.1-2), libxcb1 (= 1.13.1-2), libxdmcp6 (= 1:1.1.2-3), libxext6 (= 2:1.3.3-1+b2), libxi6 (= 2:1.7.9-1), libxml2 (= 2.9.4+dfsg1-7+b3), libxmu6 (= 2:1.1.2-2+b3), libxpm4 (= 1:3.5.12-1), libxrender1 (= 1:0.9.10-1), libxt6 (= 1:1.1.5-1+b3), libxxhash0 (= 0.6.5-3), libzstd1 (= 1.3.8+dfsg-3), libzzip-0-13 (= 0.13.62-3.2), linux-libc-dev (= 4.19.37-1), login (= 1:4.5-1.1), lsb-base (= 10.2019031300), m4 (= 1.4.18-2), make (= 4.2.1-1.2), man-db (= 2.8.5-2), mawk (= 1.3.3-17+b3), ncurses-base (= 6.1+20181013-2), ncurses-bin (= 6.1+20181013-2), patch (= 2.7.6-3), perl (= 5.28.1-6), perl-base (= 5.28.1-6), perl-modules-5.28 (= 5.28.1-6), po-debconf (= 1.0.21), poppler-data (= 0.4.9-2), sed (= 4.7-1), sensible-utils (= 0.0.12), sysvinit-utils (= 2.93-8), t1utils (= 1.41-3), tar (= 1.30+dfsg-6), tex-common (= 6.11), texlive-base (= 2018.20190227-2), texlive-binaries (= 2018.20181218.49446-2), texlive-latex-base (= 2018.20190227-2), texlive-latex-recommended (= 2018.20190227-2), ucf (= 3.0038+nmu1), util-linux (= 2.33.1-0.1), x11-common (= 1:7.7+19), xdg-utils (= 1.1.3-1), xz-utils (= 5.2.4-1), zlib1g (= 1:1.2.11.dfsg-1), zlib1g-dev (= 1:1.2.11.dfsg-1) Environment: DEB_BUILD_OPTIONS="nocheck parallel=1" DEB_BUILD_PROFILES="cross nocheck" LANG="en_US.UTF-8" LC_ALL="POSIX" SOURCE_DATE_EPOCH="1530778661" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ velvet-dbgsym_1.2.10+dfsg1-5_mips64el.deb ----------------------------------------- new Debian package, version 2.0. size 1041068 bytes: control archive=704 bytes. 507 bytes, 12 lines control 424 bytes, 4 lines md5sums Package: velvet-dbgsym Source: velvet Version: 1.2.10+dfsg1-5 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Debian package, version 2.0. size 205208 bytes: control archive=1460 bytes. 1004 bytes, 22 lines control 1499 bytes, 23 lines md5sums Package: velvet-long Source: velvet Version: 1.2.10+dfsg1-5 Architecture: mips64el Maintainer: Debian Med Packaging Team Installed-Size: 2299 Depends: libc6 (>= 2.7), libgomp1 (>= 4.9), zlib1g (>= 1:1.2.0.2), velvet Section: science Priority: optional Homepage: http://www.ebi.ac.uk/~zerbino/velvet/ Description: Nucleic acid sequence assembler for very short reads, long version Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI), near Cambridge, in the United Kingdom. . Velvet currently takes in short read sequences, removes errors then produces high quality unique contigs. It then uses paired read information, if available, to retrieve the repeated areas between contigs. . This package installs special long-mode versions of Velvet, as recommended in the Velvet tutorials. drwxr-xr-x root/root 0 2018-07-05 08:17 ./ drwxr-xr-x root/root 0 2018-07-05 08:17 ./usr/ drwxr-xr-x root/root 0 2018-07-05 08:17 ./usr/bin/ -rwxr-xr-x root/root 354984 2018-07-05 08:17 ./usr/bin/velvetg_127 -rwxr-xr-x root/root 354984 2018-07-05 08:17 ./usr/bin/velvetg_127_long -rwxr-xr-x root/root 354984 2018-07-05 08:17 ./usr/bin/velvetg_63 -rwxr-xr-x root/root 354984 2018-07-05 08:17 ./usr/bin/velvetg_63_long -rwxr-xr-x root/root 354968 2018-07-05 08:17 ./usr/bin/velvetg_long -rwxr-xr-x root/root 106480 2018-07-05 08:17 ./usr/bin/velveth_127 -rwxr-xr-x root/root 106480 2018-07-05 08:17 ./usr/bin/velveth_127_long -rwxr-xr-x root/root 106480 2018-07-05 08:17 ./usr/bin/velveth_63 -rwxr-xr-x root/root 106480 2018-07-05 08:17 ./usr/bin/velveth_63_long -rwxr-xr-x root/root 106464 2018-07-05 08:17 ./usr/bin/velveth_long drwxr-xr-x root/root 0 2018-07-05 08:17 ./usr/share/ drwxr-xr-x root/root 0 2018-07-05 08:17 ./usr/share/doc/ drwxr-xr-x root/root 0 2018-07-05 08:17 ./usr/share/doc/velvet-long/ -rw-r--r-- root/root 4917 2018-07-05 08:17 ./usr/share/doc/velvet-long/changelog.Debian.gz -rw-r--r-- root/root 4572 2013-06-06 20:00 ./usr/share/doc/velvet-long/changelog.gz -rw-r--r-- root/root 4435 2018-07-05 08:17 ./usr/share/doc/velvet-long/copyright drwxr-xr-x root/root 0 2018-07-05 08:17 ./usr/share/man/ drwxr-xr-x root/root 0 2018-07-05 08:17 ./usr/share/man/man1/ -rw-r--r-- root/root 1488 2018-07-05 08:17 ./usr/share/man/man1/velvetg_127.1.gz -rw-r--r-- root/root 1508 2018-07-05 08:17 ./usr/share/man/man1/velvetg_127_long.1.gz -rw-r--r-- root/root 1487 2018-07-05 08:17 ./usr/share/man/man1/velvetg_63.1.gz -rw-r--r-- root/root 1507 2018-07-05 08:17 ./usr/share/man/man1/velvetg_63_long.1.gz -rw-r--r-- root/root 1483 2018-07-05 08:17 ./usr/share/man/man1/velvetg_long.1.gz -rw-r--r-- root/root 1442 2018-07-05 08:17 ./usr/share/man/man1/velveth_127.1.gz -rw-r--r-- root/root 1463 2018-07-05 08:17 ./usr/share/man/man1/velveth_127_long.1.gz -rw-r--r-- root/root 1441 2018-07-05 08:17 ./usr/share/man/man1/velveth_63.1.gz -rw-r--r-- root/root 1462 2018-07-05 08:17 ./usr/share/man/man1/velveth_63_long.1.gz -rw-r--r-- root/root 1454 2018-07-05 08:17 ./usr/share/man/man1/velveth_long.1.gz velvet_1.2.10+dfsg1-5_mips64el.deb ---------------------------------- new Debian package, version 2.0. size 656304 bytes: control archive=1332 bytes. 882 bytes, 19 lines control 1154 bytes, 18 lines md5sums Package: velvet Version: 1.2.10+dfsg1-5 Architecture: mips64el Maintainer: Debian Med Packaging Team Installed-Size: 1453 Depends: libc6 (>= 2.7), libgomp1 (>= 4.9), zlib1g (>= 1:1.2.0.2) Suggests: velvet-example Section: science Priority: optional Homepage: http://www.ebi.ac.uk/~zerbino/velvet/ Description: Nucleic acid sequence assembler for very short reads Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI), near Cambridge, in the United Kingdom. . Velvet currently takes in short read sequences, removes errors then produces high quality unique contigs. It then uses paired read information, if available, to retrieve the repeated areas between contigs. drwxr-xr-x root/root 0 2018-07-05 08:17 ./ drwxr-xr-x root/root 0 2018-07-05 08:17 ./usr/ drwxr-xr-x root/root 0 2018-07-05 08:17 ./usr/bin/ -rwxr-xr-x root/root 354968 2018-07-05 08:17 ./usr/bin/velvetg -rwxr-xr-x root/root 354936 2018-07-05 08:17 ./usr/bin/velvetg_de -rwxr-xr-x root/root 106464 2018-07-05 08:17 ./usr/bin/velveth -rwxr-xr-x root/root 106728 2018-07-05 08:17 ./usr/bin/velveth_de drwxr-xr-x root/root 0 2018-07-05 08:17 ./usr/share/ drwxr-xr-x root/root 0 2018-07-05 08:17 ./usr/share/doc-base/ -rw-r--r-- root/root 243 2018-07-05 08:17 ./usr/share/doc-base/velvet drwxr-xr-x root/root 0 2018-07-05 08:17 ./usr/share/doc/ drwxr-xr-x root/root 0 2018-07-05 08:17 ./usr/share/doc/velvet/ -rw-r--r-- root/root 1956 2013-06-06 20:00 ./usr/share/doc/velvet/CREDITS.txt -rw-r--r-- root/root 90140 2018-07-05 08:17 ./usr/share/doc/velvet/Columbus_manual.pdf -rw-r--r-- root/root 430447 2018-07-05 08:17 ./usr/share/doc/velvet/Manual.pdf -rw-r--r-- root/root 220 2018-07-05 08:17 ./usr/share/doc/velvet/README.Debian -rw-r--r-- root/root 405 2018-07-05 08:17 ./usr/share/doc/velvet/README.test -rw-r--r-- root/root 1117 2013-06-06 20:00 ./usr/share/doc/velvet/README.txt -rw-r--r-- root/root 4917 2018-07-05 08:17 ./usr/share/doc/velvet/changelog.Debian.gz -rw-r--r-- root/root 4572 2013-06-06 20:00 ./usr/share/doc/velvet/changelog.gz -rw-r--r-- root/root 4435 2018-07-05 08:17 ./usr/share/doc/velvet/copyright drwxr-xr-x root/root 0 2018-07-05 08:17 ./usr/share/man/ drwxr-xr-x root/root 0 2018-07-05 08:17 ./usr/share/man/man1/ -rw-r--r-- root/root 1460 2018-07-05 08:17 ./usr/share/man/man1/velvetg.1.gz -rw-r--r-- root/root 1479 2018-07-05 08:17 ./usr/share/man/man1/velvetg_de.1.gz -rw-r--r-- root/root 1422 2018-07-05 08:17 ./usr/share/man/man1/velveth.1.gz -rw-r--r-- root/root 1453 2018-07-05 08:17 ./usr/share/man/man1/velveth_de.1.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any Build-Space: 89576 Build-Time: 134 Distribution: unstable Foreign Architectures: mips64el Host Architecture: mips64el Install-Time: 45 Job: velvet_1.2.10+dfsg1-5 Lintian: pass Machine Architecture: amd64 Package: velvet Package-Time: 190 Source-Version: 1.2.10+dfsg1-5 Space: 89576 Status: successful Version: 1.2.10+dfsg1-5 -------------------------------------------------------------------------------- Finished at 2019-05-10T05:14:45Z Build needed 00:03:10, 89576k disk space