sbuild (Debian sbuild) 0.73.0 (23 Dec 2016) on gcc131.bak.milne.osuosl.org +==============================================================================+ | velvet 1.2.10+dfsg1-5 (ppc64el) Tue, 19 Feb 2019 04:36:44 +0000 | +==============================================================================+ Package: velvet Version: 1.2.10+dfsg1-5 Source Version: 1.2.10+dfsg1-5 Distribution: unstable Machine Architecture: amd64 Host Architecture: ppc64el Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any I: NOTICE: Log filtering will replace 'var/run/schroot/mount/unstable-amd64-sbuild-f6771de1-0a07-4dd3-9dea-cc12f677f4d9' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 http://debian.oregonstate.edu/debian unstable InRelease [242 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 2019-02-18-0809.24.pdiff [2626 B] Get:5 http://debian.oregonstate.edu/debian unstable/main Sources 2019-02-18-1416.48.pdiff [11.0 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main Sources 2019-02-18-2010.59.pdiff [9566 B] Get:7 http://debian.oregonstate.edu/debian unstable/main Sources 2019-02-19-0208.15.pdiff [7692 B] Get:7 http://debian.oregonstate.edu/debian unstable/main Sources 2019-02-19-0208.15.pdiff [7692 B] Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2019-02-18-0809.24.pdiff [1057 B] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2019-02-18-1416.48.pdiff [12.8 kB] Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2019-02-18-2010.59.pdiff [15.9 kB] Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2019-02-19-0208.15.pdiff [12.1 kB] Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2019-02-19-0208.15.pdiff [12.1 kB] Get:12 http://debian.oregonstate.edu/debian unstable/main ppc64el Packages [8115 kB] Fetched 8486 kB in 2s (4628 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: diffutils libsystemd0 libudev1 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 843 kB of archives. After this operation, 2048 B of additional disk space will be used. Get:1 http://debian.oregonstate.edu/debian unstable/main amd64 diffutils amd64 1:3.7-2 [371 kB] Get:2 http://debian.oregonstate.edu/debian unstable/main amd64 libsystemd0 amd64 240-6 [326 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 libudev1 amd64 240-6 [146 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 843 kB in 0s (15.5 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11871 files and directories currently installed.) Preparing to unpack .../diffutils_1%3a3.7-2_amd64.deb ... Unpacking diffutils (1:3.7-2) over (1:3.7-1) ... Setting up diffutils (1:3.7-2) ... (Reading database ... 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Processing triggers for libc-bin (2.28-7) ... +------------------------------------------------------------------------------+ | 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 1s (12.3 MB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/velvet-s18GTI/velvet-1.2.10+dfsg1' with '<>' I: NOTICE: Log filtering will replace 'build/velvet-s18GTI' with '<>' +------------------------------------------------------------------------------+ | Install crossbuild-essential | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: build-essential:amd64, fakeroot:amd64, crossbuild-essential-ppc64el:amd64 Filtered Build-Depends: build-essential:amd64, fakeroot:amd64, crossbuild-essential-ppc64el:amd64 dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-EbjcLO/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-EbjcLO/apt_archive ./ InRelease Get:2 copy:/<>/resolver-EbjcLO/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-EbjcLO/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-EbjcLO/apt_archive ./ Sources [361 B] Get:5 copy:/<>/resolver-EbjcLO/apt_archive ./ Packages [452 B] Fetched 1770 B in 0s (98.3 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-powerpc64le-linux-gnu cpp-8-powerpc64le-linux-gnu cpp-powerpc64le-linux-gnu cross-config crossbuild-essential-ppc64el dpkg-cross file g++-8-powerpc64le-linux-gnu g++-powerpc64le-linux-gnu gcc-8-cross-base gcc-8-powerpc64le-linux-gnu gcc-8-powerpc64le-linux-gnu-base gcc-powerpc64le-linux-gnu libasan5-ppc64el-cross libatomic1-ppc64el-cross libc6-dev-ppc64el-cross libc6-ppc64el-cross libconfig-auto-perl libconfig-inifiles-perl libdebian-dpkgcross-perl libfile-homedir-perl libfile-which-perl libgcc-8-dev-ppc64el-cross libgcc1-ppc64el-cross libgomp1-ppc64el-cross libicu63 libio-string-perl libitm1-ppc64el-cross liblocale-gettext-perl liblsan0-ppc64el-cross libmagic-mgc libmagic1 libquadmath0-ppc64el-cross libstdc++-8-dev-ppc64el-cross libstdc++6-ppc64el-cross libtsan0-ppc64el-cross libubsan1-ppc64el-cross libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev-ppc64el-cross sensible-utils ucf Suggested packages: binutils-doc gcc-8-locales cpp-doc binutils-multiarch gcc-8-doc libstdc++6-8-dbg-ppc64el-cross libgcc1-dbg-ppc64el-cross libgomp1-dbg-ppc64el-cross libitm1-dbg-ppc64el-cross libatomic1-dbg-ppc64el-cross libasan5-dbg-ppc64el-cross liblsan0-dbg-ppc64el-cross libtsan0-dbg-ppc64el-cross libubsan1-dbg-ppc64el-cross libmpx2-dbg-ppc64el-cross libquadmath0-dbg-ppc64el-cross manpages-dev autoconf automake libtool flex bison gdb-powerpc64le-linux-gnu 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-powerpc64le-linux-gnu cpp-8-powerpc64le-linux-gnu cpp-powerpc64le-linux-gnu cross-config crossbuild-essential-ppc64el dpkg-cross file g++-8-powerpc64le-linux-gnu g++-powerpc64le-linux-gnu gcc-8-cross-base gcc-8-powerpc64le-linux-gnu gcc-8-powerpc64le-linux-gnu-base gcc-powerpc64le-linux-gnu libasan5-ppc64el-cross libatomic1-ppc64el-cross libc6-dev-ppc64el-cross libc6-ppc64el-cross libconfig-auto-perl libconfig-inifiles-perl libdebian-dpkgcross-perl libfile-homedir-perl libfile-which-perl libgcc-8-dev-ppc64el-cross libgcc1-ppc64el-cross libgomp1-ppc64el-cross libicu63 libio-string-perl libitm1-ppc64el-cross liblocale-gettext-perl liblsan0-ppc64el-cross libmagic-mgc libmagic1 libquadmath0-ppc64el-cross libstdc++-8-dev-ppc64el-cross libstdc++6-ppc64el-cross libtsan0-ppc64el-cross libubsan1-ppc64el-cross libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev-ppc64el-cross sbuild-build-depends-core-dummy:ppc64el sensible-utils ucf 0 upgraded, 48 newly installed, 0 to remove and 0 not upgraded. Need to get 43.9 MB of archives. After this operation, 169 MB of additional disk space will be used. Get:1 copy:/<>/resolver-EbjcLO/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 1:5.35-2 [242 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic1 amd64 1:5.35-2 [117 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 file amd64 1:5.35-2 [66.1 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-powerpc64le-linux-gnu amd64 2.31.1-12 [2424 kB] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-8-powerpc64le-linux-gnu-base amd64 8.2.0-20cross1 [190 kB] Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-8-powerpc64le-linux-gnu amd64 8.2.0-20cross1 [6591 kB] Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-powerpc64le-linux-gnu amd64 4:8.2.0-2 [16.4 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 8.2.0-20cross1 [185 kB] Get:14 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-ppc64el-cross all 2.28-4cross1 [1605 kB] Get:15 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc1-ppc64el-cross all 1:8.2.0-20cross1 [30.3 kB] Get:16 http://debian.oregonstate.edu/debian unstable/main amd64 libgomp1-ppc64el-cross all 8.2.0-20cross1 [77.5 kB] Get:17 http://debian.oregonstate.edu/debian unstable/main amd64 libitm1-ppc64el-cross all 8.2.0-20cross1 [29.0 kB] Get:18 http://debian.oregonstate.edu/debian unstable/main amd64 libatomic1-ppc64el-cross all 8.2.0-20cross1 [9636 B] Get:19 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++6-ppc64el-cross all 8.2.0-20cross1 [399 kB] Get:20 http://debian.oregonstate.edu/debian unstable/main amd64 libasan5-ppc64el-cross all 8.2.0-20cross1 [374 kB] Get:21 http://debian.oregonstate.edu/debian unstable/main amd64 liblsan0-ppc64el-cross all 8.2.0-20cross1 [141 kB] Get:22 http://debian.oregonstate.edu/debian unstable/main amd64 libtsan0-ppc64el-cross all 8.2.0-20cross1 [283 kB] Get:23 http://debian.oregonstate.edu/debian unstable/main amd64 libubsan1-ppc64el-cross all 8.2.0-20cross1 [131 kB] Get:24 http://debian.oregonstate.edu/debian unstable/main amd64 libquadmath0-ppc64el-cross all 8.2.0-20cross1 [136 kB] Get:25 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc-8-dev-ppc64el-cross all 8.2.0-20cross1 [1200 kB] Get:26 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-8-powerpc64le-linux-gnu amd64 8.2.0-20cross1 [7027 kB] Get:27 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-powerpc64le-linux-gnu amd64 4:8.2.0-2 [1472 B] Get:28 http://debian.oregonstate.edu/debian unstable/main amd64 linux-libc-dev-ppc64el-cross all 4.19.13-1cross1 [1208 kB] Get:29 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-dev-ppc64el-cross all 2.28-4cross1 [2747 kB] Get:30 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++-8-dev-ppc64el-cross all 8.2.0-20cross1 [1565 kB] Get:31 http://debian.oregonstate.edu/debian unstable/main amd64 g++-8-powerpc64le-linux-gnu amd64 8.2.0-20cross1 [7170 kB] Get:32 http://debian.oregonstate.edu/debian unstable/main amd64 g++-powerpc64le-linux-gnu amd64 4:8.2.0-2 [1184 B] Get:33 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-inifiles-perl all 3.000001-1 [51.9 kB] Get:34 http://debian.oregonstate.edu/debian unstable/main amd64 libio-string-perl all 1.08-3 [12.3 kB] Get:35 http://debian.oregonstate.edu/debian unstable/main amd64 libicu63 amd64 63.1-6 [8292 kB] Get:36 http://debian.oregonstate.edu/debian unstable/main amd64 libxml2 amd64 2.9.4+dfsg1-7+b3 [687 kB] Get:37 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-namespacesupport-perl all 1.12-1 [14.8 kB] Get:38 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-base-perl all 1.09-1 [20.4 kB] Get:39 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-perl all 1.00+dfsg-1 [58.6 kB] Get:40 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-libxml-perl amd64 2.0134+dfsg-1 [344 kB] Get:41 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-simple-perl all 2.25-1 [72.0 kB] Get:42 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-perl all 1.27-1 [66.8 kB] Get:43 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-auto-perl all 0.44-1 [19.5 kB] Get:44 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-which-perl all 1.23-1 [16.6 kB] Get:45 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-homedir-perl all 1.004-1 [42.7 kB] Get:46 http://debian.oregonstate.edu/debian unstable/main amd64 libdebian-dpkgcross-perl all 2.6.15-2 [38.5 kB] Get:47 http://debian.oregonstate.edu/debian unstable/main amd64 dpkg-cross all 2.6.15-2 [49.3 kB] Get:48 http://debian.oregonstate.edu/debian unstable/main amd64 crossbuild-essential-ppc64el all 12.5 [6548 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 43.9 MB in 1s (64.5 MB/s) Selecting previously unselected package liblocale-gettext-perl. (Reading database ... 11871 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%3a5.35-2_amd64.deb ... Unpacking libmagic-mgc (1:5.35-2) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../03-libmagic1_1%3a5.35-2_amd64.deb ... Unpacking libmagic1:amd64 (1:5.35-2) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.35-2_amd64.deb ... Unpacking file (1:5.35-2) ... 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) ... Selecting previously unselected package binutils-powerpc64le-linux-gnu. Preparing to unpack .../06-binutils-powerpc64le-linux-gnu_2.31.1-12_amd64.deb ... Unpacking binutils-powerpc64le-linux-gnu (2.31.1-12) ... Selecting previously unselected package gcc-8-powerpc64le-linux-gnu-base:amd64. Preparing to unpack .../07-gcc-8-powerpc64le-linux-gnu-base_8.2.0-20cross1_amd64.deb ... Unpacking gcc-8-powerpc64le-linux-gnu-base:amd64 (8.2.0-20cross1) ... Selecting previously unselected package cpp-8-powerpc64le-linux-gnu. Preparing to unpack .../08-cpp-8-powerpc64le-linux-gnu_8.2.0-20cross1_amd64.deb ... Unpacking cpp-8-powerpc64le-linux-gnu (8.2.0-20cross1) ... Selecting previously unselected package cpp-powerpc64le-linux-gnu. Preparing to unpack .../09-cpp-powerpc64le-linux-gnu_4%3a8.2.0-2_amd64.deb ... Unpacking cpp-powerpc64le-linux-gnu (4:8.2.0-2) ... Selecting previously unselected package cross-config. Preparing to unpack .../10-cross-config_2.6.15-2_all.deb ... Unpacking cross-config (2.6.15-2) ... Selecting previously unselected package gcc-8-cross-base. Preparing to unpack .../11-gcc-8-cross-base_8.2.0-20cross1_all.deb ... Unpacking gcc-8-cross-base (8.2.0-20cross1) ... Selecting previously unselected package libc6-ppc64el-cross. Preparing to unpack .../12-libc6-ppc64el-cross_2.28-4cross1_all.deb ... Unpacking libc6-ppc64el-cross (2.28-4cross1) ... Selecting previously unselected package libgcc1-ppc64el-cross. Preparing to unpack .../13-libgcc1-ppc64el-cross_1%3a8.2.0-20cross1_all.deb ... Unpacking libgcc1-ppc64el-cross (1:8.2.0-20cross1) ... Selecting previously unselected package libgomp1-ppc64el-cross. Preparing to unpack .../14-libgomp1-ppc64el-cross_8.2.0-20cross1_all.deb ... Unpacking libgomp1-ppc64el-cross (8.2.0-20cross1) ... Selecting previously unselected package libitm1-ppc64el-cross. Preparing to unpack .../15-libitm1-ppc64el-cross_8.2.0-20cross1_all.deb ... Unpacking libitm1-ppc64el-cross (8.2.0-20cross1) ... Selecting previously unselected package libatomic1-ppc64el-cross. Preparing to unpack .../16-libatomic1-ppc64el-cross_8.2.0-20cross1_all.deb ... Unpacking libatomic1-ppc64el-cross (8.2.0-20cross1) ... Selecting previously unselected package libstdc++6-ppc64el-cross. Preparing to unpack .../17-libstdc++6-ppc64el-cross_8.2.0-20cross1_all.deb ... Unpacking libstdc++6-ppc64el-cross (8.2.0-20cross1) ... Selecting previously unselected package libasan5-ppc64el-cross. Preparing to unpack .../18-libasan5-ppc64el-cross_8.2.0-20cross1_all.deb ... Unpacking libasan5-ppc64el-cross (8.2.0-20cross1) ... Selecting previously unselected package liblsan0-ppc64el-cross. Preparing to unpack .../19-liblsan0-ppc64el-cross_8.2.0-20cross1_all.deb ... Unpacking liblsan0-ppc64el-cross (8.2.0-20cross1) ... Selecting previously unselected package libtsan0-ppc64el-cross. Preparing to unpack .../20-libtsan0-ppc64el-cross_8.2.0-20cross1_all.deb ... Unpacking libtsan0-ppc64el-cross (8.2.0-20cross1) ... 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Unpacking gcc-powerpc64le-linux-gnu (4:8.2.0-2) ... Selecting previously unselected package linux-libc-dev-ppc64el-cross. Preparing to unpack .../26-linux-libc-dev-ppc64el-cross_4.19.13-1cross1_all.deb ... Unpacking linux-libc-dev-ppc64el-cross (4.19.13-1cross1) ... Selecting previously unselected package libc6-dev-ppc64el-cross. Preparing to unpack .../27-libc6-dev-ppc64el-cross_2.28-4cross1_all.deb ... Unpacking libc6-dev-ppc64el-cross (2.28-4cross1) ... Selecting previously unselected package libstdc++-8-dev-ppc64el-cross. Preparing to unpack .../28-libstdc++-8-dev-ppc64el-cross_8.2.0-20cross1_all.deb ... Unpacking libstdc++-8-dev-ppc64el-cross (8.2.0-20cross1) ... Selecting previously unselected package g++-8-powerpc64le-linux-gnu. Preparing to unpack .../29-g++-8-powerpc64le-linux-gnu_8.2.0-20cross1_amd64.deb ... Unpacking g++-8-powerpc64le-linux-gnu (8.2.0-20cross1) ... Selecting previously unselected package g++-powerpc64le-linux-gnu. Preparing to unpack .../30-g++-powerpc64le-linux-gnu_4%3a8.2.0-2_amd64.deb ... Unpacking g++-powerpc64le-linux-gnu (4:8.2.0-2) ... Selecting previously unselected package libconfig-inifiles-perl. Preparing to unpack .../31-libconfig-inifiles-perl_3.000001-1_all.deb ... Unpacking libconfig-inifiles-perl (3.000001-1) ... Selecting previously unselected package libio-string-perl. Preparing to unpack .../32-libio-string-perl_1.08-3_all.deb ... Unpacking libio-string-perl (1.08-3) ... Selecting previously unselected package libicu63:amd64. Preparing to unpack .../33-libicu63_63.1-6_amd64.deb ... Unpacking libicu63:amd64 (63.1-6) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../34-libxml2_2.9.4+dfsg1-7+b3_amd64.deb ... Unpacking libxml2:amd64 (2.9.4+dfsg1-7+b3) ... Selecting previously unselected package libxml-namespacesupport-perl. Preparing to unpack .../35-libxml-namespacesupport-perl_1.12-1_all.deb ... Unpacking libxml-namespacesupport-perl (1.12-1) ... Selecting previously unselected package libxml-sax-base-perl. Preparing to unpack .../36-libxml-sax-base-perl_1.09-1_all.deb ... Unpacking libxml-sax-base-perl (1.09-1) ... Selecting previously unselected package libxml-sax-perl. Preparing to unpack .../37-libxml-sax-perl_1.00+dfsg-1_all.deb ... Unpacking libxml-sax-perl (1.00+dfsg-1) ... Selecting previously unselected package libxml-libxml-perl. Preparing to unpack .../38-libxml-libxml-perl_2.0134+dfsg-1_amd64.deb ... Unpacking libxml-libxml-perl (2.0134+dfsg-1) ... Selecting previously unselected package libxml-simple-perl. Preparing to unpack .../39-libxml-simple-perl_2.25-1_all.deb ... Unpacking libxml-simple-perl (2.25-1) ... Selecting previously unselected package libyaml-perl. Preparing to unpack .../40-libyaml-perl_1.27-1_all.deb ... Unpacking libyaml-perl (1.27-1) ... Selecting previously unselected package libconfig-auto-perl. Preparing to unpack .../41-libconfig-auto-perl_0.44-1_all.deb ... Unpacking libconfig-auto-perl (0.44-1) ... Selecting previously unselected package libfile-which-perl. Preparing to unpack .../42-libfile-which-perl_1.23-1_all.deb ... Unpacking libfile-which-perl (1.23-1) ... Selecting previously unselected package libfile-homedir-perl. Preparing to unpack .../43-libfile-homedir-perl_1.004-1_all.deb ... Unpacking libfile-homedir-perl (1.004-1) ... Selecting previously unselected package libdebian-dpkgcross-perl. Preparing to unpack .../44-libdebian-dpkgcross-perl_2.6.15-2_all.deb ... Unpacking libdebian-dpkgcross-perl (2.6.15-2) ... Selecting previously unselected package dpkg-cross. Preparing to unpack .../45-dpkg-cross_2.6.15-2_all.deb ... Unpacking dpkg-cross (2.6.15-2) ... Selecting previously unselected package crossbuild-essential-ppc64el. Preparing to unpack .../46-crossbuild-essential-ppc64el_12.5_all.deb ... Unpacking crossbuild-essential-ppc64el (12.5) ... Selecting previously unselected package sbuild-build-depends-core-dummy:ppc64el. Preparing to unpack .../47-sbuild-build-depends-core-dummy_0.invalid.0_ppc64el.deb ... Unpacking sbuild-build-depends-core-dummy:ppc64el (0.invalid.0) ... Setting up gcc-8-cross-base (8.2.0-20cross1) ... Setting up libconfig-inifiles-perl (3.000001-1) ... Setting up libxml-namespacesupport-perl (1.12-1) ... Setting up libicu63:amd64 (63.1-6) ... Setting up libfile-which-perl (1.23-1) ... Setting up libc6-ppc64el-cross (2.28-4cross1) ... Setting up libfile-homedir-perl (1.004-1) ... Setting up binutils-powerpc64le-linux-gnu (2.31.1-12) ... Setting up gcc-8-powerpc64le-linux-gnu-base:amd64 (8.2.0-20cross1) ... Setting up libyaml-perl (1.27-1) ... Setting up linux-libc-dev-ppc64el-cross (4.19.13-1cross1) ... Setting up libquadmath0-ppc64el-cross (8.2.0-20cross1) ... Setting up libxml2:amd64 (2.9.4+dfsg1-7+b3) ... Setting up libmagic-mgc (1:5.35-2) ... Setting up libmagic1:amd64 (1:5.35-2) ... Setting up libxml-sax-base-perl (1.09-1) ... Setting up sensible-utils (0.0.12) ... Setting up libgcc1-ppc64el-cross (1:8.2.0-20cross1) ... Setting up cross-config (2.6.15-2) ... Setting up libitm1-ppc64el-cross (8.2.0-20cross1) ... Setting up libio-string-perl (1.08-3) ... Setting up liblocale-gettext-perl (1.07-3+b4) ... Setting up libatomic1-ppc64el-cross (8.2.0-20cross1) ... Setting up libstdc++6-ppc64el-cross (8.2.0-20cross1) ... Setting up libubsan1-ppc64el-cross (8.2.0-20cross1) ... Setting up libasan5-ppc64el-cross (8.2.0-20cross1) ... Setting up cpp-8-powerpc64le-linux-gnu (8.2.0-20cross1) ... Setting up libgomp1-ppc64el-cross (8.2.0-20cross1) ... Setting up libc6-dev-ppc64el-cross (2.28-4cross1) ... Setting up liblsan0-ppc64el-cross (8.2.0-20cross1) ... Setting up file (1:5.35-2) ... Setting up ucf (3.0038+nmu1) ... Setting up libtsan0-ppc64el-cross (8.2.0-20cross1) ... 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 cpp-powerpc64le-linux-gnu (4:8.2.0-2) ... Setting up libgcc-8-dev-ppc64el-cross (8.2.0-20cross1) ... Setting up gcc-8-powerpc64le-linux-gnu (8.2.0-20cross1) ... 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 gcc-powerpc64le-linux-gnu (4:8.2.0-2) ... Setting up libstdc++-8-dev-ppc64el-cross (8.2.0-20cross1) ... Setting up g++-8-powerpc64le-linux-gnu (8.2.0-20cross1) ... Setting up libxml-simple-perl (2.25-1) ... Setting up g++-powerpc64le-linux-gnu (4:8.2.0-2) ... 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-ppc64el (12.5) ... Setting up sbuild-build-depends-core-dummy:ppc64el (0.invalid.0) ... Processing triggers for libc-bin (2.28-7) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (ppc64el included in any all) Setup apt archive ----------------- dpkg-deb: building package 'sbuild-build-depends-essential-dummy' in '/<>/resolver-EbjcLO/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-EbjcLO/apt_archive ./ InRelease Get:2 copy:/<>/resolver-EbjcLO/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-EbjcLO/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-EbjcLO/apt_archive ./ Sources [481 B] Get:5 copy:/<>/resolver-EbjcLO/apt_archive ./ Packages [572 B] Fetched 2016 B in 0s (133 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:ppc64el 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-EbjcLO/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:ppc64el. (Reading database ... 15106 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-essential-dummy_0.invalid.0_ppc64el.deb ... Unpacking sbuild-build-depends-essential-dummy:ppc64el (0.invalid.0) ... Setting up sbuild-build-depends-essential-dummy:ppc64el (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-EbjcLO/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-EbjcLO/apt_archive ./ InRelease Get:2 copy:/<>/resolver-EbjcLO/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-EbjcLO/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-EbjcLO/apt_archive ./ Sources [663 B] Get:5 copy:/<>/resolver-EbjcLO/apt_archive ./ Packages [748 B] Fetched 2374 B in 0s (0 B/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:ppc64el gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasan5:ppc64el libatomic1:ppc64el libavahi-client3 libavahi-common-data libavahi-common3 libbrotli1 libbsd0 libc6:ppc64el libc6-dev:ppc64el libcairo2 libcroco3 libcups2 libcupsimage2 libdbus-1-3 libelf1 libexpat1 libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libgcc-8-dev:ppc64el libgcc1:ppc64el libglib2.0-0 libgomp1:ppc64el libgraphite2-3 libgs9 libgs9-common libgssapi-krb5-2 libharfbuzz-icu0 libharfbuzz0b libice6 libidn11 libijs-0.35 libitm1:ppc64el libjbig0 libjbig2dec0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkpathsea6 libkrb5-3 libkrb5support0 liblcms2-2 liblsan0:ppc64el libncurses6 libopenjp2-7 libpaper-utils libpaper1 libpipeline1 libpixman-1-0 libpng16-16 libpotrace0 libptexenc1 libquadmath0:ppc64el libsigsegv2 libsm6 libssl1.1 libstdc++-8-dev:ppc64el libstdc++6:ppc64el libsynctex2 libteckit0 libtexlua52 libtexlua53 libtexluajit2 libtiff5 libtool libtsan0:ppc64el libubsan1:ppc64el 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:ppc64el 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:ppc64el zlib1g-dev:ppc64el Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff glibc-doc:ppc64el libc-l10n:ppc64el locales:ppc64el manpages-dev:ppc64el cups-common krb5-doc krb5-user liblcms2-utils libstdc++-8-doc:ppc64el 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:ppc64el 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:ppc64el gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasan5:ppc64el libatomic1:ppc64el libavahi-client3 libavahi-common-data libavahi-common3 libbrotli1 libbsd0 libc6:ppc64el libc6-dev:ppc64el libcairo2 libcroco3 libcups2 libcupsimage2 libdbus-1-3 libelf1 libexpat1 libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libgcc-8-dev:ppc64el libgcc1:ppc64el libglib2.0-0 libgomp1:ppc64el libgraphite2-3 libgs9 libgs9-common libgssapi-krb5-2 libharfbuzz-icu0 libharfbuzz0b libice6 libidn11 libijs-0.35 libitm1:ppc64el libjbig0 libjbig2dec0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkpathsea6 libkrb5-3 libkrb5support0 liblcms2-2 liblsan0:ppc64el libncurses6 libopenjp2-7 libpaper-utils libpaper1 libpipeline1 libpixman-1-0 libpng16-16 libpotrace0 libptexenc1 libquadmath0:ppc64el libsigsegv2 libsm6 libssl1.1 libstdc++-8-dev:ppc64el libstdc++6:ppc64el libsynctex2 libteckit0 libtexlua52 libtexlua53 libtexluajit2 libtiff5 libtool libtsan0:ppc64el libubsan1:ppc64el 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:ppc64el lsb-base m4 man-db po-debconf poppler-data sbuild-build-depends-velvet-dummy:ppc64el t1utils tex-common texlive-base texlive-binaries texlive-latex-base texlive-latex-recommended x11-common xdg-utils zlib1g:ppc64el zlib1g-dev:ppc64el 0 upgraded, 121 newly installed, 0 to remove and 0 not upgraded. Need to get 96.3 MB of archives. After this operation, 354 MB of additional disk space will be used. Get:1 copy:/<>/resolver-EbjcLO/apt_archive ./ sbuild-build-depends-velvet-dummy 0.invalid.0 [908 B] Get:2 http://debian.oregonstate.edu/debian unstable/main amd64 libbsd0 amd64 0.9.1-1 [99.3 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 1.22.4-2 [917 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 6.10 [53.0 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 2.4.6-9 [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 1.1.1-1 [19.7 kB] Get:21 http://debian.oregonstate.edu/debian unstable/main amd64 dh-strip-nondeterminism all 1.1.1-1 [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 [1015 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 2.004.5-5 [4539 kB] Get:34 http://debian.oregonstate.edu/debian unstable/main ppc64el gcc-8-base ppc64el 8.2.0-21 [190 kB] Get:35 http://debian.oregonstate.edu/debian unstable/main ppc64el libgcc1 ppc64el 1:8.2.0-21 [30.2 kB] Get:36 http://debian.oregonstate.edu/debian unstable/main ppc64el libc6 ppc64el 2.28-7 [2888 kB] Get:37 http://debian.oregonstate.edu/debian unstable/main ppc64el libstdc++6 ppc64el 8.2.0-21 [438 kB] Get:38 http://debian.oregonstate.edu/debian unstable/main ppc64el libasan5 ppc64el 8.2.0-21 [381 kB] Get:39 http://debian.oregonstate.edu/debian unstable/main ppc64el libatomic1 ppc64el 8.2.0-21 [9684 B] Get:40 http://debian.oregonstate.edu/debian unstable/main amd64 libavahi-common-data amd64 0.7-4+b1 [122 kB] Get:41 http://debian.oregonstate.edu/debian unstable/main amd64 libavahi-common3 amd64 0.7-4+b1 [54.6 kB] Get:42 http://debian.oregonstate.edu/debian unstable/main amd64 libdbus-1-3 amd64 1.12.12-1 [212 kB] Get:43 http://debian.oregonstate.edu/debian unstable/main amd64 libavahi-client3 amd64 0.7-4+b1 [58.1 kB] Get:44 http://debian.oregonstate.edu/debian unstable/main amd64 libbrotli1 amd64 1.0.7-2 [270 kB] Get:45 http://debian.oregonstate.edu/debian unstable/main ppc64el linux-libc-dev ppc64el 4.19.20-1 [1135 kB] Get:46 http://debian.oregonstate.edu/debian unstable/main ppc64el libc6-dev ppc64el 2.28-7 [2747 kB] Get:47 http://debian.oregonstate.edu/debian unstable/main amd64 libexpat1 amd64 2.2.6-1 [105 kB] Get:48 http://debian.oregonstate.edu/debian unstable/main amd64 libpng16-16 amd64 1.6.36-5 [292 kB] Get:49 http://debian.oregonstate.edu/debian unstable/main amd64 libfreetype6 amd64 2.9.1-3 [379 kB] Get:50 http://debian.oregonstate.edu/debian unstable/main amd64 libfontconfig1 amd64 2.13.1-2 [346 kB] Get:51 http://debian.oregonstate.edu/debian unstable/main amd64 libpixman-1-0 amd64 0.36.0-1 [537 kB] Get:52 http://debian.oregonstate.edu/debian unstable/main amd64 libxau6 amd64 1:1.0.8-1+b2 [19.9 kB] Get:53 http://debian.oregonstate.edu/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get:54 http://debian.oregonstate.edu/debian unstable/main amd64 libxcb1 amd64 1.13.1-2 [137 kB] Get:55 http://debian.oregonstate.edu/debian unstable/main amd64 libx11-data all 2:1.6.7-1 [298 kB] Get:56 http://debian.oregonstate.edu/debian unstable/main amd64 libx11-6 amd64 2:1.6.7-1 [754 kB] Get:57 http://debian.oregonstate.edu/debian unstable/main amd64 libxcb-render0 amd64 1.13.1-2 [109 kB] Get:58 http://debian.oregonstate.edu/debian unstable/main amd64 libxcb-shm0 amd64 1.13.1-2 [99.2 kB] Get:59 http://debian.oregonstate.edu/debian unstable/main amd64 libxext6 amd64 2:1.3.3-1+b2 [52.5 kB] Get:60 http://debian.oregonstate.edu/debian unstable/main amd64 libxrender1 amd64 1:0.9.10-1 [33.0 kB] Get:61 http://debian.oregonstate.edu/debian unstable/main amd64 libcairo2 amd64 1.16.0-2 [690 kB] Get:62 http://debian.oregonstate.edu/debian unstable/main amd64 libkeyutils1 amd64 1.6-2 [14.5 kB] Get:63 http://debian.oregonstate.edu/debian unstable/main amd64 libkrb5support0 amd64 1.17-1 [65.5 kB] Get:64 http://debian.oregonstate.edu/debian unstable/main amd64 libk5crypto3 amd64 1.17-1 [121 kB] Get:65 http://debian.oregonstate.edu/debian unstable/main amd64 libssl1.1 amd64 1.1.1a-1 [1527 kB] Get:66 http://debian.oregonstate.edu/debian unstable/main amd64 libkrb5-3 amd64 1.17-1 [368 kB] Get:67 http://debian.oregonstate.edu/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.17-1 [159 kB] Get:68 http://debian.oregonstate.edu/debian unstable/main amd64 libcups2 amd64 2.2.10-4 [324 kB] Get:69 http://debian.oregonstate.edu/debian unstable/main amd64 libcupsimage2 amd64 2.2.10-4 [132 kB] Get:70 http://debian.oregonstate.edu/debian unstable/main ppc64el libgomp1 ppc64el 8.2.0-21 [79.0 kB] Get:71 http://debian.oregonstate.edu/debian unstable/main ppc64el libitm1 ppc64el 8.2.0-21 [29.3 kB] Get:72 http://debian.oregonstate.edu/debian unstable/main ppc64el liblsan0 ppc64el 8.2.0-21 [142 kB] Get:73 http://debian.oregonstate.edu/debian unstable/main ppc64el libtsan0 ppc64el 8.2.0-21 [291 kB] Get:74 http://debian.oregonstate.edu/debian unstable/main ppc64el libubsan1 ppc64el 8.2.0-21 [132 kB] Get:75 http://debian.oregonstate.edu/debian unstable/main ppc64el libquadmath0 ppc64el 8.2.0-21 [136 kB] Get:76 http://debian.oregonstate.edu/debian unstable/main ppc64el libgcc-8-dev ppc64el 8.2.0-21 [1190 kB] Get:77 http://debian.oregonstate.edu/debian unstable/main amd64 libgraphite2-3 amd64 1.3.13-7 [80.7 kB] Get:78 http://debian.oregonstate.edu/debian unstable/main amd64 libgs9-common all 9.26a~dfsg-2 [5136 kB] Get:79 http://debian.oregonstate.edu/debian unstable/main amd64 libidn11 amd64 1.33-2.2 [116 kB] Get:80 http://debian.oregonstate.edu/debian unstable/main amd64 libijs-0.35 amd64 0.35-13 [18.5 kB] Get:81 http://debian.oregonstate.edu/debian unstable/main amd64 libjbig2dec0 amd64 0.15-2 [61.7 kB] Get:82 http://debian.oregonstate.edu/debian unstable/main amd64 libjpeg62-turbo amd64 1:1.5.2-2+b1 [134 kB] Get:83 http://debian.oregonstate.edu/debian unstable/main amd64 liblcms2-2 amd64 2.9-3 [145 kB] Get:84 http://debian.oregonstate.edu/debian unstable/main amd64 libopenjp2-7 amd64 2.3.0-1.1 [158 kB] Get:85 http://debian.oregonstate.edu/debian unstable/main amd64 libpaper1 amd64 1.1.26 [20.8 kB] Get:86 http://debian.oregonstate.edu/debian unstable/main amd64 libjbig0 amd64 2.1-3.1+b2 [31.0 kB] Get:87 http://debian.oregonstate.edu/debian unstable/main amd64 libwebp6 amd64 0.6.1-2 [263 kB] Get:88 http://debian.oregonstate.edu/debian unstable/main amd64 libtiff5 amd64 4.0.10-4 [257 kB] Get:89 http://debian.oregonstate.edu/debian unstable/main amd64 libgs9 amd64 9.26a~dfsg-2 [2198 kB] Get:90 http://debian.oregonstate.edu/debian unstable/main amd64 libharfbuzz0b amd64 2.3.1-1 [1187 kB] Get:91 http://debian.oregonstate.edu/debian unstable/main amd64 libharfbuzz-icu0 amd64 2.3.1-1 [834 kB] Get:92 http://debian.oregonstate.edu/debian unstable/main amd64 lsb-base all 10.2018112800 [28.3 kB] Get:93 http://debian.oregonstate.edu/debian unstable/main amd64 x11-common all 1:7.7+19 [251 kB] Get:94 http://debian.oregonstate.edu/debian unstable/main amd64 libice6 amd64 2:1.0.9-2 [58.7 kB] Get:95 http://debian.oregonstate.edu/debian unstable/main amd64 libkpathsea6 amd64 2018.20181218.49446-1 [167 kB] Get:96 http://debian.oregonstate.edu/debian unstable/main amd64 libpaper-utils amd64 1.1.26 [17.9 kB] Get:97 http://debian.oregonstate.edu/debian unstable/main amd64 libpotrace0 amd64 1.15-1 [26.3 kB] Get:98 http://debian.oregonstate.edu/debian unstable/main amd64 libptexenc1 amd64 2018.20181218.49446-1 [61.0 kB] Get:99 http://debian.oregonstate.edu/debian unstable/main amd64 libsm6 amd64 2:1.2.3-1 [35.1 kB] Get:100 http://debian.oregonstate.edu/debian unstable/main ppc64el libstdc++-8-dev ppc64el 8.2.0-21 [1589 kB] Get:101 http://debian.oregonstate.edu/debian unstable/main amd64 libsynctex2 amd64 2018.20181218.49446-1 [80.5 kB] Get:102 http://debian.oregonstate.edu/debian unstable/main amd64 libteckit0 amd64 2.5.8+ds2-5 [318 kB] Get:103 http://debian.oregonstate.edu/debian unstable/main amd64 libtexlua52 amd64 2018.20181218.49446-1 [112 kB] Get:104 http://debian.oregonstate.edu/debian unstable/main amd64 libtexlua53 amd64 2018.20181218.49446-1 [126 kB] Get:105 http://debian.oregonstate.edu/debian unstable/main amd64 libtexluajit2 amd64 2018.20181218.49446-1 [256 kB] Get:106 http://debian.oregonstate.edu/debian unstable/main amd64 libwoff1 amd64 1.0.2-1 [43.2 kB] Get:107 http://debian.oregonstate.edu/debian unstable/main amd64 libxt6 amd64 1:1.1.5-1 [188 kB] Get:108 http://debian.oregonstate.edu/debian unstable/main amd64 libxmu6 amd64 2:1.1.2-2 [60.3 kB] Get:109 http://debian.oregonstate.edu/debian unstable/main amd64 libxpm4 amd64 1:3.5.12-1 [49.1 kB] Get:110 http://debian.oregonstate.edu/debian unstable/main amd64 libxaw7 amd64 2:1.0.13-1+b2 [201 kB] Get:111 http://debian.oregonstate.edu/debian unstable/main amd64 libxi6 amd64 2:1.7.9-1 [82.6 kB] Get:112 http://debian.oregonstate.edu/debian unstable/main amd64 libxxhash0 amd64 0.6.5-2 [7156 B] Get:113 http://debian.oregonstate.edu/debian unstable/main amd64 libzzip-0-13 amd64 0.13.62-3.1 [55.4 kB] Get:114 http://debian.oregonstate.edu/debian unstable/main amd64 t1utils amd64 1.41-3 [62.3 kB] Get:115 http://debian.oregonstate.edu/debian unstable/main amd64 texlive-binaries amd64 2018.20181218.49446-1 [11.3 MB] Get:116 http://debian.oregonstate.edu/debian unstable/main amd64 xdg-utils all 1.1.3-1 [73.3 kB] Get:117 http://debian.oregonstate.edu/debian unstable/main amd64 texlive-base all 2018.20190131-1 [19.7 MB] Get:118 http://debian.oregonstate.edu/debian unstable/main amd64 texlive-latex-base all 2018.20190131-1 [985 kB] Get:119 http://debian.oregonstate.edu/debian unstable/main amd64 texlive-latex-recommended all 2018.20190131-1 [15.2 MB] Get:120 http://debian.oregonstate.edu/debian unstable/main ppc64el zlib1g ppc64el 1:1.2.11.dfsg-1 [96.4 kB] Get:121 http://debian.oregonstate.edu/debian unstable/main ppc64el zlib1g-dev ppc64el 1:1.2.11.dfsg-1 [216 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 96.3 MB in 2s (61.1 MB/s) Selecting previously unselected package libbsd0:amd64. (Reading database ... 15106 files and directories currently installed.) Preparing to unpack .../000-libbsd0_0.9.1-1_amd64.deb ... Unpacking libbsd0:amd64 (0.9.1-1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../001-bsdmainutils_11.1.2+b1_amd64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../002-libuchardet0_0.0.6-3_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../003-groff-base_1.22.4-2_amd64.deb ... Unpacking groff-base (1.22.4-2) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../004-libpipeline1_1.5.1-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../005-man-db_2.8.5-2_amd64.deb ... Unpacking man-db (2.8.5-2) ... Selecting previously unselected package poppler-data. 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Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../019-dh-strip-nondeterminism_1.1.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.1.1-1) ... Selecting previously unselected package libelf1:amd64. Preparing to unpack .../020-libelf1_0.176-1_amd64.deb ... Unpacking libelf1:amd64 (0.176-1) ... Selecting previously unselected package dwz. Preparing to unpack .../021-dwz_0.12-3_amd64.deb ... Unpacking dwz (0.12-3) ... Selecting previously unselected package libglib2.0-0:amd64. Preparing to unpack .../022-libglib2.0-0_2.58.3-1_amd64.deb ... Unpacking libglib2.0-0:amd64 (2.58.3-1) ... Selecting previously unselected package libcroco3:amd64. Preparing to unpack .../023-libcroco3_0.6.12-3_amd64.deb ... Unpacking libcroco3:amd64 (0.6.12-3) ... Selecting previously unselected package libncurses6:amd64. Preparing to unpack .../024-libncurses6_6.1+20181013-2_amd64.deb ... Unpacking libncurses6:amd64 (6.1+20181013-2) ... Selecting previously unselected package gettext. Preparing to unpack .../025-gettext_0.19.8.1-9_amd64.deb ... Unpacking gettext (0.19.8.1-9) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../026-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../027-po-debconf_1.0.21_all.deb ... Unpacking po-debconf (1.0.21) ... Selecting previously unselected package debhelper. Preparing to unpack .../028-debhelper_12.1_all.deb ... Unpacking debhelper (12.1) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../029-fonts-dejavu-core_2.37-1_all.deb ... Unpacking fonts-dejavu-core (2.37-1) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../030-fontconfig-config_2.13.1-2_all.deb ... Unpacking fontconfig-config (2.13.1-2) ... Selecting previously unselected package fonts-lmodern. Preparing to unpack .../031-fonts-lmodern_2.004.5-5_all.deb ... Unpacking fonts-lmodern (2.004.5-5) ... Selecting previously unselected package gcc-8-base:ppc64el. Preparing to unpack .../032-gcc-8-base_8.2.0-21_ppc64el.deb ... Unpacking gcc-8-base:ppc64el (8.2.0-21) ... Selecting previously unselected package libgcc1:ppc64el. Preparing to unpack .../033-libgcc1_1%3a8.2.0-21_ppc64el.deb ... Unpacking libgcc1:ppc64el (1:8.2.0-21) ... Selecting previously unselected package libc6:ppc64el. Preparing to unpack .../034-libc6_2.28-7_ppc64el.deb ... Unpacking libc6:ppc64el (2.28-7) ... Selecting previously unselected package libstdc++6:ppc64el. Preparing to unpack .../035-libstdc++6_8.2.0-21_ppc64el.deb ... Unpacking libstdc++6:ppc64el (8.2.0-21) ... Selecting previously unselected package libasan5:ppc64el. Preparing to unpack .../036-libasan5_8.2.0-21_ppc64el.deb ... Unpacking libasan5:ppc64el (8.2.0-21) ... Selecting previously unselected package libatomic1:ppc64el. Preparing to unpack .../037-libatomic1_8.2.0-21_ppc64el.deb ... Unpacking libatomic1:ppc64el (8.2.0-21) ... Selecting previously unselected package libavahi-common-data:amd64. Preparing to unpack .../038-libavahi-common-data_0.7-4+b1_amd64.deb ... Unpacking libavahi-common-data:amd64 (0.7-4+b1) ... Selecting previously unselected package libavahi-common3:amd64. Preparing to unpack .../039-libavahi-common3_0.7-4+b1_amd64.deb ... Unpacking libavahi-common3:amd64 (0.7-4+b1) ... Selecting previously unselected package libdbus-1-3:amd64. Preparing to unpack .../040-libdbus-1-3_1.12.12-1_amd64.deb ... Unpacking libdbus-1-3:amd64 (1.12.12-1) ... Selecting previously unselected package libavahi-client3:amd64. Preparing to unpack .../041-libavahi-client3_0.7-4+b1_amd64.deb ... Unpacking libavahi-client3:amd64 (0.7-4+b1) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../042-libbrotli1_1.0.7-2_amd64.deb ... Unpacking libbrotli1:amd64 (1.0.7-2) ... Selecting previously unselected package linux-libc-dev:ppc64el. Preparing to unpack .../043-linux-libc-dev_4.19.20-1_ppc64el.deb ... Unpacking linux-libc-dev:ppc64el (4.19.20-1) ... Selecting previously unselected package libc6-dev:ppc64el. Preparing to unpack .../044-libc6-dev_2.28-7_ppc64el.deb ... Unpacking libc6-dev:ppc64el (2.28-7) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../045-libexpat1_2.2.6-1_amd64.deb ... Unpacking libexpat1:amd64 (2.2.6-1) ... Selecting previously unselected package libpng16-16:amd64. Preparing to unpack .../046-libpng16-16_1.6.36-5_amd64.deb ... Unpacking libpng16-16:amd64 (1.6.36-5) ... Selecting previously unselected package libfreetype6:amd64. Preparing to unpack .../047-libfreetype6_2.9.1-3_amd64.deb ... Unpacking libfreetype6:amd64 (2.9.1-3) ... Selecting previously unselected package libfontconfig1:amd64. Preparing to unpack .../048-libfontconfig1_2.13.1-2_amd64.deb ... Unpacking libfontconfig1:amd64 (2.13.1-2) ... Selecting previously unselected package libpixman-1-0:amd64. Preparing to unpack .../049-libpixman-1-0_0.36.0-1_amd64.deb ... Unpacking libpixman-1-0:amd64 (0.36.0-1) ... Selecting previously unselected package libxau6:amd64. Preparing to unpack .../050-libxau6_1%3a1.0.8-1+b2_amd64.deb ... Unpacking libxau6:amd64 (1:1.0.8-1+b2) ... Selecting previously unselected package libxdmcp6:amd64. Preparing to unpack .../051-libxdmcp6_1%3a1.1.2-3_amd64.deb ... Unpacking libxdmcp6:amd64 (1:1.1.2-3) ... Selecting previously unselected package libxcb1:amd64. Preparing to unpack .../052-libxcb1_1.13.1-2_amd64.deb ... Unpacking libxcb1:amd64 (1.13.1-2) ... Selecting previously unselected package libx11-data. Preparing to unpack .../053-libx11-data_2%3a1.6.7-1_all.deb ... Unpacking libx11-data (2:1.6.7-1) ... Selecting previously unselected package libx11-6:amd64. Preparing to unpack .../054-libx11-6_2%3a1.6.7-1_amd64.deb ... Unpacking libx11-6:amd64 (2:1.6.7-1) ... Selecting previously unselected package libxcb-render0:amd64. Preparing to unpack .../055-libxcb-render0_1.13.1-2_amd64.deb ... Unpacking libxcb-render0:amd64 (1.13.1-2) ... Selecting previously unselected package libxcb-shm0:amd64. Preparing to unpack .../056-libxcb-shm0_1.13.1-2_amd64.deb ... Unpacking libxcb-shm0:amd64 (1.13.1-2) ... Selecting previously unselected package libxext6:amd64. Preparing to unpack .../057-libxext6_2%3a1.3.3-1+b2_amd64.deb ... Unpacking libxext6:amd64 (2:1.3.3-1+b2) ... Selecting previously unselected package libxrender1:amd64. Preparing to unpack .../058-libxrender1_1%3a0.9.10-1_amd64.deb ... Unpacking libxrender1:amd64 (1:0.9.10-1) ... Selecting previously unselected package libcairo2:amd64. Preparing to unpack .../059-libcairo2_1.16.0-2_amd64.deb ... Unpacking libcairo2:amd64 (1.16.0-2) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../060-libkeyutils1_1.6-2_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6-2) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../061-libkrb5support0_1.17-1_amd64.deb ... Unpacking libkrb5support0:amd64 (1.17-1) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../062-libk5crypto3_1.17-1_amd64.deb ... Unpacking libk5crypto3:amd64 (1.17-1) ... Selecting previously unselected package libssl1.1:amd64. Preparing to unpack .../063-libssl1.1_1.1.1a-1_amd64.deb ... Unpacking libssl1.1:amd64 (1.1.1a-1) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../064-libkrb5-3_1.17-1_amd64.deb ... Unpacking libkrb5-3:amd64 (1.17-1) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../065-libgssapi-krb5-2_1.17-1_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.17-1) ... Selecting previously unselected package libcups2:amd64. Preparing to unpack .../066-libcups2_2.2.10-4_amd64.deb ... Unpacking libcups2:amd64 (2.2.10-4) ... Selecting previously unselected package libcupsimage2:amd64. Preparing to unpack .../067-libcupsimage2_2.2.10-4_amd64.deb ... Unpacking libcupsimage2:amd64 (2.2.10-4) ... Selecting previously unselected package libgomp1:ppc64el. Preparing to unpack .../068-libgomp1_8.2.0-21_ppc64el.deb ... Unpacking libgomp1:ppc64el (8.2.0-21) ... Selecting previously unselected package libitm1:ppc64el. Preparing to unpack .../069-libitm1_8.2.0-21_ppc64el.deb ... Unpacking libitm1:ppc64el (8.2.0-21) ... Selecting previously unselected package liblsan0:ppc64el. Preparing to unpack .../070-liblsan0_8.2.0-21_ppc64el.deb ... Unpacking liblsan0:ppc64el (8.2.0-21) ... Selecting previously unselected package libtsan0:ppc64el. Preparing to unpack .../071-libtsan0_8.2.0-21_ppc64el.deb ... Unpacking libtsan0:ppc64el (8.2.0-21) ... Selecting previously unselected package libubsan1:ppc64el. Preparing to unpack .../072-libubsan1_8.2.0-21_ppc64el.deb ... 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Setting up libjpeg62-turbo:amd64 (1:1.5.2-2+b1) ... Setting up tex-common (6.10) ... update-language: texlive-base not installed and configured, doing nothing! Setting up libarchive-zip-perl (1.64-1) ... Setting up libwoff1:amd64 (1.0.2-1) ... Setting up libpng16-16:amd64 (1.6.36-5) ... Setting up liblcms2-2:amd64 (2.9-3) ... Setting up libjbig0:amd64 (2.1-3.1+b2) ... Setting up libsigsegv2:amd64 (2.12-2) ... Setting up fonts-dejavu-core (2.37-1) ... Setting up poppler-data (0.4.9-2) ... Setting up libelf1:amd64 (0.176-1) ... Setting up libglib2.0-0:amd64 (2.58.3-1) ... No schema files found: doing nothing. Setting up libtexlua53:amd64 (2018.20181218.49446-1) ... Setting up linux-libc-dev:ppc64el (4.19.20-1) ... Setting up gettext-base (0.19.8.1-9) ... Setting up libsynctex2:amd64 (2018.20181218.49446-1) ... Setting up libpipeline1:amd64 (1.5.1-2) ... Setting up m4 (1.4.18-2) ... Setting up libxxhash0:amd64 (0.6.5-2) ... Setting up libbsd0:amd64 (0.9.1-1) ... Setting up libuchardet0:amd64 (0.0.6-3) ... Setting up libfreetype6:amd64 (2.9.1-3) ... Setting up lsb-base (10.2018112800) ... Setting up libgraphite2-3:amd64 (1.3.13-7) ... Setting up libcroco3:amd64 (0.6.12-3) ... Setting up libjbig2dec0:amd64 (0.15-2) ... Setting up libpixman-1-0:amd64 (0.36.0-1) ... Setting up dwz (0.12-3) ... Setting up autotools-dev (20180224.1) ... Setting up t1utils (1.41-3) ... Setting up libssl1.1:amd64 (1.1.1a-1) ... Setting up gcc-8-base:ppc64el (8.2.0-21) ... Setting up libijs-0.35:amd64 (0.35-13) ... Setting up libpotrace0:amd64 (1.15-1) ... Setting up libteckit0:amd64 (2.5.8+ds2-5) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up libkeyutils1:amd64 (1.6-2) ... 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 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 libzzip-0-13:amd64 (0.13.62-3.1) ... Setting up xdg-utils (1.1.3-1) ... Setting up libncurses6:amd64 (6.1+20181013-2) ... Setting up libtexluajit2:amd64 (2018.20181218.49446-1) ... Setting up libx11-data (2:1.6.7-1) ... Setting up libxau6:amd64 (1:1.0.8-1+b2) ... Setting up autopoint (0.19.8.1-9) ... Setting up libidn11:amd64 (1.33-2.2) ... Setting up libdbus-1-3:amd64 (1.12.12-1) ... Setting up fonts-lmodern (2.004.5-5) ... Setting up libavahi-common-data:amd64 (0.7-4+b1) ... Setting up libwebp6:amd64 (0.6.1-2) ... Setting up libfile-stripnondeterminism-perl (1.1.1-1) ... Setting up libtool (2.4.6-9) ... Setting up fontconfig-config (2.13.1-2) ... Setting up gettext (0.19.8.1-9) ... Setting up groff-base (1.22.4-2) ... Setting up libharfbuzz0b:amd64 (2.3.1-1) ... Setting up libtiff5:amd64 (4.0.10-4) ... Setting up autoconf (2.69-11) ... Setting up libkrb5support0:amd64 (1.17-1) ... Setting up intltool-debian (0.35.0+20060710.5) ... 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 libice6:amd64 (2:1.0.9-2) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libavahi-common3:amd64 (0.7-4+b1) ... Setting up libxcb1:amd64 (1.13.1-2) ... Setting up libfontconfig1:amd64 (2.13.1-2) ... Setting up libsm6:amd64 (2:1.2.3-1) ... Setting up libk5crypto3:amd64 (1.17-1) ... Setting up libxcb-render0:amd64 (1.13.1-2) ... Setting up libharfbuzz-icu0:amd64 (2.3.1-1) ... Setting up po-debconf (1.0.21) ... Setting up libx11-6:amd64 (2:1.6.7-1) ... Setting up libxcb-shm0:amd64 (1.13.1-2) ... Setting up libxpm4:amd64 (1:3.5.12-1) ... Setting up libxt6:amd64 (1:1.1.5-1) ... Setting up libxrender1:amd64 (1:0.9.10-1) ... Setting up libavahi-client3:amd64 (0.7-4+b1) ... Setting up libkrb5-3:amd64 (1.17-1) ... Setting up libxext6:amd64 (2:1.3.3-1+b2) ... Setting up libxmu6:amd64 (2:1.1.2-2) ... Setting up libgssapi-krb5-2:amd64 (1.17-1) ... Setting up libcups2:amd64 (2.2.10-4) ... Setting up libxi6:amd64 (2:1.7.9-1) ... Setting up libxaw7:amd64 (2:1.0.13-1+b2) ... Setting up libcairo2:amd64 (1.16.0-2) ... Setting up libcupsimage2:amd64 (2.2.10-4) ... Setting up libgs9:amd64 (9.26a~dfsg-2) ... Setting up texlive-binaries (2018.20181218.49446-1) ... 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 (2018.20190131-1) ... tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/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 (2018.20190131-1) ... Setting up texlive-latex-recommended (2018.20190131-1) ... Setting up dh-strip-nondeterminism (1.1.1-1) ... Setting up libgcc1:ppc64el (1:8.2.0-21) ... Setting up debhelper (12.1) ... Setting up dh-autoreconf (19) ... Setting up libc6:ppc64el (2.28-7) ... Setting up libstdc++6:ppc64el (8.2.0-21) ... Setting up libc6-dev:ppc64el (2.28-7) ... Setting up libasan5:ppc64el (8.2.0-21) ... Setting up libitm1:ppc64el (8.2.0-21) ... Setting up libubsan1:ppc64el (8.2.0-21) ... Setting up libquadmath0:ppc64el (8.2.0-21) ... Setting up libgomp1:ppc64el (8.2.0-21) ... Setting up libatomic1:ppc64el (8.2.0-21) ... Setting up zlib1g:ppc64el (1:1.2.11.dfsg-1) ... Setting up libtsan0:ppc64el (8.2.0-21) ... Setting up liblsan0:ppc64el (8.2.0-21) ... Setting up libgcc-8-dev:ppc64el (8.2.0-21) ... Setting up zlib1g-dev:ppc64el (1:1.2.11.dfsg-1) ... Setting up libstdc++-8-dev:ppc64el (8.2.0-21) ... Setting up sbuild-build-depends-velvet-dummy:ppc64el (0.invalid.0) ... Processing triggers for libc-bin (2.28-7) ... Processing triggers for tex-common (6.10) ... 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_2.31.1-12 dpkg-dev_1.19.4 g++-8_8.2.0-21 gcc-8_8.2.0-21 libc6-dev_2.28-7 libstdc++-8-dev_8.2.0-21 libstdc++-8-dev-ppc64el-cross_8.2.0-20cross1 libstdc++6_8.2.0-21 libstdc++6-ppc64el-cross_8.2.0-20cross1 linux-libc-dev_4.19.20-1 Package versions: adduser_3.118 apt_1.8.0~rc3 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_10.1 base-passwd_3.5.46 bash_5.0-2 binutils_2.31.1-12 binutils-common_2.31.1-12 binutils-powerpc64le-linux-gnu_2.31.1-12 binutils-x86-64-linux-gnu_2.31.1-12 bsdmainutils_11.1.2+b1 bsdutils_1:2.33.1-0.1 build-essential_12.5 bzip2_1.0.6-9 coreutils_8.30-1 cpp_4:8.2.0-2 cpp-8_8.2.0-21 cpp-8-powerpc64le-linux-gnu_8.2.0-20cross1 cpp-powerpc64le-linux-gnu_4:8.2.0-2 cross-config_2.6.15-2 crossbuild-essential-ppc64el_12.5 dash_0.5.10.2-5 debconf_1.5.70 debhelper_12.1 debian-archive-keyring_2018.1 debianutils_4.8.6.1 dh-autoreconf_19 dh-strip-nondeterminism_1.1.1-1 diffutils_1:3.7-2 dpkg_1.19.4 dpkg-cross_2.6.15-2 dpkg-dev_1.19.4 dwz_0.12-3 e2fsprogs_1.44.5-1 fakeroot_1.23-1 fdisk_2.33.1-0.1 file_1:5.35-2 findutils_4.6.0+git+20190209-2 fontconfig-config_2.13.1-2 fonts-dejavu-core_2.37-1 fonts-lmodern_2.004.5-5 g++_4:8.2.0-2 g++-8_8.2.0-21 g++-8-powerpc64le-linux-gnu_8.2.0-20cross1 g++-powerpc64le-linux-gnu_4:8.2.0-2 gcc_4:8.2.0-2 gcc-8_8.2.0-21 gcc-8-base_8.2.0-21 gcc-8-cross-base_8.2.0-20cross1 gcc-8-powerpc64le-linux-gnu_8.2.0-20cross1 gcc-8-powerpc64le-linux-gnu-base_8.2.0-20cross1 gcc-powerpc64le-linux-gnu_4:8.2.0-2 gettext_0.19.8.1-9 gettext-base_0.19.8.1-9 gpgv_2.2.12-1 grep_3.3-1 groff-base_1.22.4-2 gzip_1.9-3 hostname_3.21 init-system-helpers_1.56+nmu1 intltool-debian_0.35.0+20060710.5 libacl1_2.2.52-5 libapt-pkg5.0_1.8.0~rc3 libarchive-zip-perl_1.64-1 libasan5_8.2.0-21 libasan5-ppc64el-cross_8.2.0-20cross1 libatomic1_8.2.0-21 libatomic1-ppc64el-cross_8.2.0-20cross1 libattr1_1:2.4.47-4 libaudit-common_1:2.8.4-2 libaudit1_1:2.8.4-2 libavahi-client3_0.7-4+b1 libavahi-common-data_0.7-4+b1 libavahi-common3_0.7-4+b1 libbinutils_2.31.1-12 libblkid1_2.33.1-0.1 libbrotli1_1.0.7-2 libbsd0_0.9.1-1 libbz2-1.0_1.0.6-9 libc-bin_2.28-7 libc-dev-bin_2.28-7 libc6_2.28-7 libc6-dev_2.28-7 libc6-dev-ppc64el-cross_2.28-4cross1 libc6-ppc64el-cross_2.28-4cross1 libcairo2_1.16.0-2 libcap-ng0_0.7.9-2 libcc1-0_8.2.0-21 libcom-err2_1.44.5-1 libconfig-auto-perl_0.44-1 libconfig-inifiles-perl_3.000001-1 libcroco3_0.6.12-3 libcups2_2.2.10-4 libcupsimage2_2.2.10-4 libdb5.3_5.3.28+dfsg1-0.3 libdbus-1-3_1.12.12-1 libdebconfclient0_0.247 libdebian-dpkgcross-perl_2.6.15-2 libdpkg-perl_1.19.4 libelf1_0.176-1 libexpat1_2.2.6-1 libext2fs2_1.44.5-1 libfakeroot_1.23-1 libfdisk1_2.33.1-0.1 libffi6_3.2.1-9 libfile-homedir-perl_1.004-1 libfile-stripnondeterminism-perl_1.1.1-1 libfile-which-perl_1.23-1 libfontconfig1_2.13.1-2 libfreetype6_2.9.1-3 libgcc-8-dev_8.2.0-21 libgcc-8-dev-ppc64el-cross_8.2.0-20cross1 libgcc1_1:8.2.0-21 libgcc1-ppc64el-cross_1:8.2.0-20cross1 libgcrypt20_1.8.4-5 libgdbm-compat4_1.18.1-3 libgdbm6_1.18.1-3 libglib2.0-0_2.58.3-1 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.6-2 libgomp1_8.2.0-21 libgomp1-ppc64el-cross_8.2.0-20cross1 libgpg-error0_1.35-1 libgraphite2-3_1.3.13-7 libgs9_9.26a~dfsg-2 libgs9-common_9.26a~dfsg-2 libgssapi-krb5-2_1.17-1 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 libio-string-perl_1.08-3 libisl19_0.20-2 libitm1_8.2.0-21 libitm1-ppc64el-cross_8.2.0-20cross1 libjbig0_2.1-3.1+b2 libjbig2dec0_0.15-2 libjpeg62-turbo_1:1.5.2-2+b1 libk5crypto3_1.17-1 libkeyutils1_1.6-2 libkpathsea6_2018.20181218.49446-1 libkrb5-3_1.17-1 libkrb5support0_1.17-1 liblcms2-2_2.9-3 liblocale-gettext-perl_1.07-3+b4 liblsan0_8.2.0-21 liblsan0-ppc64el-cross_8.2.0-20cross1 liblz4-1_1.8.3-1 liblzma5_5.2.4-1 libmagic-mgc_1:5.35-2 libmagic1_1:5.35-2 libmount1_2.33.1-0.1 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libmpx2_8.2.0-21 libncurses6_6.1+20181013-2 libncursesw6_6.1+20181013-2 libnettle6_3.4.1-1 libopenjp2-7_2.3.0-1.1 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_2:8.39-11 libperl5.28_5.28.1-4 libpipeline1_1.5.1-2 libpixman-1-0_0.36.0-1 libpng16-16_1.6.36-5 libpotrace0_1.15-1 libptexenc1_2018.20181218.49446-1 libquadmath0_8.2.0-21 libquadmath0-ppc64el-cross_8.2.0-20cross1 libseccomp2_2.3.3-4 libselinux1_2.8-1+b1 libsemanage-common_2.8-2 libsemanage1_2.8-2 libsepol1_2.8-1 libsigsegv2_2.12-2 libsm6_2:1.2.3-1 libsmartcols1_2.33.1-0.1 libss2_1.44.5-1 libssl1.1_1.1.1a-1 libstdc++-8-dev_8.2.0-21 libstdc++-8-dev-ppc64el-cross_8.2.0-20cross1 libstdc++6_8.2.0-21 libstdc++6-ppc64el-cross_8.2.0-20cross1 libsynctex2_2018.20181218.49446-1 libsystemd0_240-6 libtasn1-6_4.13-3 libteckit0_2.5.8+ds2-5 libtexlua52_2018.20181218.49446-1 libtexlua53_2018.20181218.49446-1 libtexluajit2_2018.20181218.49446-1 libtiff5_4.0.10-4 libtinfo6_6.1+20181013-2 libtool_2.4.6-9 libtsan0_8.2.0-21 libtsan0-ppc64el-cross_8.2.0-20cross1 libubsan1_8.2.0-21 libubsan1-ppc64el-cross_8.2.0-20cross1 libuchardet0_0.0.6-3 libudev1_240-6 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 libxpm4_1:3.5.12-1 libxrender1_1:0.9.10-1 libxt6_1:1.1.5-1 libxxhash0_0.6.5-2 libyaml-perl_1.27-1 libzstd1_1.3.8+dfsg-3 libzzip-0-13_0.13.62-3.1 linux-libc-dev_4.19.20-1 linux-libc-dev-ppc64el-cross_4.19.13-1cross1 login_1:4.5-1.1 lsb-base_10.2018112800 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_5.28.1-4 perl-base_5.28.1-4 perl-modules-5.28_5.28.1-4 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-5 tex-common_6.10 texlive-base_2018.20190131-1 texlive-binaries_2018.20181218.49446-1 texlive-latex-base_2018.20190131-1 texlive-latex-recommended_2018.20190131-1 tzdata_2018i-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.ppc64el 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-f6771de1-0a07-4dd3-9dea-cc12f677f4d9 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 powerpc64le-linux-gnu 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 ppc64el 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=powerpc64le-linux-gnu-pkg-config CXX=powerpc64le-linux-gnu-g\+\+ CC=powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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 'velvetifySequence': src/readSet.c:247:3: warning: case label value is less than minimum value for type case EOF: ^~~~ 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; ^~~~~~~~~~~~ powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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=powerpc64le-linux-gnu-pkg-config CXX=powerpc64le-linux-gnu-g\+\+ CC=powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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 'velvetifySequence': src/readSet.c:247:3: warning: case label value is less than minimum value for type case EOF: ^~~~ 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; ^~~~~~~~~~~~ powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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=powerpc64le-linux-gnu-pkg-config CXX=powerpc64le-linux-gnu-g\+\+ CC=powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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 'velvetifySequence': src/readSet.c:247:3: warning: case label value is less than minimum value for type case EOF: ^~~~ 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; ^~~~~~~~~~~~ powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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=powerpc64le-linux-gnu-pkg-config CXX=powerpc64le-linux-gnu-g\+\+ CC=powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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 'velvetifySequence': src/readSet.c:247:3: warning: case label value is less than minimum value for type case EOF: ^~~~ 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; ^~~~~~~~~~~~ powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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=powerpc64le-linux-gnu-pkg-config CXX=powerpc64le-linux-gnu-g\+\+ CC=powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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 'velvetifySequence': src/readSet.c:247:3: warning: case label value is less than minimum value for type case EOF: ^~~~ 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; ^~~~~~~~~~~~ powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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=powerpc64le-linux-gnu-pkg-config CXX=powerpc64le-linux-gnu-g\+\+ CC=powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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 'velvetifySequence': src/readSet.c:247:3: warning: case label value is less than minimum value for type case EOF: ^~~~ 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; ^~~~~~~~~~~~ powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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=powerpc64le-linux-gnu-pkg-config CXX=powerpc64le-linux-gnu-g\+\+ CC=powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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 'velvetifySequence': src/readSet.c:247:3: warning: case label value is less than minimum value for type case EOF: ^~~~ 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; ^~~~~~~~~~~~ powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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 powerpc64le-linux-gnu-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_ppc64el.deb'. dpkg-deb: building package 'velvet-dbgsym' in '../velvet-dbgsym_1.2.10+dfsg1-5_ppc64el.deb'. dpkg-deb: building package 'velvet-long' in '../velvet-long_1.2.10+dfsg1-5_ppc64el.deb'. dpkg-deb: building package 'velvet-long-dbgsym' in '../velvet-long-dbgsym_1.2.10+dfsg1-5_ppc64el.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../velvet_1.2.10+dfsg1-5_ppc64el.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 2019-02-19T04:39:30Z 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-EbjcLO/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-EbjcLO/apt_archive ./ InRelease Get:2 copy:/<>/resolver-EbjcLO/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-EbjcLO/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-EbjcLO/apt_archive ./ Sources [782 B] Get:5 copy:/<>/resolver-EbjcLO/apt_archive ./ Packages [861 B] Fetched 2606 B in 0s (0 B/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 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 libreadline7 libsqlite3-0 libstruct-dumb-perl libsub-name-perl libtext-levenshtein-perl libtimedate-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 libperlio-gzip-perl The following NEW packages will be installed: diffstat gpg gpgconf libapt-pkg-perl libassuan0 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 libreadline7 libsqlite3-0 libstruct-dumb-perl libsub-name-perl libtext-levenshtein-perl libtimedate-perl liburi-perl libyaml-0-2 libyaml-libyaml-perl lintian netbase patchutils perl-openssl-defaults readline-common sbuild-build-depends-lintian-dummy:ppc64el 0 upgraded, 43 newly installed, 0 to remove and 0 not upgraded. Need to get 6078 kB of archives. After this operation, 16.0 MB of additional disk space will be used. Get:1 copy:/<>/resolver-EbjcLO/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 2.2.12-1 [509 kB] Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 libsqlite3-0 amd64 3.27.1-1 [640 kB] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 gpg amd64 2.2.12-1 [862 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 libhtml-tagset-perl all 3.20-3 [12.7 kB] Get:12 http://debian.oregonstate.edu/debian unstable/main amd64 liburi-perl all 1.76-1 [89.9 kB] Get:13 http://debian.oregonstate.edu/debian unstable/main amd64 libhtml-parser-perl amd64 3.72-3+b3 [105 kB] Get:14 http://debian.oregonstate.edu/debian unstable/main amd64 libcgi-pm-perl all 4.40-1 [222 kB] Get:15 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-name-perl amd64 0.21-1+b3 [13.6 kB] Get:16 http://debian.oregonstate.edu/debian unstable/main amd64 libclass-accessor-perl all 0.51-1 [23.2 kB] Get:17 http://debian.oregonstate.edu/debian unstable/main amd64 libclone-perl amd64 0.41-1+b1 [14.6 kB] Get:18 http://debian.oregonstate.edu/debian unstable/main amd64 libdigest-hmac-perl all 1.03+dfsg-2 [10.6 kB] Get:19 http://debian.oregonstate.edu/debian unstable/main amd64 libtimedate-perl all 2.3000-2 [42.2 kB] Get:20 http://debian.oregonstate.edu/debian unstable/main amd64 perl-openssl-defaults amd64 3 [6782 B] Get:21 http://debian.oregonstate.edu/debian unstable/main amd64 libnet-ssleay-perl amd64 1.85-2+b1 [308 kB] Get:22 http://debian.oregonstate.edu/debian unstable/main amd64 libio-socket-ssl-perl all 2.060-3 [207 kB] Get:23 http://debian.oregonstate.edu/debian unstable/main amd64 libnet-smtp-ssl-perl all 1.04-1 [6184 B] Get:24 http://debian.oregonstate.edu/debian unstable/main amd64 libmailtools-perl all 2.18-1 [88.5 kB] Get:25 http://debian.oregonstate.edu/debian unstable/main amd64 libnet-ip-perl all 1.26-2 [29.0 kB] Get:26 http://debian.oregonstate.edu/debian unstable/main amd64 libnet-dns-perl all 1.19-1 [372 kB] Get:27 http://debian.oregonstate.edu/debian unstable/main amd64 libnet-domain-tld-perl all 1.75-1 [33.3 kB] Get:28 http://debian.oregonstate.edu/debian unstable/main amd64 libemail-valid-perl all 1.202-1 [23.0 kB] Get:29 http://debian.oregonstate.edu/debian unstable/main amd64 libexporter-tiny-perl all 1.002001-1 [36.9 kB] Get:30 http://debian.oregonstate.edu/debian unstable/main amd64 libipc-system-simple-perl all 1.25-4 [26.5 kB] Get:31 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-basedir-perl all 0.08-1 [17.7 kB] Get:32 http://debian.oregonstate.edu/debian unstable/main amd64 libfuture-perl all 0.39-1 [74.5 kB] Get:33 http://debian.oregonstate.edu/debian unstable/main amd64 libstruct-dumb-perl all 0.09-1 [11.1 kB] Get:34 http://debian.oregonstate.edu/debian unstable/main amd64 libio-async-perl all 0.72-1 [262 kB] Get:35 http://debian.oregonstate.edu/debian unstable/main amd64 libio-pty-perl amd64 1:1.08-1.1+b5 [33.7 kB] Get:36 http://debian.oregonstate.edu/debian unstable/main amd64 libipc-run-perl all 20180523.0-1 [101 kB] Get:37 http://debian.oregonstate.edu/debian unstable/main amd64 liblist-moreutils-perl amd64 0.416-1+b4 [64.2 kB] Get:38 http://debian.oregonstate.edu/debian unstable/main amd64 libparse-debianchangelog-perl all 1.2.0-13 [59.5 kB] Get:39 http://debian.oregonstate.edu/debian unstable/main amd64 libtext-levenshtein-perl all 0.13-1 [11.1 kB] Get:40 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-0-2 amd64 0.2.1-1 [47.2 kB] Get:41 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-libyaml-perl amd64 0.76+repack-1 [33.1 kB] Get:42 http://debian.oregonstate.edu/debian unstable/main amd64 patchutils amd64 0.3.4-2 [90.4 kB] Get:43 http://debian.oregonstate.edu/debian unstable/main amd64 lintian all 2.7.0 [1193 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 6078 kB in 0s (51.7 MB/s) Selecting previously unselected package netbase. (Reading database ... 25234 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_2.2.12-1_amd64.deb ... Unpacking gpgconf (2.2.12-1) ... Selecting previously unselected package libsqlite3-0:amd64. 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I: Lintian run was successful. +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ velvet_1.2.10+dfsg1-5_ppc64el.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: ppc64el 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: 9e92096e2c8d05a16fb05d2504dd04390cbd8962 986244 velvet-dbgsym_1.2.10+dfsg1-5_ppc64el.deb d7c84aa98d80ab35f0e972759dfb6431b9b67364 1957816 velvet-long-dbgsym_1.2.10+dfsg1-5_ppc64el.deb d360c6618bbf0197bc80c95905ce9cf589e97f40 228248 velvet-long_1.2.10+dfsg1-5_ppc64el.deb 16910debe1d6d23817bdb22532f051099d2f855a 7534 velvet_1.2.10+dfsg1-5_ppc64el.buildinfo e6bc989f539b2f2e36a33077dd5fbe220eb9ca96 674868 velvet_1.2.10+dfsg1-5_ppc64el.deb Checksums-Sha256: 50a51af04b6f96f5afadfd89c094a9c9b456b315fafe1c6e909fb6dcf3207658 986244 velvet-dbgsym_1.2.10+dfsg1-5_ppc64el.deb 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+------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: velvet Binary: velvet velvet-long velvet-example velvet-tests Architecture: ppc64el Version: 1.2.10+dfsg1-5 Checksums-Md5: dd5f9b9a1cf7b74f1494a1e7cae263f5 986244 velvet-dbgsym_1.2.10+dfsg1-5_ppc64el.deb 9799405b7575fdb784a20558ed77c6e9 1957816 velvet-long-dbgsym_1.2.10+dfsg1-5_ppc64el.deb 32c88793a2b0a7409658b6d9c90eb649 228248 velvet-long_1.2.10+dfsg1-5_ppc64el.deb 4f7433eb30f8e1648a9b8a3578646cc7 674868 velvet_1.2.10+dfsg1-5_ppc64el.deb Checksums-Sha1: 9e92096e2c8d05a16fb05d2504dd04390cbd8962 986244 velvet-dbgsym_1.2.10+dfsg1-5_ppc64el.deb d7c84aa98d80ab35f0e972759dfb6431b9b67364 1957816 velvet-long-dbgsym_1.2.10+dfsg1-5_ppc64el.deb d360c6618bbf0197bc80c95905ce9cf589e97f40 228248 velvet-long_1.2.10+dfsg1-5_ppc64el.deb e6bc989f539b2f2e36a33077dd5fbe220eb9ca96 674868 velvet_1.2.10+dfsg1-5_ppc64el.deb Checksums-Sha256: 50a51af04b6f96f5afadfd89c094a9c9b456b315fafe1c6e909fb6dcf3207658 986244 velvet-dbgsym_1.2.10+dfsg1-5_ppc64el.deb a0581b55a8a61c985b39f41ab3b14659bad6eceaa8f798e898ab2abc28755ffe 1957816 velvet-long-dbgsym_1.2.10+dfsg1-5_ppc64el.deb 827375a46992d6d0fd75b598b318c21df17e69b4007cf3a8727dc6d51c860604 228248 velvet-long_1.2.10+dfsg1-5_ppc64el.deb fa546cbd687873f4a86d5dd4978375e271976882711871dd66348ceed5162f6d 674868 velvet_1.2.10+dfsg1-5_ppc64el.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Tue, 19 Feb 2019 04:39:30 +0000 Build-Path: /<>/velvet-1.2.10+dfsg1 Installed-Build-Depends: autoconf (= 2.69-11), automake (= 1:1.16.1-4), autopoint (= 0.19.8.1-9), autotools-dev (= 20180224.1), base-files (= 10.1), base-passwd (= 3.5.46), bash (= 5.0-2), binutils (= 2.31.1-12), binutils-common (= 2.31.1-12), binutils-x86-64-linux-gnu (= 2.31.1-12), bsdmainutils (= 11.1.2+b1), bsdutils (= 1:2.33.1-0.1), build-essential (= 12.5), bzip2 (= 1.0.6-9), coreutils (= 8.30-1), cpp (= 4:8.2.0-2), cpp-8 (= 8.2.0-21), dash (= 0.5.10.2-5), debconf (= 1.5.70), debhelper (= 12.1), debianutils (= 4.8.6.1), dh-autoreconf (= 19), dh-strip-nondeterminism (= 1.1.1-1), diffutils (= 1:3.7-2), dpkg (= 1.19.4), dpkg-dev (= 1.19.4), dwz (= 0.12-3), fdisk (= 2.33.1-0.1), file (= 1:5.35-2), findutils (= 4.6.0+git+20190209-2), fontconfig-config (= 2.13.1-2), fonts-dejavu-core (= 2.37-1), fonts-lmodern (= 2.004.5-5), g++ (= 4:8.2.0-2), g++-8 (= 8.2.0-21), gcc (= 4:8.2.0-2), gcc-8 (= 8.2.0-21), gcc-8-base (= 8.2.0-21), gettext (= 0.19.8.1-9), gettext-base (= 0.19.8.1-9), grep (= 3.3-1), groff-base (= 1.22.4-2), gzip (= 1.9-3), hostname (= 3.21), init-system-helpers (= 1.56+nmu1), intltool-debian (= 0.35.0+20060710.5), libacl1 (= 2.2.52-5), libarchive-zip-perl (= 1.64-1), libasan5 (= 8.2.0-21), libatomic1 (= 8.2.0-21), libattr1 (= 1:2.4.47-4), libaudit-common (= 1:2.8.4-2), libaudit1 (= 1:2.8.4-2), libavahi-client3 (= 0.7-4+b1), libavahi-common-data (= 0.7-4+b1), libavahi-common3 (= 0.7-4+b1), libbinutils (= 2.31.1-12), libblkid1 (= 2.33.1-0.1), libbrotli1 (= 1.0.7-2), libbsd0 (= 0.9.1-1), libbz2-1.0 (= 1.0.6-9), libc-bin (= 2.28-7), libc-dev-bin (= 2.28-7), libc6 (= 2.28-7), libc6-dev (= 2.28-7), libcairo2 (= 1.16.0-2), libcap-ng0 (= 0.7.9-2), libcc1-0 (= 8.2.0-21), libcom-err2 (= 1.44.5-1), libcroco3 (= 0.6.12-3), libcups2 (= 2.2.10-4), libcupsimage2 (= 2.2.10-4), libdb5.3 (= 5.3.28+dfsg1-0.3), libdbus-1-3 (= 1.12.12-1), libdebconfclient0 (= 0.247), libdpkg-perl (= 1.19.4), libelf1 (= 0.176-1), libexpat1 (= 2.2.6-1), libfdisk1 (= 2.33.1-0.1), libffi6 (= 3.2.1-9), libfile-stripnondeterminism-perl (= 1.1.1-1), libfontconfig1 (= 2.13.1-2), libfreetype6 (= 2.9.1-3), libgcc-8-dev (= 8.2.0-21), libgcc1 (= 1:8.2.0-21), libgcrypt20 (= 1.8.4-5), libgdbm-compat4 (= 1.18.1-3), libgdbm6 (= 1.18.1-3), libglib2.0-0 (= 2.58.3-1), libgmp10 (= 2:6.1.2+dfsg-4), libgnutls30 (= 3.6.6-2), libgomp1 (= 8.2.0-21), libgpg-error0 (= 1.35-1), libgraphite2-3 (= 1.3.13-7), libgs9 (= 9.26a~dfsg-2), libgs9-common (= 9.26a~dfsg-2), libgssapi-krb5-2 (= 1.17-1), 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 (= 8.2.0-21), libjbig0 (= 2.1-3.1+b2), libjbig2dec0 (= 0.15-2), libjpeg62-turbo (= 1:1.5.2-2+b1), libk5crypto3 (= 1.17-1), libkeyutils1 (= 1.6-2), libkpathsea6 (= 2018.20181218.49446-1), libkrb5-3 (= 1.17-1), libkrb5support0 (= 1.17-1), liblcms2-2 (= 2.9-3), liblsan0 (= 8.2.0-21), liblz4-1 (= 1.8.3-1), liblzma5 (= 5.2.4-1), libmagic-mgc (= 1:5.35-2), libmagic1 (= 1:5.35-2), libmount1 (= 2.33.1-0.1), libmpc3 (= 1.1.0-1), libmpfr6 (= 4.0.2-1), libmpx2 (= 8.2.0-21), libncurses6 (= 6.1+20181013-2), libncursesw6 (= 6.1+20181013-2), libnettle6 (= 3.4.1-1), libopenjp2-7 (= 2.3.0-1.1), 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 (= 2:8.39-11), libperl5.28 (= 5.28.1-4), libpipeline1 (= 1.5.1-2), libpixman-1-0 (= 0.36.0-1), libpng16-16 (= 1.6.36-5), libpotrace0 (= 1.15-1), libptexenc1 (= 2018.20181218.49446-1), libquadmath0 (= 8.2.0-21), 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 (= 1.1.1a-1), libstdc++-8-dev (= 8.2.0-21), libstdc++6 (= 8.2.0-21), libsynctex2 (= 2018.20181218.49446-1), libsystemd0 (= 240-6), libtasn1-6 (= 4.13-3), libteckit0 (= 2.5.8+ds2-5), libtexlua52 (= 2018.20181218.49446-1), libtexlua53 (= 2018.20181218.49446-1), libtexluajit2 (= 2018.20181218.49446-1), libtiff5 (= 4.0.10-4), libtinfo6 (= 6.1+20181013-2), libtool (= 2.4.6-9), libtsan0 (= 8.2.0-21), libubsan1 (= 8.2.0-21), libuchardet0 (= 0.0.6-3), libudev1 (= 240-6), 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), libxpm4 (= 1:3.5.12-1), libxrender1 (= 1:0.9.10-1), libxt6 (= 1:1.1.5-1), libxxhash0 (= 0.6.5-2), libzstd1 (= 1.3.8+dfsg-3), libzzip-0-13 (= 0.13.62-3.1), linux-libc-dev (= 4.19.20-1), login (= 1:4.5-1.1), lsb-base (= 10.2018112800), 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 (= 5.28.1-4), perl-base (= 5.28.1-4), perl-modules-5.28 (= 5.28.1-4), 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-5), tex-common (= 6.10), texlive-base (= 2018.20190131-1), texlive-binaries (= 2018.20181218.49446-1), texlive-latex-base (= 2018.20190131-1), texlive-latex-recommended (= 2018.20190131-1), 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) 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_ppc64el.deb ---------------------------------------- new Debian package, version 2.0. size 986244 bytes: control archive=704 bytes. 506 bytes, 12 lines control 424 bytes, 4 lines md5sums Package: velvet-dbgsym Source: velvet Version: 1.2.10+dfsg1-5 Auto-Built-Package: 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./usr/share/doc/velvet-long-dbgsym -> velvet-long velvet-long_1.2.10+dfsg1-5_ppc64el.deb -------------------------------------- new Debian package, version 2.0. size 228248 bytes: control archive=1456 bytes. 1004 bytes, 22 lines control 1499 bytes, 23 lines md5sums Package: velvet-long Source: velvet Version: 1.2.10+dfsg1-5 Architecture: ppc64el Maintainer: Debian Med Packaging Team Installed-Size: 2634 Depends: libc6 (>= 2.17), 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 396136 2018-07-05 08:17 ./usr/bin/velvetg_127 -rwxr-xr-x root/root 396136 2018-07-05 08:17 ./usr/bin/velvetg_127_long -rwxr-xr-x root/root 396136 2018-07-05 08:17 ./usr/bin/velvetg_63 -rwxr-xr-x root/root 396136 2018-07-05 08:17 ./usr/bin/velvetg_63_long -rwxr-xr-x root/root 396120 2018-07-05 08:17 ./usr/bin/velvetg_long -rwxr-xr-x root/root 133840 2018-07-05 08:17 ./usr/bin/velveth_127 -rwxr-xr-x root/root 133840 2018-07-05 08:17 ./usr/bin/velveth_127_long -rwxr-xr-x root/root 133840 2018-07-05 08:17 ./usr/bin/velveth_63 -rwxr-xr-x root/root 133840 2018-07-05 08:17 ./usr/bin/velveth_63_long -rwxr-xr-x root/root 133824 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_ppc64el.deb --------------------------------- new Debian package, version 2.0. size 674868 bytes: control archive=1332 bytes. 882 bytes, 19 lines control 1154 bytes, 18 lines md5sums Package: velvet Version: 1.2.10+dfsg1-5 Architecture: ppc64el Maintainer: Debian Med Packaging Team Installed-Size: 1586 Depends: libc6 (>= 2.17), 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 396120 2018-07-05 08:17 ./usr/bin/velvetg -rwxr-xr-x root/root 396120 2018-07-05 08:17 ./usr/bin/velvetg_de -rwxr-xr-x root/root 133824 2018-07-05 08:17 ./usr/bin/velveth -rwxr-xr-x root/root 133832 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: 85928 Build-Time: 113 Distribution: unstable Foreign Architectures: ppc64el Host Architecture: ppc64el Install-Time: 39 Job: velvet_1.2.10+dfsg1-5 Lintian: pass Machine Architecture: amd64 Package: velvet Package-Time: 166 Source-Version: 1.2.10+dfsg1-5 Space: 85928 Status: successful Version: 1.2.10+dfsg1-5 -------------------------------------------------------------------------------- Finished at 2019-02-19T04:39:30Z Build needed 00:02:46, 85928k disk space