=> Building biology/velvet Started : Sunday, 7 JUL 2019 at 04:56:02 UTC Platform: 5.7-DEVELOPMENT DragonFly v5.7.0.83.g49866-DEVELOPMENT #40: Sun Jun 30 03:00:04 PDT 2019 root@pkgbox64.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 -------------------------------------------------- -- Environment -------------------------------------------------- UNAME_r=5.4-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.4-SYNTH UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 TERM=dumb PKG_CACHEDIR=/var/cache/pkg8 PKG_DBDIR=/var/db/pkg8 PORTSDIR=/xports LANG=C HOME=/root USER=root -------------------------------------------------- -- Options -------------------------------------------------- ===> The following configuration options are available for velvet-1.2.10_2: DOCS=on: Build and/or install documentation ===> Use 'make config' to modify these settings -------------------------------------------------- -- CONFIGURE_ENV -------------------------------------------------- ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl PERL_USE_UNSAFE_INC=1 MAKE=gmake PYTHON="/usr/local/bin/python3.6" XDG_DATA_HOME=/construction/biology/velvet XDG_CONFIG_HOME=/construction/biology/velvet HOME=/construction/biology/velvet TMPDIR="/tmp" PATH=/construction/biology/velvet/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc80 -------------------------------------------------- -- CONFIGURE_ARGS -------------------------------------------------- -------------------------------------------------- -- MAKE_ENV -------------------------------------------------- MAXKMERLENGTH=31 CATEGORIES=2 PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/construction/biology/velvet XDG_CONFIG_HOME=/construction/biology/velvet HOME=/construction/biology/velvet TMPDIR="/tmp" PATH=/construction/biology/velvet/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES CCVER=gcc80 PREFIX=/usr/local LOCALBASE=/usr/local NOPROFILE=1 CC="cc" CFLAGS="-pipe -O2 -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="c++" CXXFLAGS=" -pipe -O2 -fno-strict-aliasing " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" -------------------------------------------------- -- MAKE_ARGS -------------------------------------------------- DESTDIR=/construction/biology/velvet/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- PORTDOCS="" PYTHON_INCLUDEDIR=include/python3.6m PYTHON_LIBDIR=lib/python3.6 PYTHON_PLATFORM=dragonfly5 PYTHON_SITELIBDIR=lib/python3.6/site-packages PYTHON_SUFFIX=36 PYTHON_VER=3.6 PYTHON_VERSION=python3.6 PYTHON2="@comment " PYTHON3="" OSREL=5.4 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.28.2 PERL_VER=5.28 PERL5_MAN1=lib/perl5/site_perl/man/man1 PERL5_MAN3=lib/perl5/site_perl/man/man3 SITE_PERL=lib/perl5/site_perl SITE_ARCH=lib/perl5/site_perl/mach/5.28 PROFILE="@comment " DOCSDIR="share/doc/velvet" EXAMPLESDIR="share/examples/velvet" DATADIR="share/velvet" WWWDIR="www/velvet" ETCDIR="etc/velvet" -------------------------------------------------- -- SUB_LIST -------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/velvet DOCSDIR=/usr/local/share/doc/velvet EXAMPLESDIR=/usr/local/share/examples/velvet WWWDIR=/usr/local/www/velvet ETCDIR=/usr/local/etc/velvet -------------------------------------------------- -- /etc/make.conf -------------------------------------------------- SYNTHPROFILE=Release-5.4 USE_PACKAGE_DEPENDS_ONLY=yes PACKAGE_BUILDING=yes BATCH=yes PKG_CREATE_VERBOSE=yes PORTSDIR=/xports DISTDIR=/distfiles WRKDIRPREFIX=/construction PORT_DBDIR=/options PACKAGES=/packages MAKE_JOBS_NUMBER_LIMIT=5 HAVE_COMPAT_IA32_KERN= CONFIGURE_MAX_CMD_LEN=262144 _PERL5_FROM_BIN=5.28.1 _ALTCCVERSION_921dbbb2=none _OBJC_ALTCCVERSION_921dbbb2=none _SMP_CPUS=8 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500400 OSVERSION=9999999 OSREL=5.4 _OSRELEASE=5.4-SYNTH PYTHONBASE=/usr/local _PKG_CHECKED=1 -------------------------------------------------------------------------------- -- Phase: check-sanity -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> velvet-1.2.10_2 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.11.1.txz Installing pkg-1.11.1... Extracting pkg-1.11.1: .......... done ===> velvet-1.2.10_2 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of velvet-1.2.10_2 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> Fetching all distfiles required by velvet-1.2.10_2 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> Fetching all distfiles required by velvet-1.2.10_2 for building => SHA256 Checksum OK for velvet_1.2.10.tgz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> Fetching all distfiles required by velvet-1.2.10_2 for building ===> Extracting for velvet-1.2.10_2 => SHA256 Checksum OK for velvet_1.2.10.tgz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for velvet-1.2.10_2 ===> Applying ports patches for velvet-1.2.10_2 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> velvet-1.2.10_2 depends on executable: gmake - not found ===> Installing existing package /packages/All/gmake-4.2.1_3.txz Installing gmake-4.2.1_3... `-- Installing gettext-runtime-0.20.1... | `-- Installing indexinfo-0.3.1... | `-- Extracting indexinfo-0.3.1: .... done `-- Extracting gettext-runtime-0.20.1: .......... done Extracting gmake-4.2.1_3: .......... done ===> velvet-1.2.10_2 depends on executable: gmake - found ===> Returning to build of velvet-1.2.10_2 ===> velvet-1.2.10_2 depends on file: /usr/local/bin/python3.6 - not found ===> Installing existing package /packages/All/python36-3.6.8_2.txz Installing python36-3.6.8_2... `-- Installing expat-2.2.6_1... `-- Extracting expat-2.2.6_1: .......... done `-- Installing libffi-3.2.1_3... `-- Extracting libffi-3.2.1_3: .......... done `-- Installing libressl-2.9.2... `-- Extracting libressl-2.9.2: .......... done `-- Installing ncurses-6.1.20190525... `-- Extracting ncurses-6.1.20190525: .......... done `-- Installing readline-8.0.0... `-- Extracting readline-8.0.0: .......... done Extracting python36-3.6.8_2: .......... done Message from python36-3.6.8_2: =========================================================================== Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py36-gdbm databases/py-gdbm@py36 py36-sqlite3 databases/py-sqlite3@py36 py36-tkinter x11-toolkits/py-tkinter@py36 =========================================================================== ===> velvet-1.2.10_2 depends on file: /usr/local/bin/python3.6 - found ===> Returning to build of velvet-1.2.10_2 -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for velvet-1.2.10_2 -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for velvet-1.2.10_2 gmake[1]: Entering directory '/construction/biology/velvet/velvet_1.2.10' rm obj/*.o obj/dbg/*.o rm: obj/*.o: No such file or directory rm: obj/dbg/*.o: No such file or directory gmake[1]: [Makefile:51: cleanobj] Error 1 (ignored) mkdir -p obj cc -pipe -O2 -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/tightString.c -o obj/tightString.o cc -pipe -O2 -fno-strict-aliasing -Wall -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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ cc -pipe -O2 -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/splay.c -o obj/splay.o cc -pipe -O2 -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/splayTable.c -o obj/splayTable.o src/splayTable.c: In function 'inputSequenceArrayIntoSplayTableAndArchive': src/splayTable.c:1060:14: warning: variable 'refElem' set but not used [-Wunused-but-set-variable] RefInfo refElem; ^~~~~~~ cc -pipe -O2 -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/graph.c -o obj/graph.o cc -pipe -O2 -fno-strict-aliasing -Wall -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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ cc -pipe -O2 -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/fibHeap.c -o obj/fibHeap.o cc -pipe -O2 -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/fib.c -o obj/fib.o cc -pipe -O2 -fno-strict-aliasing -Wall -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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ cc -pipe -O2 -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/passageMarker.c -o obj/passageMarker.o src/passageMarker.c: In function 'readPassageMarker': src/passageMarker.c:289:4: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict] (long) getNodeID(getNode(marker))); ^ src/passageMarker.c:293:4: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict] (long) getNodeID(getNode(marker))); ^ src/passageMarker.c:296:3: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict] sprintf(s, "%s -> FINISH", s); ^~~~~~~ src/passageMarker.c:299:4: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict] (long) getNodeID(getNode(getNextInSequence(marker)))); ^ In file included from src/passageMarker.c:29: src/passageMarker.c: At top level: 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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ cc -pipe -O2 -fno-strict-aliasing -Wall -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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ cc -pipe -O2 -fno-strict-aliasing -Wall -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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ cc -pipe -O2 -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/dfib.c -o obj/dfib.o cc -pipe -O2 -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/dfibHeap.c -o obj/dfibHeap.o cc -pipe -O2 -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/recycleBin.c -o obj/recycleBin.o cc -pipe -O2 -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/readSet.c -o obj/readSet.o src/readSet.c: In function 'readFastXFile': src/readSet.c:641:21: warning: assignment to 'gzFile' {aka 'struct gzFile_s *'} from incompatible pointer type 'AutoFile *' {aka 'struct *'} [-Wincompatible-pointer-types] file.gzFile = file.autoFile = NULL; ^ src/readSet.c: In function 'readFastXPair': src/readSet.c:680:22: warning: assignment to 'gzFile' {aka 'struct gzFile_s *'} from incompatible pointer type 'AutoFile *' {aka 'struct *'} [-Wincompatible-pointer-types] file1.gzFile = file1.autoFile = NULL; ^ src/readSet.c:681:22: warning: assignment to 'gzFile' {aka 'struct gzFile_s *'} from incompatible pointer type 'AutoFile *' {aka 'struct *'} [-Wincompatible-pointer-types] file2.gzFile = file2.autoFile = NULL; ^ src/readSet.c: In function 'addMapping': src/readSet.c:748:4: warning: passing argument 1 to restrict-qualified parameter aliases with argument 4 [-Wrestrict] snprintf(buffer, *buffer_size, "%sM\t%li\t%lli\n", buffer, (long) orientation * refCoord->referenceID, (long long) (pos - refCoord->start)); ^~~~~~~~ src/readSet.c:750:4: warning: passing argument 1 to restrict-qualified parameter aliases with argument 4 [-Wrestrict] snprintf(buffer, *buffer_size, "%sM\t%li\t%lli\n", buffer, (long) - orientation * refCoord->referenceID, (long long) (refCoord->finish - pos - strlen(seq))); ^~~~~~~~ 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; ^~~~~~~~~~~~ cc -pipe -O2 -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/binarySequences.c -o obj/binarySequences.o src/binarySequences.c: In function 'importCnyReadSet': src/binarySequences.c:314:12: warning: variable 'refElem' set but not used [-Wunused-but-set-variable] RefInfo refElem; ^~~~~~~ cc -pipe -O2 -fno-strict-aliasing -Wall -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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ cc -pipe -O2 -fno-strict-aliasing -Wall -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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ cc -pipe -O2 -fno-strict-aliasing -Wall -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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ cc -pipe -O2 -fno-strict-aliasing -Wall -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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ cc -pipe -O2 -fno-strict-aliasing -Wall -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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ cc -pipe -O2 -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/preGraphConstruction.c -o obj/preGraphConstruction.o src/preGraphConstruction.c: In function 'createPreNodes': src/preGraphConstruction.c:414:2: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (sequenceCount_pg(preGraph) > 0 && !fgets(line, lineLength, file)) ^~ src/preGraphConstruction.c:416:3: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' seqReadInfo->m_pFile = file; ^~~~~~~~~~~ cc -pipe -O2 -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o cc -pipe -O2 -fno-strict-aliasing -Wall -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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ cc -pipe -O2 -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/utility.c -o obj/utility.o cc -pipe -O2 -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/kmer.c -o obj/kmer.o src/kmer.c:31:22: warning: 'charLeftFilter' defined but not used [-Wunused-const-variable=] static const uint8_t charLeftFilter = (uint8_t) 3 << 6; ^~~~~~~~~~~~~~ src/kmer.c:30:23: warning: 'intLeftFilter' defined but not used [-Wunused-const-variable=] static const uint16_t intLeftFilter = (uint16_t) 3 << 14; ^~~~~~~~~~~~~ src/kmer.c:29:23: warning: 'longLeftFilter' defined but not used [-Wunused-const-variable=] static const uint32_t longLeftFilter = (uint32_t) 3 << 30; ^~~~~~~~~~~~~~ src/kmer.c:28:23: warning: 'longLongLeftFilter' defined but not used [-Wunused-const-variable=] static const uint64_t longLongLeftFilter = (uint64_t) 3 << 62; ^~~~~~~~~~~~~~~~~~ cc -pipe -O2 -fno-strict-aliasing -Wall -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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ cc -pipe -O2 -fno-strict-aliasing -Wall -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); ^~~~~~~~~~~~~~~~~~~~~~~~~~ cc -pipe -O2 -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/allocArray.c -o obj/allocArray.o cc -pipe -O2 -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/autoOpen.c -o obj/autoOpen.o src/autoOpen.c: In function 'pcloseNoStderr': src/autoOpen.c:49:6: warning: variable 'rc' set but not used [-Wunused-but-set-variable] int rc, status; ^~ src/autoOpen.c: At top level: src/autoOpen.c:56:19: warning: duplicate 'const' declaration specifier [-Wduplicate-decl-specifier] static const char const* decompressors[] = {"","pigz", "gunzip", "pbunzip2", "bunzip2", NULL}; ^~~~~ cc -pipe -O2 -fno-strict-aliasing -Wall -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 cc -pipe -O2 -fno-strict-aliasing -Wall -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 gmake[1]: Leaving directory '/construction/biology/velvet/velvet_1.2.10' -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- ===> velvet-1.2.10_2 depends on file: /usr/local/bin/python3.6 - found ===> velvet-1.2.10_2 depends on package: perl5>=5.28.r1<5.29 - not found ===> Installing existing package /packages/All/perl5-5.28.2.txz Installing perl5-5.28.2... Extracting perl5-5.28.2: .......... done Message from perl5-5.28.2: The /usr/bin/perl symlink has been removed starting with Perl 5.20. For shebangs, you should either use: #!/usr/local/bin/perl or #!/usr/bin/env perl The first one will only work if you have a /usr/local/bin/perl, the second will work as long as perl is in PATH. ===> velvet-1.2.10_2 depends on package: perl5>=5.28.r1<5.29 - found ===> Returning to build of velvet-1.2.10_2 -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for velvet-1.2.10_2 ===> Generating temporary packing list install -s -m 555 /construction/biology/velvet/velvet_1.2.10/velvetg /construction/biology/velvet/stage/usr/local/bin install -s -m 555 /construction/biology/velvet/velvet_1.2.10/velveth /construction/biology/velvet/stage/usr/local/bin install -m 555 /construction/biology/velvet/velvet_1.2.10/contrib/shuffleSequences_fasta/shuffleSequences_fasta.pl /construction/biology/velvet/stage/usr/local/bin/shuffleSequences_fasta.pl install -m 555 /construction/biology/velvet/velvet_1.2.10/contrib/shuffleSequences_fasta/shuffleSequences_fastq.pl /construction/biology/velvet/stage/usr/local/bin/shuffleSequences_fastq.pl install -m 555 /construction/biology/velvet/velvet_1.2.10/contrib/VelvetOptimiser-2.2.4/VelvetOptimiser.pl /construction/biology/velvet/stage/usr/local/bin/VelvetOptimiser.pl install -m 555 /construction/biology/velvet/velvet_1.2.10/contrib/afg_handling/asmbly_splitter.pl /construction/biology/velvet/stage/usr/local/bin/asmbly_splitter.pl install -m 555 /construction/biology/velvet/velvet_1.2.10/contrib/afg_handling/snp_view.pl /construction/biology/velvet/stage/usr/local/bin/snp_view.pl install -m 555 /construction/biology/velvet/velvet_1.2.10/contrib/columbus_scripts/enlarge_exons.pl /construction/biology/velvet/stage/usr/local/bin/enlarge_exons.pl install -m 555 /construction/biology/velvet/velvet_1.2.10/contrib/columbus_scripts/gff2fasta.pl /construction/biology/velvet/stage/usr/local/bin/gff2fasta.pl install -m 555 /construction/biology/velvet/velvet_1.2.10/contrib/columbus_scripts/merge_gtf_exons.pl /construction/biology/velvet/stage/usr/local/bin/merge_gtf_exons.pl install -m 555 /construction/biology/velvet/velvet_1.2.10/contrib/estimate-exp_cov/velvet-estimate-exp_cov.pl /construction/biology/velvet/stage/usr/local/bin/velvet-estimate-exp_cov.pl install -m 555 /construction/biology/velvet/velvet_1.2.10/contrib/extractContigReads/extractContigReads.pl /construction/biology/velvet/stage/usr/local/bin/extractContigReads.pl install -m 555 /construction/biology/velvet/velvet_1.2.10/contrib/fasta2agp/fasta2agp.pl /construction/biology/velvet/stage/usr/local/bin/fasta2agp.pl install -m 555 /construction/biology/velvet/velvet_1.2.10/contrib/observed-insert-length.pl/observed-insert-length.pl /construction/biology/velvet/stage/usr/local/bin/observed-insert-length.pl install -m 555 /construction/biology/velvet/velvet_1.2.10/contrib/read_prepare/pe_read_prepare.0.1.pl /construction/biology/velvet/stage/usr/local/bin/pe_read_prepare.0.1.pl install -m 555 /construction/biology/velvet/velvet_1.2.10/contrib/select_paired/select_paired.pl /construction/biology/velvet/stage/usr/local/bin/select_paired.pl install -m 555 /construction/biology/velvet/velvet_1.2.10/contrib/show_repeats/show_repeats.pl /construction/biology/velvet/stage/usr/local/bin/show_repeats.pl install -m 555 /construction/biology/velvet/velvet_1.2.10/contrib/AssemblyAssembler1.3/AssemblyAssembler1.3.py /construction/biology/velvet/stage/usr/local/bin/AssemblyAssembler1.3.py /bin/mkdir -p /construction/biology/velvet/stage/usr/local/lib/perl5/site_perl/VelvetOpt install -m 0644 /construction/biology/velvet/velvet_1.2.10/contrib/VelvetOptimiser-2.2.4/VelvetOpt/Assembly.pm /construction/biology/velvet/stage/usr/local/lib/perl5/site_perl/VelvetOpt/Assembly.pm install -m 0644 /construction/biology/velvet/velvet_1.2.10/contrib/VelvetOptimiser-2.2.4/VelvetOpt/Utils.pm /construction/biology/velvet/stage/usr/local/lib/perl5/site_perl/VelvetOpt/Utils.pm install -m 0644 /construction/biology/velvet/velvet_1.2.10/contrib/VelvetOptimiser-2.2.4/VelvetOpt/gwrap.pm /construction/biology/velvet/stage/usr/local/lib/perl5/site_perl/VelvetOpt/gwrap.pm install -m 0644 /construction/biology/velvet/velvet_1.2.10/contrib/VelvetOptimiser-2.2.4/VelvetOpt/hwrap.pm /construction/biology/velvet/stage/usr/local/lib/perl5/site_perl/VelvetOpt/hwrap.pm install -m 0644 /construction/biology/velvet/velvet_1.2.10/ChangeLog /construction/biology/velvet/velvet_1.2.10/Manual.pdf /construction/biology/velvet/velvet_1.2.10/Columbus_manual.pdf /construction/biology/velvet/stage/usr/local/share/doc/velvet ====> Compressing man pages (compress-man) -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for velvet-1.2.10_2 file sizes/checksums [25]: . done packing files [25]: . done packing directories [1]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Sunday, 7 JUL 2019 at 04:56:36 UTC Duration: 00:00:34