------------------------------------------------------------------------------- -- Phase: Environment ------------------------------------------------------------------------------- NO_DEPENDS=1 UNAME_r=5.9 UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=unknown UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 LANG=C HOME=/root USER=root TERM=dumb SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: showconfig ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ENV ------------------------------------------------------------------------------- MAKE=gmake XDG_DATA_HOME=/construction/biology/subread XDG_CONFIG_HOME=/construction/biology/subread HOME=/construction/biology/subread TMPDIR="/tmp" PATH=/construction/biology/subread/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc80 CMAKE_PREFIX_PATH="/usr/local" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ARGS ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: MAKE_ENV ------------------------------------------------------------------------------- XDG_DATA_HOME=/construction/biology/subread XDG_CONFIG_HOME=/construction/biology/subread HOME=/construction/biology/subread TMPDIR="/tmp" PATH=/construction/biology/subread/.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 -fcommon -O2 -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" -L/usr/local/lib " LIBS="" CXX="c++" CXXFLAGS=" -pipe -fcommon -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include " 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" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: MAKE_ARGS ------------------------------------------------------------------------------- DESTDIR=/construction/biology/subread/stage SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: PLIST_SUB ------------------------------------------------------------------------------- OSREL=5.9 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/subread" EXAMPLESDIR="share/examples/subread" DATADIR="share/subread" WWWDIR="www/subread" ETCDIR="etc/subread" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: SUB_LIST ------------------------------------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/subread DOCSDIR=/usr/local/share/doc/subread EXAMPLESDIR=/usr/local/share/examples/subread WWWDIR=/usr/local/www/subread ETCDIR=/usr/local/etc/subread SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: /etc/make.conf ------------------------------------------------------------------------------- DPORTS_BUILDER=yes DISABLE_LICENSES=yes DEFAULT_VERSIONS=ssl=openssl FORCE_PACKAGE=yes DEVELOPER=yes USE_PACKAGE_DEPENDS_ONLY=yes PORTSDIR=/xports PORT_DBDIR=/options PKG_DBDIR=/var/db/pkg PKG_CACHEDIR=/var/cache/pkg PKG_SUFX=.txz DEVELOPER=1 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500908 OSVERSION=9999999 OSREL=5.9 _OSRELEASE=5.9-SYNTH DISTDIR=/distfiles WRKDIRPREFIX=/construction BATCH=yes PACKAGE_BUILDING=yes PKG_CREATE_VERBOSE=yes MAKE_JOBS_NUMBER=10 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/indexinfo-0.3.1.txz Installing /packages/All/gettext-runtime-0.21.txz Installing /packages/All/gmake-4.3_2.txz Installing /packages/All/libsysinfo-0.0.3_2.txz SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> subread-2.0.1 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> subread-2.0.1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by subread-2.0.1 for building SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> subread-2.0.1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by subread-2.0.1 for building => SHA256 Checksum OK for subread-2.0.1-source.tar.gz. SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> subread-2.0.1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by subread-2.0.1 for building ===> Extracting for subread-2.0.1 => SHA256 Checksum OK for subread-2.0.1-source.tar.gz. Extracted Memory Use: 74.15M SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for subread-2.0.1 ===> Applying ports patches for subread-2.0.1 from /xports/biology/subread/files ===> Applying dragonfly patches for subread-2.0.1 from /xports/biology/subread/dragonfly SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> subread-2.0.1 depends on package: gmake>=4.3 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- ===> subread-2.0.1 depends on shared library: libsysinfo.so - found (/usr/local/lib/libsysinfo.so) SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> subread-2.0.1 depends on package: gmake>=4.3 - found ===> subread-2.0.1 depends on shared library: libsysinfo.so - found (/usr/local/lib/libsysinfo.so) ===> Configuring for subread-2.0.1 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for subread-2.0.1 gmake[1]: Entering directory '/construction/biology/subread/subread-2.0.1-source/src' cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -pipe -fcommon -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -c -o core.o core.c cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -pipe -fcommon -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -c -o core-junction.o core-junction.c cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -pipe -fcommon -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -c -o core-indel.o core-indel.c cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -pipe -fcommon -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -c -o sambam-file.o sambam-file.c cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -pipe -fcommon -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -c -o sublog.o sublog.c cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -pipe -fcommon -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -c -o gene-algorithms.o gene-algorithms.c cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -pipe -fcommon -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -c -o hashtable.o hashtable.c cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -pipe -fcommon -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -c -o input-files.o input-files.c cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -pipe -fcommon -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -c -o sorted-hashtable.o sorted-hashtable.c cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -pipe -fcommon -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -c -o gene-value-index.o gene-value-index.c cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -pipe -fcommon -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -c -o exon-algorithms.o exon-algorithms.c cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -pipe -fcommon -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -c -o HelperFunctions.o HelperFunctions.c cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -pipe -fcommon -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -c -o interval_merge.o interval_merge.c cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -pipe -fcommon -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -c -o long-hashtable.o long-hashtable.c cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -pipe -fcommon -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -c -o core-bigtable.o core-bigtable.c cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -pipe -fcommon -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -c -o seek-zlib.o seek-zlib.c cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -pipe -fcommon -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -c -o input-blc.o input-blc.c cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -o genRandomReads gen_rand_reads.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -L/usr/local/lib -DMAKE_FOR_EXON -DMAKE_STANDALONE -pthread -lsysinfo -lz -lm cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -o detectionCall detection-calls.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -L/usr/local/lib -DMAKE_FOR_EXON -DMAKE_STANDALONE -pthread -lsysinfo -lz -lm echo " " > longread-one/make.version cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -o repair read-repair.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -L/usr/local/lib -DMAKE_FOR_EXON -DMAKE_STANDALONE -pthread -lsysinfo -lz -lm rm -f longread-one/*.o cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -o txUnique tx-unique.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -L/usr/local/lib -DMAKE_FOR_EXON -DMAKE_STANDALONE -pthread -lsysinfo -lz -lm cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -o featureCounts readSummary.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -L/usr/local/lib -DMAKE_FOR_EXON -DMAKE_STANDALONE -pthread -lsysinfo -lz -lm cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -o removeDup removeDupReads.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -L/usr/local/lib -DMAKE_FOR_EXON -DMAKE_STANDALONE -pthread -lsysinfo -lz -lm cd longread-one && gmake cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -o exactSNP SNPCalling.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -L/usr/local/lib -DMAKE_FOR_EXON -DMAKE_STANDALONE -pthread -lsysinfo -lz -lm cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -o subread-buildindex index-builder.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -L/usr/local/lib -DMAKE_FOR_EXON -DMAKE_STANDALONE -pthread -lsysinfo -lz -lm cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -o subindel SUBindel.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -L/usr/local/lib -DMAKE_FOR_EXON -DMAKE_STANDALONE -pthread -lsysinfo -lz -lm gmake[2]: Entering directory '/construction/biology/subread/subread-2.0.1-source/src/longread-one' cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -o LRMsorted-hashtable.o -c -pipe -fcommon -O2 -isystem /usr/local/include -fno-strict-aliasing -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.1"\" LRMsorted-hashtable.c cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -o LRMbase-index.o -c -pipe -fcommon -O2 -isystem /usr/local/include -fno-strict-aliasing -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.1"\" LRMbase-index.c cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -o LRMchro-event.o -c -pipe -fcommon -O2 -isystem /usr/local/include -fno-strict-aliasing -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.1"\" LRMchro-event.c cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -o LRMhelper.o -c -pipe -fcommon -O2 -isystem /usr/local/include -fno-strict-aliasing -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.1"\" LRMhelper.c cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -o LRMseek-zlib.o -c -pipe -fcommon -O2 -isystem /usr/local/include -fno-strict-aliasing -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.1"\" LRMseek-zlib.c cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -o subread-align core-interface-aligner.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -L/usr/local/lib -DMAKE_FOR_EXON -DMAKE_STANDALONE -pthread -lsysinfo -lz -lm cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -o subjunc core-interface-subjunc.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -L/usr/local/lib -DMAKE_FOR_EXON -DMAKE_STANDALONE -pthread -lsysinfo -lz -lm cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -o LRMfile-io.o -c -pipe -fcommon -O2 -isystem /usr/local/include -fno-strict-aliasing -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.1"\" LRMfile-io.c cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -o LRMhashtable.o -c -pipe -fcommon -O2 -isystem /usr/local/include -fno-strict-aliasing -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.1"\" LRMhashtable.c cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -o qualityScores qualityScores.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -L/usr/local/lib -DMAKE_FOR_EXON -DMAKE_STANDALONE -pthread -lsysinfo -lz -lm cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -o subread-fullscan fullscan.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -L/usr/local/lib -DMAKE_FOR_EXON -DMAKE_STANDALONE -pthread -lsysinfo -lz -lm cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -o propmapped propmapped.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -L/usr/local/lib -DMAKE_FOR_EXON -DMAKE_STANDALONE -pthread -lsysinfo -lz -lm cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -o flattenGTF flattenAnnotations.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -L/usr/local/lib -DMAKE_FOR_EXON -DMAKE_STANDALONE -pthread -lsysinfo -lz -lm cc -DMAKE_FOR_EXON -DMAKE_STANDALONE -DSUBREAD_VERSION=\""2.0.1"\" -D_FILE_OFFSET_BITS=64 -o LRM -pipe -fcommon -O2 -isystem /usr/local/include -fno-strict-aliasing -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.1"\" longread-mapping.c LRMsorted-hashtable.o LRMbase-index.o LRMchro-event.o LRMhelper.o LRMseek-zlib.o LRMfile-io.o LRMhashtable.o -L/usr/local/lib -DMAKE_FOR_EXON -DMAKE_STANDALONE -pthread -lsysinfo -lz -lm -lpthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE gmake[2]: Leaving directory '/construction/biology/subread/subread-2.0.1-source/src/longread-one' mkdir -p ../bin/utilities mv longread-one/LRM longread-one/sublong mv longread-one/sublong subread-align subjunc featureCounts subindel exactSNP subread-buildindex ../bin/ mv detectionCall genRandomReads repair propmapped qualityScores removeDup subread-fullscan txUnique flattenGTF ../bin/utilities gmake[1]: Leaving directory '/construction/biology/subread/subread-2.0.1-source/src' SUCCEEDED 00:00:10 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- ===> Staging for subread-2.0.1 ===> Generating temporary packing list gmake[1]: Entering directory '/construction/biology/subread/subread-2.0.1-source/src' mkdir -p /construction/biology/subread/stage/usr/local/bin install -c \ ../bin/exactSNP \ ../bin/featureCounts \ ../bin/sub* \ ../bin/utilities/* \ /construction/biology/subread/stage/usr/local/bin strip /construction/biology/subread/stage/usr/local/bin/* gmake[1]: Leaving directory '/construction/biology/subread/subread-2.0.1-source/src' ====> Compressing man pages (compress-man) ====> Running Q/A tests (stage-qa) Warning: You have disabled the licenses framework with DISABLE_LICENSES, unable to run checks SUCCEEDED 00:00:02 ------------------------------------------------------------------------------- -- Phase: check-plist ------------------------------------------------------------------------------- ====> Checking for pkg-plist issues (check-plist) ===> Parsing plist ===> Checking for items in STAGEDIR missing from pkg-plist ===> Checking for items in pkg-plist which are not in STAGEDIR ===> No pkg-plist issues found (check-plist) SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: package ------------------------------------------------------------------------------- ===> Building package for subread-2.0.1 file sizes/checksums [16]: 0% file sizes/checksums [16]: 100% packing files [16]: 0% packing files [16]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:00:06 TOTAL TIME 00:00:21