=> Building biology/ssaha Started : Sunday, 1 OCT 2017 at 02:46:00 UTC Platform: 4.9-DEVELOPMENT DragonFly v4.9.0.699.g39a93-DEVELOPMENT #22: Tue Sep 19 22:06:52 PDT 2017 root@pkgbox64.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 -------------------------------------------------- -- Environment -------------------------------------------------- UNAME_r=5.0-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.0-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 -------------------------------------------------- -------------------------------------------------- -- CONFIGURE_ENV -------------------------------------------------- MAKE=gmake XDG_DATA_HOME=/construction/biology/ssaha XDG_CONFIG_HOME=/construction/biology/ssaha HOME=/construction/biology/ssaha TMPDIR="/tmp" SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc50 -------------------------------------------------- -- CONFIGURE_ARGS -------------------------------------------------- -------------------------------------------------- -- MAKE_ENV -------------------------------------------------- CCC="g++" OPTIM=" -pipe -O2 -fno-strict-aliasing" THREAD_LIB="-pthread" XDG_DATA_HOME=/construction/biology/ssaha XDG_CONFIG_HOME=/construction/biology/ssaha HOME=/construction/biology/ssaha TMPDIR="/tmp" NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES CCVER=gcc50 PREFIX=/usr/local LOCALBASE=/usr/local LIBDIR="/usr/lib" NOPROFILE=1 CC="gcc" CFLAGS="-pipe -O2 -fno-strict-aliasing" CPP="cpp" CPPFLAGS="" LDFLAGS="" LIBS="" CXX="g++" 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/ssaha/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- OSREL=5.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local PORTDOCS="" PORTEXAMPLES="" LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/ssaha" EXAMPLESDIR="share/examples/ssaha" DATADIR="share/ssaha" WWWDIR="www/ssaha" ETCDIR="etc/ssaha" -------------------------------------------------- -- SUB_LIST -------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/ssaha DOCSDIR=/usr/local/share/doc/ssaha EXAMPLESDIR=/usr/local/share/examples/ssaha WWWDIR=/usr/local/www/ssaha ETCDIR=/usr/local/etc/ssaha -------------------------------------------------- -- /etc/make.conf -------------------------------------------------- SYNTHPROFILE=Release-5.0 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 _SMP_CPUS=8 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500000 OSVERSION=9999999 OSREL=5.0 _OSRELEASE=5.0-SYNTH -------------------------------------------------------------------------------- -- Phase: check-sanity -------------------------------------------------------------------------------- ===> NOTICE: The ssaha port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> ssaha-3.1c_5 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.1.txz Installing pkg-1.10.1... Extracting pkg-1.10.1: .......... done ===> ssaha-3.1c_5 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of ssaha-3.1c_5 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> NOTICE: The ssaha port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port ===> Fetching all distfiles required by ssaha-3.1c_5 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> NOTICE: The ssaha port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port ===> Fetching all distfiles required by ssaha-3.1c_5 for building => SHA256 Checksum OK for ssaha_v31c.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> NOTICE: The ssaha port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port ===> Fetching all distfiles required by ssaha-3.1c_5 for building ===> Extracting for ssaha-3.1c_5 => SHA256 Checksum OK for ssaha_v31c.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for ssaha-3.1c_5 ===> Applying ports patches for ssaha-3.1c_5 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> ssaha-3.1c_5 depends on executable: gmake - not found ===> Installing existing package /packages/All/gmake-4.2.1_1.txz Installing gmake-4.2.1_1... `-- Installing gettext-runtime-0.19.8.1_1... | `-- Installing indexinfo-0.2.6... | `-- Extracting indexinfo-0.2.6: .... done `-- Extracting gettext-runtime-0.19.8.1_1: .......... done Extracting gmake-4.2.1_1: .......... done ===> ssaha-3.1c_5 depends on executable: gmake - found ===> Returning to build of ssaha-3.1c_5 -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for ssaha-3.1c_5 -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for ssaha-3.1c_5 gmake[1]: Entering directory '/construction/biology/ssaha/ssaha-3.1c_5/Binary' g++ -c -pipe -O2 -fno-strict-aliasing -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/../ -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/..//Global -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/..//SequenceReader -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/..//HashTable -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/..//QueryManager -D_REENTRANT /construction/biology/ssaha/ssaha-3.1c_5/Binary/..//Global/GlobalDefinitions.cpp g++ -c -pipe -O2 -fno-strict-aliasing -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/../ -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/..//Global -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/..//SequenceReader -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/..//HashTable -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/..//QueryManager -D_REENTRANT /construction/biology/ssaha/ssaha-3.1c_5/Binary/..//HashTable/HashTable.cpp g++ -c -pipe -O2 -fno-strict-aliasing -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/../ -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/..//Global -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/..//SequenceReader -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/..//HashTable -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/..//QueryManager -D_REENTRANT /construction/biology/ssaha/ssaha-3.1c_5/Binary/..//HashTable/HashTablePacked.cpp g++ -c -pipe -O2 -fno-strict-aliasing -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/../ -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/..//Global -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/..//SequenceReader -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/..//HashTable -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/..//QueryManager -D_REENTRANT /construction/biology/ssaha/ssaha-3.1c_5/Binary/..//HashTable/HashTableGeneric.cpp g++ -c -pipe -O2 -fno-strict-aliasing -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/../ -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/..//Global -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/..//SequenceReader -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/..//HashTable -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/..//QueryManager -D_REENTRANT /construction/biology/ssaha/ssaha-3.1c_5/Binary/..//HashTable/HashTableTranslated.cpp g++ -c -pipe -O2 -fno-strict-aliasing -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/../ -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/..//Global -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/..//SequenceReader -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/..//HashTable -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/..//QueryManager -D_REENTRANT /construction/biology/ssaha/ssaha-3.1c_5/Binary/..//SequenceReader/SequenceReader.cpp g++ -c -pipe -O2 -fno-strict-aliasing -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/../ -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/..//Global -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/..//SequenceReader -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/..//HashTable -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/..//QueryManager -D_REENTRANT /construction/biology/ssaha/ssaha-3.1c_5/Binary/..//SequenceReader/SequenceEncoder.cpp g++ -c -pipe -O2 -fno-strict-aliasing -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/../ -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/..//Global -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/..//SequenceReader -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/..//HashTable -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/..//QueryManager -D_REENTRANT /construction/biology/ssaha/ssaha-3.1c_5/Binary/..//SequenceReader/SequenceReaderMulti.cpp g++ -c -pipe -O2 -fno-strict-aliasing -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/../ -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/..//Global -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/..//SequenceReader -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/..//HashTable -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/..//QueryManager -D_REENTRANT /construction/biology/ssaha/ssaha-3.1c_5/Binary/..//SequenceReader/SequenceReaderFasta.cpp In file included from /usr/include/c++/5.0/backward/strstream:50:0, from /construction/biology/ssaha/ssaha-3.1c_5/Binary/..//SequenceReader/SequenceReaderFasta.cpp:36: /usr/include/c++/5.0/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] #warning \ ^ g++ -c -pipe -O2 -fno-strict-aliasing -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/../ -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/..//Global -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/..//SequenceReader -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/..//HashTable -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/..//QueryManager -D_REENTRANT /construction/biology/ssaha/ssaha-3.1c_5/Binary/..//SequenceReader/SequenceReaderFastq.cpp In file included from /usr/include/c++/5.0/backward/strstream:50:0, from /construction/biology/ssaha/ssaha-3.1c_5/Binary/..//SequenceReader/SequenceReaderFastq.cpp:36: /usr/include/c++/5.0/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] #warning \ ^ g++ -c -pipe -O2 -fno-strict-aliasing -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/../ -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/..//Global -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/..//SequenceReader -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/..//HashTable -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/..//QueryManager -D_REENTRANT /construction/biology/ssaha/ssaha-3.1c_5/Binary/..//SequenceReader/SequenceReaderFilter.cpp In file included from /usr/include/c++/5.0/backward/strstream:50:0, from /construction/biology/ssaha/ssaha-3.1c_5/Binary/..//SequenceReader/SequenceReaderFilter.cpp:34: /usr/include/c++/5.0/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] #warning \ ^ g++ -c -pipe -O2 -fno-strict-aliasing -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/../ -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/..//Global -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/..//SequenceReader -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/..//HashTable -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/..//QueryManager -D_REENTRANT /construction/biology/ssaha/ssaha-3.1c_5/Binary/..//QueryManager/QueryManager.cpp g++ -c -pipe -O2 -fno-strict-aliasing -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/../ -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/..//Global -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/..//SequenceReader -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/..//HashTable -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/..//QueryManager -D_REENTRANT /construction/biology/ssaha/ssaha-3.1c_5/Binary/..//QueryManager/MatchStoreUngapped.cpp g++ -c -pipe -O2 -fno-strict-aliasing -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/../ -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/..//Global -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/..//SequenceReader -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/..//HashTable -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/..//QueryManager -D_REENTRANT /construction/biology/ssaha/ssaha-3.1c_5/Binary/..//QueryManager/MatchStoreGapped.cpp g++ -c -pipe -O2 -fno-strict-aliasing -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/../ -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/..//Global -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/..//SequenceReader -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/..//HashTable -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/..//QueryManager -D_REENTRANT /construction/biology/ssaha/ssaha-3.1c_5/Binary/..//QueryManager/MatchStore.cpp g++ -c -pipe -O2 -fno-strict-aliasing -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/../ -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/..//Global -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/..//SequenceReader -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/..//HashTable -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/..//QueryManager -D_REENTRANT /construction/biology/ssaha/ssaha-3.1c_5/Binary/..//QueryManager/MatchAligner.cpp g++ -c -pipe -O2 -fno-strict-aliasing -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/../ -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/..//Global -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/..//SequenceReader -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/..//HashTable -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/..//QueryManager -D_REENTRANT /construction/biology/ssaha/ssaha-3.1c_5/Binary/..//Global/SSAHAMain.cpp g++ -c -pipe -O2 -fno-strict-aliasing -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/../ -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/..//Global -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/..//SequenceReader -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/..//HashTable -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/..//QueryManager -D_REENTRANT /construction/biology/ssaha/ssaha-3.1c_5/Binary/..//Global/TimeStamp.cpp g++ -pipe -O2 -fno-strict-aliasing -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/../ -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/..//Global -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/..//SequenceReader -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/..//HashTable -I/construction/biology/ssaha/ssaha-3.1c_5/Binary/..//QueryManager -D_REENTRANT -Wl,-S -o ssaha GlobalDefinitions.o HashTable.o HashTablePacked.o HashTableGeneric.o HashTableTranslated.o SequenceReader.o SequenceEncoder.o SequenceReaderMulti.o SequenceReaderFasta.o SequenceReaderFastq.o SequenceReaderFilter.o QueryManager.o MatchStoreUngapped.o MatchStoreGapped.o MatchStore.o MatchAligner.o SSAHAMain.o TimeStamp.o gmake[1]: Leaving directory '/construction/biology/ssaha/ssaha-3.1c_5/Binary' -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for ssaha-3.1c_5 ===> Generating temporary packing list (cd /construction/biology/ssaha/ssaha-3.1c_5/Binary && install -s -m 555 ssaha /construction/biology/ssaha/stage/usr/local/bin) (cd /construction/biology/ssaha/ssaha-3.1c_5/Binary && install -m 555 testSSAHA.csh /construction/biology/ssaha/stage/usr/local/share/ssaha) (cd /construction/biology/ssaha/ssaha-3.1c_5/Binary && install -m 0644 test.fasta /construction/biology/ssaha/stage/usr/local/share/ssaha) (cd /construction/biology/ssaha/ssaha-3.1c_5/Binary && install -m 0644 test_extract.fasta /construction/biology/ssaha/stage/usr/local/share/ssaha) (cd /construction/biology/ssaha/ssaha-3.1c_5/Binary && install -m 0644 test_filter.fail /construction/biology/ssaha/stage/usr/local/share/ssaha) (cd /construction/biology/ssaha/ssaha-3.1c_5/Binary && install -m 0644 test_filter.fastq /construction/biology/ssaha/stage/usr/local/share/ssaha) (cd /construction/biology/ssaha/ssaha-3.1c_5/Binary && install -m 0644 test_protein.fasta /construction/biology/ssaha/stage/usr/local/share/ssaha) (cd /construction/biology/ssaha/ssaha-3.1c_5/Binary && install -m 0644 README /construction/biology/ssaha/stage/usr/local/share/ssaha) ====> Compressing man pages (compress-man) -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for ssaha-3.1c_5 file sizes/checksums [8]: . done packing files [8]: . done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Sunday, 1 OCT 2017 at 02:46:20 UTC Duration: 00:00:19