=> Building biology/pear-merger Started : Thursday, 30 AUG 2018 at 13:03:07 UTC Platform: 5.3-DEVELOPMENT DragonFly 5.3-DEVELOPMENT #140: Wed Aug 29 22:06:30 PDT 2018 root@test.backplane.com:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 -------------------------------------------------- -- Environment -------------------------------------------------- UNAME_r=5.3-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.3-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 -------------------------------------------------- XDG_DATA_HOME=/construction/biology/pear-merger XDG_CONFIG_HOME=/construction/biology/pear-merger HOME=/construction/biology/pear-merger TMPDIR="/tmp" PATH=/construction/biology/pear-merger/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc50 CONFIG_SITE=/xports/Templates/config.site lt_cv_sys_max_cmd_len=262144 -------------------------------------------------- -- CONFIGURE_ARGS -------------------------------------------------- --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} -------------------------------------------------- -- MAKE_ENV -------------------------------------------------- XDG_DATA_HOME=/construction/biology/pear-merger XDG_CONFIG_HOME=/construction/biology/pear-merger HOME=/construction/biology/pear-merger TMPDIR="/tmp" PATH=/construction/biology/pear-merger/.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=gcc50 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/pear-merger/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- PORTDOCS="" PORTEXAMPLES="" OSREL=5.3 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/pear" EXAMPLESDIR="share/examples/pear" DATADIR="share/pear" WWWDIR="www/pear" ETCDIR="etc/pear" -------------------------------------------------- -- SUB_LIST -------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/pear DOCSDIR=/usr/local/share/doc/pear EXAMPLESDIR=/usr/local/share/examples/pear WWWDIR=/usr/local/www/pear ETCDIR=/usr/local/etc/pear -------------------------------------------------- -- /etc/make.conf -------------------------------------------------- SYNTHPROFILE=LiveSystem 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=12 _ALTCCVERSION_921dbbb2=none _OBJC_ALTCCVERSION_921dbbb2=none _SMP_CPUS=32 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500316 OSVERSION=9999999 OSREL=5.3 _OSRELEASE=5.3-SYNTH PYTHONBASE=/usr/local _PKG_CHECKED=1 -------------------------------------------------------------------------------- -- Phase: check-sanity -------------------------------------------------------------------------------- ===> License CC-BY-NC-SA-3.0 accepted by the user -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> pear-merger-0.9.6 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.5_1.txz Installing pkg-1.10.5_1... Extracting pkg-1.10.5_1: .......... done ===> pear-merger-0.9.6 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of pear-merger-0.9.6 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> License CC-BY-NC-SA-3.0 accepted by the user ===> Fetching all distfiles required by pear-merger-0.9.6 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> License CC-BY-NC-SA-3.0 accepted by the user ===> Fetching all distfiles required by pear-merger-0.9.6 for building => SHA256 Checksum OK for pear_0.9.6_src_all.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> License CC-BY-NC-SA-3.0 accepted by the user ===> Fetching all distfiles required by pear-merger-0.9.6 for building ===> Extracting for pear-merger-0.9.6 => SHA256 Checksum OK for pear_0.9.6_src_all.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for pear-merger-0.9.6 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for pear-merger-0.9.6 configure: loading site script /xports/Templates/config.site checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... (cached) /bin/mkdir -p checking for gawk... (cached) /usr/bin/awk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes test: -pipe: unexpected operator checking for gcc... cc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking whether cc understands -c and -o together... yes checking for style of include used by make... GNU checking dependency style of cc... gcc3 checking for log in -lm... yes checking for main in -lpthread... yes checking how to run the C preprocessor... cpp checking for grep that handles long lines and -e... (cached) /usr/bin/grep checking for egrep... (cached) /usr/bin/egrep checking for ANSI C header files... (cached) yes checking for sys/types.h... (cached) yes checking for sys/stat.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for memory.h... (cached) yes checking for strings.h... (cached) yes checking for inttypes.h... (cached) yes checking for stdint.h... (cached) yes checking for unistd.h... (cached) yes checking for stdint.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for inline... inline checking for size_t... (cached) yes checking for uint32_t... (cached) yes checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... (cached) yes checking for working strtod... (cached) yes checking for memmove... (cached) yes checking for pow... yes checking for strtol... (cached) yes checking for library containing pthread_create... none required checking for library containing BZ2_bzCompress... -lbz2 checking for library containing zlibVersion... -lz checking for pthread.h... (cached) yes checking bzlib.h usability... yes checking bzlib.h presence... yes checking for bzlib.h... yes checking for zlib.h... (cached) yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating man/Makefile config.status: creating src/config.h config.status: executing depfiles commands -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for pear-merger-0.9.6 --- all-recursive --- Making all in src --- all --- /usr/bin/make all-am --- pear-args.o --- --- pear-pear-pt.o --- --- pear-reader.o --- --- pear-statistics.o --- --- pear-args.o --- cc -DHAVE_CONFIG_H -I. -O3 -fomit-frame-pointer -funroll-loops -Wall -Wredundant-decls -Wreturn-type -Wswitch-default -Wimplicit -Wimplicit-function-declaration -Wimplicit-int -Wimport -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wstrict-prototypes -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value -Wunused-variable -Wformat -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -pipe -O2 -fno-strict-aliasing -MT pear-args.o -MD -MP -MF .deps/pear-args.Tpo -c -o pear-args.o `test -f 'args.c' || echo './'`args.c --- pear-pear-pt.o --- cc -DHAVE_CONFIG_H -I. -O3 -fomit-frame-pointer -funroll-loops -Wall -Wredundant-decls -Wreturn-type -Wswitch-default -Wimplicit -Wimplicit-function-declaration -Wimplicit-int -Wimport -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wstrict-prototypes -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value -Wunused-variable -Wformat -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -pipe -O2 -fno-strict-aliasing -MT pear-pear-pt.o -MD -MP -MF .deps/pear-pear-pt.Tpo -c -o pear-pear-pt.o `test -f 'pear-pt.c' || echo './'`pear-pt.c --- pear-reader.o --- cc -DHAVE_CONFIG_H -I. -O3 -fomit-frame-pointer -funroll-loops -Wall -Wredundant-decls -Wreturn-type -Wswitch-default -Wimplicit -Wimplicit-function-declaration -Wimplicit-int -Wimport -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wstrict-prototypes -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value -Wunused-variable -Wformat -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -pipe -O2 -fno-strict-aliasing -MT pear-reader.o -MD -MP -MF .deps/pear-reader.Tpo -c -o pear-reader.o `test -f 'reader.c' || echo './'`reader.c --- pear-statistics.o --- cc -DHAVE_CONFIG_H -I. -O3 -fomit-frame-pointer -funroll-loops -Wall -Wredundant-decls -Wreturn-type -Wswitch-default -Wimplicit -Wimplicit-function-declaration -Wimplicit-int -Wimport -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wstrict-prototypes -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value -Wunused-variable -Wformat -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -pipe -O2 -fno-strict-aliasing -MT pear-statistics.o -MD -MP -MF .deps/pear-statistics.Tpo -c -o pear-statistics.o `test -f 'statistics.c' || echo './'`statistics.c --- pear-args.o --- mv -f .deps/pear-args.Tpo .deps/pear-args.Po --- pear-reader.o --- reader.c: In function 'db_read_fastq_block': reader.c:766:20: warning: 'nBytes' may be used uninitialized in this function [-Wmaybe-uninitialized] block->rawdata[nBytes + remainder] = '\0'; ^ --- pear-statistics.o --- mv -f .deps/pear-statistics.Tpo .deps/pear-statistics.Po --- pear-reader.o --- mv -f .deps/pear-reader.Tpo .deps/pear-reader.Po --- pear-pear-pt.o --- mv -f .deps/pear-pear-pt.Tpo .deps/pear-pear-pt.Po --- pear --- cc -O3 -fomit-frame-pointer -funroll-loops -Wall -Wredundant-decls -Wreturn-type -Wswitch-default -Wimplicit -Wimplicit-function-declaration -Wimplicit-int -Wimport -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wstrict-prototypes -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value -Wunused-variable -Wformat -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -pipe -O2 -fno-strict-aliasing -o pear pear-pear-pt.o pear-args.o pear-statistics.o pear-reader.o -lz -lbz2 -lpthread -lm Making all in man -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for pear-merger-0.9.6 ===> Generating temporary packing list install -s -m 555 /construction/biology/pear-merger/pear-0.9.6-src/src/pear /construction/biology/pear-merger/stage/usr/local/bin/pearRM install -m 444 /construction/biology/pear-merger/pear-0.9.6-src/man/pearRM.1 /construction/biology/pear-merger/stage/usr/local/man/man1 ====> Compressing man pages (compress-man) -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for pear-merger-0.9.6 file sizes/checksums [5]: . done packing files [5]: . done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Thursday, 30 AUG 2018 at 13:03:29 UTC Duration: 00:00:22