=> Building biology/treepuzzle Started : Thursday, 7 MAR 2019 at 18:41:18 UTC Platform: 5.5-DEVELOPMENT DragonFly v5.5.0.192.g15ae7f0-DEVELOPMENT #34: Tue Feb 19 09:07:07 PST 2019 root@pkgbox64.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 -------------------------------------------------- -- Environment -------------------------------------------------- UNAME_r=5.5-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.5-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/treepuzzle XDG_CONFIG_HOME=/construction/biology/treepuzzle HOME=/construction/biology/treepuzzle TMPDIR="/tmp" PATH=/construction/biology/treepuzzle/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc80 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/treepuzzle XDG_CONFIG_HOME=/construction/biology/treepuzzle HOME=/construction/biology/treepuzzle TMPDIR="/tmp" PATH=/construction/biology/treepuzzle/.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/treepuzzle/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- OSREL=5.5 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/treepuzzle" EXAMPLESDIR="share/examples/treepuzzle" DATADIR="share/treepuzzle" WWWDIR="www/treepuzzle" ETCDIR="etc/treepuzzle" -------------------------------------------------- -- SUB_LIST -------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/treepuzzle DOCSDIR=/usr/local/share/doc/treepuzzle EXAMPLESDIR=/usr/local/share/examples/treepuzzle WWWDIR=/usr/local/www/treepuzzle ETCDIR=/usr/local/etc/treepuzzle -------------------------------------------------- -- /etc/make.conf -------------------------------------------------- SYNTHPROFILE=Release-BE 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 LICENSES_ACCEPTED= NONE HAVE_COMPAT_IA32_KERN= CONFIGURE_MAX_CMD_LEN=262144 _PERL5_FROM_BIN=5.26.2 _ALTCCVERSION_921dbbb2=none _OBJC_ALTCCVERSION_921dbbb2=none _SMP_CPUS=8 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500500 OSVERSION=9999999 OSREL=5.5 _OSRELEASE=5.5-SYNTH PYTHONBASE=/usr/local _PKG_CHECKED=1 -------------------------------------------------------------------------------- -- Phase: check-sanity -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> treepuzzle-5.2 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.5_5.txz Installing pkg-1.10.5_5... Extracting pkg-1.10.5_5: .......... done ===> treepuzzle-5.2 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of treepuzzle-5.2 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> Fetching all distfiles required by treepuzzle-5.2 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> Fetching all distfiles required by treepuzzle-5.2 for building => SHA256 Checksum OK for tree-puzzle-5.2.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> Fetching all distfiles required by treepuzzle-5.2 for building ===> Extracting for treepuzzle-5.2 => SHA256 Checksum OK for tree-puzzle-5.2.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for treepuzzle-5.2 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for treepuzzle-5.2 --------------------------------------------- If you want to install the parallel version of tree-puzzle, you need to install from the ports and have to have a MPI-Implementation on your system. The tree-puzzle configure script will then automatically build the normal and parallel version (puzzle & ppuzzle). --------------------------------------------- configure: loading site script /xports/Templates/config.site checking build system type... x86_64-portbld-dragonfly5.5 checking host system type... x86_64-portbld-dragonfly5.5 checking target system type... x86_64-portbld-dragonfly5.5 checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for gawk... (cached) /usr/bin/awk checking whether make sets ${MAKE}... yes checking for gcc... cc checking for C compiler default output... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... 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 style of include used by make... GNU checking dependency style of cc... gcc3 checking whether cc understands -c and -o together... yes checking for a BSD-compatible install... /usr/bin/install -c checking whether make sets ${MAKE}... (cached) yes checking for mpcc... no checking for hcc... no checking for mpicc... no checking for mpicc_lam... no checking for mpicc_mpich... no checking for cc... /usr/bin/cc checking whether /usr/bin/cc works as MPI compiler... no checking whether /usr/bin/cc needs -lmpi... no checking whether cc handles quotes correctly... yes checking for main in -lm... yes checking how to run the C preprocessor... cpp 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 limits.h... (cached) yes checking for cc option to accept ANSI C... none needed checking for an ANSI C-conforming const... yes checking for size_t... (cached) yes configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating src/sprng/Makefile config.status: creating doc/Makefile config.status: creating data/Makefile config.status: creating tests/Makefile config.status: creating src/config.h config.status: executing depfiles commands -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for treepuzzle-5.2 --- all-recursive --- Making all in src --- all --- /usr/bin/make all-recursive --- all-recursive --- Making all in sprng --- makeseed.o --- --- store.o --- --- memory.o --- --- checkid.o --- --- lcg64.o --- --- makeseed.o --- cc -pipe -O2 -fno-strict-aliasing -c makeseed.c --- store.o --- cc -pipe -O2 -fno-strict-aliasing -c store.c --- memory.o --- cc -pipe -O2 -fno-strict-aliasing -c memory.c --- primes-lcg64.o --- --- lcg64.o --- cc -pipe -O2 -fno-strict-aliasing -c lcg64.c --- checkid.o --- cc -pipe -O2 -fno-strict-aliasing -c checkid.c --- primes-lcg64.o --- cc -pipe -O2 -fno-strict-aliasing -c primes-lcg64.c primes-lcg64.c: In function 'getprime': primes-lcg64.c:75:5: warning: implicit declaration of function 'memcpy' [-Wimplicit-function-declaration] memcpy(prime_array,prime_list+offset,need*sizeof(unsigned int)); ^~~~~~ primes-lcg64.c:75:5: warning: incompatible implicit declaration of built-in function 'memcpy' primes-lcg64.c:75:5: note: include '' or provide a declaration of 'memcpy' primes-lcg64.c:5:1: +#include primes-lcg64.c:75:5: memcpy(prime_array,prime_list+offset,need*sizeof(unsigned int)); ^~~~~~ --- make-sprng-objs --- --- sml1.o --- --- sml2.o --- --- smlparam.o --- --- smodel1.o --- --- make-sprng-objs --- cd sprng && /usr/bin/make makeseed.o store.o memory.o checkid.o lcg64.o primes-lcg64.o `makeseed.o' is up to date. `store.o' is up to date. `memory.o' is up to date. `checkid.o' is up to date. `lcg64.o' is up to date. `primes-lcg64.o' is up to date. --- sml1.o --- cc -DHAVE_CONFIG_H -I. -I.. -I. -I./sprng -pipe -O2 -fno-strict-aliasing -c ./ml1.c && mv ml1.o sml1.o --- sml2.o --- cc -DHAVE_CONFIG_H -I. -I.. -I. -I./sprng -pipe -O2 -fno-strict-aliasing -c ./ml2.c && mv ml2.o sml2.o --- smodel2.o --- --- smlparam.o --- cc -DHAVE_CONFIG_H -I. -I.. -I. -I./sprng -pipe -O2 -fno-strict-aliasing -c ./mlparam.c && mv mlparam.o smlparam.o --- smodel1.o --- cc -DHAVE_CONFIG_H -I. -I.. -I. -I./sprng -pipe -O2 -fno-strict-aliasing -c ./model1.c && mv model1.o smodel1.o --- smodel2.o --- cc -DHAVE_CONFIG_H -I. -I.. -I. -I./sprng -pipe -O2 -fno-strict-aliasing -c ./model2.c && mv model2.o smodel2.o --- spuzzle1.o --- cc -DHAVE_CONFIG_H -I. -I.. -I. -I./sprng -pipe -O2 -fno-strict-aliasing -c ./puzzle1.c && mv puzzle1.o spuzzle1.o --- spuzzle2.o --- cc -DHAVE_CONFIG_H -I. -I.. -I. -I./sprng -pipe -O2 -fno-strict-aliasing -c ./puzzle2.c && mv puzzle2.o spuzzle2.o --- spstep.o --- cc -DHAVE_CONFIG_H -I. -I.. -I. -I./sprng -pipe -O2 -fno-strict-aliasing -c ./pstep.c && mv pstep.o spstep.o --- sutil.o --- cc -DHAVE_CONFIG_H -I. -I.. -I. -I./sprng -pipe -O2 -fno-strict-aliasing -c ./util.c && mv util.o sutil.o --- sgamma.o --- cc -DHAVE_CONFIG_H -I. -I.. -I. -I./sprng -pipe -O2 -fno-strict-aliasing -c ./gamma.c && mv gamma.o sgamma.o --- sconsensus.o --- cc -DHAVE_CONFIG_H -I. -I.. -I. -I./sprng -pipe -O2 -fno-strict-aliasing -c ./consensus.c && mv consensus.o sconsensus.o --- streesort.o --- cc -DHAVE_CONFIG_H -I. -I.. -I. -I./sprng -pipe -O2 -fno-strict-aliasing -c ./treesort.c && mv treesort.o streesort.o --- streetest.o --- cc -DHAVE_CONFIG_H -I. -I.. -I. -I./sprng -pipe -O2 -fno-strict-aliasing -c ./treetest.c && mv treetest.o streetest.o --- puzzle --- cc -pipe -O2 -fno-strict-aliasing sgamma.o sml1.o sml2.o smlparam.o smodel1.o smodel2.o spuzzle1.o spuzzle2.o spstep.o sutil.o sconsensus.o streesort.o streetest.o sprng/makeseed.o sprng/store.o sprng/memory.o sprng/checkid.o sprng/lcg64.o sprng/primes-lcg64.o -lm -o puzzle Making all in doc --- all-recursive --- Making all in data Making all in tests -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for treepuzzle-5.2 ===> Generating temporary packing list Making install in src Making install in sprng cd sprng && /usr/bin/make makeseed.o store.o memory.o checkid.o lcg64.o primes-lcg64.o `makeseed.o' is up to date. `store.o' is up to date. `memory.o' is up to date. `checkid.o' is up to date. `lcg64.o' is up to date. `primes-lcg64.o' is up to date. cc -pipe -O2 -fno-strict-aliasing sgamma.o sml1.o sml2.o smlparam.o smodel1.o smodel2.o spuzzle1.o spuzzle2.o spstep.o sutil.o sconsensus.o streesort.o streetest.o sprng/makeseed.o sprng/store.o sprng/memory.o sprng/checkid.o sprng/lcg64.o sprng/primes-lcg64.o -lm -o puzzle cd sprng && /usr/bin/make makeseed.o store.o memory.o checkid.o lcg64.o primes-lcg64.o `makeseed.o' is up to date. `store.o' is up to date. `memory.o' is up to date. `checkid.o' is up to date. `lcg64.o' is up to date. `primes-lcg64.o' is up to date. cc -pipe -O2 -fno-strict-aliasing sgamma.o sml1.o sml2.o smlparam.o smodel1.o smodel2.o spuzzle1.o spuzzle2.o spstep.o sutil.o sconsensus.o streesort.o streetest.o sprng/makeseed.o sprng/store.o sprng/memory.o sprng/checkid.o sprng/lcg64.o sprng/primes-lcg64.o -lm -o puzzle /bin/sh ../mkinstalldirs /construction/biology/treepuzzle/stage/usr/local/bin install -s -m 555 puzzle /construction/biology/treepuzzle/stage/usr/local/bin/puzzle Making install in doc Making install in data Making install in tests ====> Compressing man pages (compress-man) -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for treepuzzle-5.2 file sizes/checksums [1]: . done packing files [1]: . done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Thursday, 7 MAR 2019 at 18:41:36 UTC Duration: 00:00:18