=> Building biology/ariadne Started : Sunday, 1 OCT 2017 at 02:26:12 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 -------------------------------------------------- ===> The following configuration options are available for ariadne-1.3: DOCS=on: Build and/or install documentation ===> Use 'make config' to modify these settings -------------------------------------------------- -- CONFIGURE_ENV -------------------------------------------------- MAKE=gmake XDG_DATA_HOME=/construction/biology/ariadne XDG_CONFIG_HOME=/construction/biology/ariadne HOME=/construction/biology/ariadne TMPDIR="/tmp" SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc50 -------------------------------------------------- -- CONFIGURE_ARGS -------------------------------------------------- -------------------------------------------------- -- MAKE_ENV -------------------------------------------------- XDG_DATA_HOME=/construction/biology/ariadne XDG_CONFIG_HOME=/construction/biology/ariadne HOME=/construction/biology/ariadne 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="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 -------------------------------------------------- CC="cc" DESTDIR=/construction/biology/ariadne/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- OSREL=5.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local PORTDOCS="" PORTEXAMPLES="" LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/ariadne" EXAMPLESDIR="share/examples/ariadne" DATADIR="share/ariadne" WWWDIR="www/ariadne" ETCDIR="etc/ariadne" -------------------------------------------------- -- SUB_LIST -------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/ariadne DOCSDIR=/usr/local/share/doc/ariadne EXAMPLESDIR=/usr/local/share/examples/ariadne WWWDIR=/usr/local/www/ariadne ETCDIR=/usr/local/etc/ariadne -------------------------------------------------- -- /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 ariadne 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 -------------------------------------------------------------------------------- ===> ariadne-1.3 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 ===> ariadne-1.3 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of ariadne-1.3 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> NOTICE: The ariadne 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 ariadne-1.3 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> NOTICE: The ariadne 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 ariadne-1.3 for building => SHA256 Checksum OK for ariadne-1.3.tar.Z. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> NOTICE: The ariadne 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 ariadne-1.3 for building ===> Extracting for ariadne-1.3 => SHA256 Checksum OK for ariadne-1.3.tar.Z. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for ariadne-1.3 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> ariadne-1.3 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 ===> ariadne-1.3 depends on executable: gmake - found ===> Returning to build of ariadne-1.3 -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for ariadne-1.3 -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for ariadne-1.3 gmake[1]: Entering directory '/construction/biology/ariadne/SRC-1.3' mkdir -p ./DragonFly cc -c -pipe -O2 -fno-strict-aliasing -g -I./Include/ -o DragonFly/cl.o cl.c; cl.c: In function 'FileDate': cl.c:673:10: warning: function returns address of local variable [-Wreturn-local-addr] return t; ^ cl.c:652:8: note: declared here char date[256], *t; ^ cc -c -pipe -O2 -fno-strict-aliasing -g -I./Include/ -o DragonFly/searchpath.o searchpath.c; cc -c -pipe -O2 -fno-strict-aliasing -g -I./Include/ -o DragonFly/readline.o readline.c; cc -c -pipe -O2 -fno-strict-aliasing -g -I./Include/ -o DragonFly/seq_util.o seq_util.c; seq_util.c: In function 'Read_nbrf_Sq': seq_util.c:676:1: warning: type of 'text_offset' defaults to 'int' [-Wimplicit-int] Read_nbrf_Sq( name, database, offset, text_offset ) ^ cc -c -pipe -O2 -fno-strict-aliasing -g -I./Include/ -o DragonFly/gaplib.o gaplib.c; cc -c -pipe -O2 -fno-strict-aliasing -g -I./Include/ -o DragonFly/cmp.o cmp.c; cc -c -pipe -O2 -fno-strict-aliasing -g -I./Include/ -o DragonFly/profile_util.o profile_util.c; cc -c -pipe -O2 -fno-strict-aliasing -g -I./Include/ -o DragonFly/profile_stat.o profile_stat.c; cc -c -pipe -O2 -fno-strict-aliasing -g -I./Include/ -o DragonFly/prospero_utils.o prospero_utils.c; cc -c -pipe -O2 -fno-strict-aliasing -g -I./Include/ -o DragonFly/topalign.o topalign.c; topalign.c: In function 'TopAlignProteinToProfile': topalign.c:96:14: warning: implicit declaration of function 'toupper' [-Wimplicit-function-declaration] int ci = toupper(seq[i]); ^ ar rscuv ./DragonFly/libseq.a ./DragonFly/cl.o ./DragonFly/searchpath.o ./DragonFly/readline.o ./DragonFly/seq_util.o ./DragonFly/gaplib.o ./DragonFly/cmp.o ./DragonFly/profile_util.o ./DragonFly/profile_stat.o ./DragonFly/prospero_utils.o ./DragonFly/topalign.o; /usr/libexec/binutils227/elf/ar: `u' modifier ignored since `D' is the default (see `U') a - ./DragonFly/cl.o a - ./DragonFly/searchpath.o a - ./DragonFly/readline.o a - ./DragonFly/seq_util.o a - ./DragonFly/gaplib.o a - ./DragonFly/cmp.o a - ./DragonFly/profile_util.o a - ./DragonFly/profile_stat.o a - ./DragonFly/prospero_utils.o a - ./DragonFly/topalign.o cc -pipe -O2 -fno-strict-aliasing -O2 -g -DDragonFly -I./Include/ -L./DragonFly -o ./DragonFly/ariadne ariadne.c -lseq -lm -lpthread cc -pipe -O2 -fno-strict-aliasing -O2 -g -DDragonFly -I./Include/ -L./DragonFly -o ./DragonFly/prospero prospero.c -lseq -lm -lpthread prospero.c: In function 'main': prospero.c:63:3: warning: implicit declaration of function 'strcpy' [-Wimplicit-function-declaration] strcpy(matname, "blosum62"); ^ prospero.c:63:3: warning: incompatible implicit declaration of built-in function 'strcpy' prospero.c:63:3: note: include '' or provide a declaration of 'strcpy' gmake[1]: Leaving directory '/construction/biology/ariadne/SRC-1.3' -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for ariadne-1.3 ===> Generating temporary packing list install -s -m 555 /construction/biology/ariadne/SRC-1.3/DragonFly/ariadne /construction/biology/ariadne/stage/usr/local/bin install -s -m 555 /construction/biology/ariadne/SRC-1.3/DragonFly/prospero /construction/biology/ariadne/stage/usr/local/bin install -m 0644 /construction/biology/ariadne/SRC-1.3/README /construction/biology/ariadne/stage/usr/local/share/doc/ariadne ====> Compressing man pages (compress-man) -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for ariadne-1.3 file sizes/checksums [3]: . done packing files [3]: . done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Sunday, 1 OCT 2017 at 02:26:20 UTC Duration: 00:00:08