=> Building biology/fasta Started : Wednesday, 18 APR 2018 at 02:04:28 UTC Platform: 5.3-DEVELOPMENT DragonFly v5.3.0.81.g32506c-DEVELOPMENT #29: Tue Apr 10 08:49:52 PDT 2018 marino@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 fasta-21.1.1: DOCS=on: Build and/or install documentation ===> Use 'make config' to modify these settings -------------------------------------------------- -- CONFIGURE_ENV -------------------------------------------------- XDG_DATA_HOME=/construction/biology/fasta XDG_CONFIG_HOME=/construction/biology/fasta HOME=/construction/biology/fasta TMPDIR="/tmp" PATH=/construction/biology/fasta/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc50 -------------------------------------------------- -- CONFIGURE_ARGS -------------------------------------------------- -------------------------------------------------- -- MAKE_ENV -------------------------------------------------- XDG_DATA_HOME=/construction/biology/fasta XDG_CONFIG_HOME=/construction/biology/fasta HOME=/construction/biology/fasta TMPDIR="/tmp" PATH=/construction/biology/fasta/.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 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 -------------------------------------------------- DESTDIR=/construction/biology/fasta/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- PORTDOCS="" PORTEXAMPLES="" OSREL=5.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/fasta" EXAMPLESDIR="share/examples/fasta" DATADIR="share/fasta" WWWDIR="www/fasta" ETCDIR="etc/fasta" -------------------------------------------------- -- SUB_LIST -------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/fasta DOCSDIR=/usr/local/share/doc/fasta EXAMPLESDIR=/usr/local/share/examples/fasta WWWDIR=/usr/local/www/fasta ETCDIR=/usr/local/etc/fasta -------------------------------------------------- -- /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 LICENSES_ACCEPTED= NONE 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 fasta 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 -------------------------------------------------------------------------------- ===> fasta-21.1.1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.5.txz Installing pkg-1.10.5... Extracting pkg-1.10.5: .......... done ===> fasta-21.1.1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of fasta-21.1.1 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> NOTICE: The fasta 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 fasta-21.1.1 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> NOTICE: The fasta 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 fasta-21.1.1 for building => SHA256 Checksum OK for fasta-21.1.1.shar.Z. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> NOTICE: The fasta 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 fasta-21.1.1 for building ===> Extracting for fasta-21.1.1 => SHA256 Checksum OK for fasta-21.1.1.shar.Z. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for fasta-21.1.1 ===> Applying ports patches for fasta-21.1.1 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for fasta-21.1.1 -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for fasta-21.1.1 --- plalign2.o --- --- plsim3.o --- --- lalign2.o --- --- apam.o --- --- lsim3.o --- --- plalign2.o --- cc -pipe -O2 -fno-strict-aliasing -DUNIX -DPGM_DOC -DBIGMEM -DSFCHAR="':'" -DEXPM1 -DPROGRESS -DGAP_OPEN -DTPLOT -c lalign2.c -o plalign2.o --- plsim3.o --- cc -pipe -O2 -fno-strict-aliasing -DUNIX -DPGM_DOC -DBIGMEM -DSFCHAR="':'" -DEXPM1 -DPROGRESS -DGAP_OPEN -DTPLOT -c lsim3.c -o plsim3.o --- lalign2.o --- cc -pipe -O2 -fno-strict-aliasing -DUNIX -DPGM_DOC -DBIGMEM -DSFCHAR="':'" -DEXPM1 -DPROGRESS -DGAP_OPEN -c lalign2.c --- apam.o --- cc -pipe -O2 -fno-strict-aliasing -DUNIX -DPGM_DOC -DBIGMEM -DSFCHAR="':'" -DEXPM1 -DPROGRESS -DGAP_OPEN -c apam.c --- lsim3.o --- cc -pipe -O2 -fno-strict-aliasing -DUNIX -DPGM_DOC -DBIGMEM -DSFCHAR="':'" -DEXPM1 -DPROGRESS -DGAP_OPEN -c lsim3.c --- lgetaa.o --- cc -pipe -O2 -fno-strict-aliasing -DUNIX -DPGM_DOC -DBIGMEM -DSFCHAR="':'" -DEXPM1 -DPROGRESS -DGAP_OPEN -DNOLIB -c nxgetaa.c -o lgetaa.o --- ndispn.o --- cc -pipe -O2 -fno-strict-aliasing -DUNIX -DPGM_DOC -DBIGMEM -DSFCHAR="':'" -DEXPM1 -DPROGRESS -DGAP_OPEN -c ndispn.c --- ag_stats.o --- cc -pipe -O2 -fno-strict-aliasing -DUNIX -DPGM_DOC -DBIGMEM -DSFCHAR="':'" -DEXPM1 -DPROGRESS -DGAP_OPEN -c ag_stats.c --- time.o --- cc -pipe -O2 -fno-strict-aliasing -DUNIX -DPGM_DOC -DBIGMEM -DSFCHAR="':'" -DEXPM1 -DPROGRESS -DGAP_OPEN -DHZ=60 -c time.c --- ps_dispn.o --- cc -pipe -O2 -fno-strict-aliasing -DUNIX -DPGM_DOC -DBIGMEM -DSFCHAR="':'" -DEXPM1 -DPROGRESS -DGAP_OPEN -c ps_dispn.c --- align.o --- cc -pipe -O2 -fno-strict-aliasing -DUNIX -DPGM_DOC -DBIGMEM -DSFCHAR="':'" -DEXPM1 -DPROGRESS -DGAP_OPEN -c align.c --- llmax.o --- cc -pipe -O2 -fno-strict-aliasing -DUNIX -DPGM_DOC -DBIGMEM -DSFCHAR="':'" -DEXPM1 -DPROGRESS -DGAP_OPEN -c llmax.c --- llmax0.o --- cc -pipe -O2 -fno-strict-aliasing -DUNIX -DPGM_DOC -DBIGMEM -DSFCHAR="':'" -DEXPM1 -DPROGRESS -DGAP_OPEN -c llmax0.c --- tgrease.o --- cc -pipe -O2 -fno-strict-aliasing -DUNIX -DPGM_DOC -DBIGMEM -DSFCHAR="':'" -DEXPM1 -DPROGRESS -DGAP_OPEN -c tgrease.c --- ps_plotsub.o --- cc -pipe -O2 -fno-strict-aliasing -DUNIX -DPGM_DOC -DBIGMEM -DSFCHAR="':'" -DEXPM1 -DPROGRESS -DGAP_OPEN -c ps_plotsub.c ps_plotsub.c: In function 'drawstr': ps_plotsub.c:97:13: warning: implicit declaration of function 'strchr' [-Wimplicit-function-declaration] for (bp = strchr(str,'('); (bp!=NULL); bp = strchr(bp+1,'(')) *bp=' '; ^ ps_plotsub.c:97:13: warning: incompatible implicit declaration of built-in function 'strchr' ps_plotsub.c:97:13: note: include '' or provide a declaration of 'strchr' ps_plotsub.c:98:13: warning: incompatible implicit declaration of built-in function 'strchr' for (bp = strchr(str,')'); (bp!=NULL); bp = strchr(bp+1,')')) *bp=' '; ^ ps_plotsub.c:98:13: note: include '' or provide a declaration of 'strchr' ps_plotsub.c: In function 'xaxis': ps_plotsub.c:132:16: warning: implicit declaration of function 'strlen' [-Wimplicit-function-declaration] move(SX(n/2)-strlen(title)*8,i); ^ ps_plotsub.c:132:16: warning: incompatible implicit declaration of built-in function 'strlen' ps_plotsub.c:132:16: note: include '' or provide a declaration of 'strlen' --- chofas.o --- cc -pipe -O2 -fno-strict-aliasing -DUNIX -DPGM_DOC -DBIGMEM -DSFCHAR="':'" -DEXPM1 -DPROGRESS -DGAP_OPEN -c chofas.c --- garnier.o --- cc -pipe -O2 -fno-strict-aliasing -DUNIX -DPGM_DOC -DBIGMEM -DSFCHAR="':'" -DEXPM1 -DPROGRESS -DGAP_OPEN -c garnier.c --- align --- cc align.o apam.o llmax.o lgetaa.o ndispn.o time.o -lm -o align --- psgrease --- cc -pipe -O2 -fno-strict-aliasing -DUNIX -DPGM_DOC -DBIGMEM -DSFCHAR="':'" -DEXPM1 -DPROGRESS -DGAP_OPEN tgrease.o lgetaa.o ps_plotsub.o -o psgrease --- align0 --- cc align.o apam.o llmax0.o lgetaa.o ndispn.o time.o -lm -o align0 --- garnier --- cc -pipe -O2 -fno-strict-aliasing -DUNIX -DPGM_DOC -DBIGMEM -DSFCHAR="':'" -DEXPM1 -DPROGRESS -DGAP_OPEN garnier.o lgetaa.o -o garnier --- plalign --- cc plalign2.o apam.o plsim3.o lgetaa.o ps_dispn.o ag_stats.o time.o -lm -o plalign --- chofas --- cc -pipe -O2 -fno-strict-aliasing -DUNIX -DPGM_DOC -DBIGMEM -DSFCHAR="':'" -DEXPM1 -DPROGRESS -DGAP_OPEN chofas.o lgetaa.o -o chofas --- lalign --- cc lalign2.o apam.o lsim3.o lgetaa.o ndispn.o ag_stats.o time.o -lm -o lalign -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for fasta-21.1.1 ===> Generating temporary packing list install -s -m 555 lalign plalign align align0 psgrease chofas garnier /construction/biology/fasta/stage/usr/local/bin install -m 444 /construction/biology/fasta/fasta/align.1 /construction/biology/fasta/fasta/fasta.1 /construction/biology/fasta/fasta/lalign.1 /construction/biology/fasta/fasta/prdf.1 /construction/biology/fasta/fasta/prss.1 /construction/biology/fasta/fasta/randseq.1 /construction/biology/fasta/fasta/ssearch.1 /construction/biology/fasta/stage/usr/local/man/man1 ln -s fasta.1.gz /construction/biology/fasta/stage/usr/local/man/man1/tfasta.1.gz ln -s fasta.1.gz /construction/biology/fasta/stage/usr/local/man/man1/lfasta.1.gz ln -s fasta.1.gz /construction/biology/fasta/stage/usr/local/man/man1/plfasta.1.gz ln -s fasta.1.gz /construction/biology/fasta/stage/usr/local/man/man1/fastx.1.gz ln -s fasta.1.gz /construction/biology/fasta/stage/usr/local/man/man1/tfastx.1.gz ln -s align.1.gz /construction/biology/fasta/stage/usr/local/man/man1/align0.1.gz ln -s align.1.gz /construction/biology/fasta/stage/usr/local/man/man1/plalign.1.gz install -m 0644 /construction/biology/fasta/fasta/COPYRIGHT /construction/biology/fasta/fasta/README.versions /construction/biology/fasta/fasta/fasta20.doc /construction/biology/fasta/fasta/fasta20.me /construction/biology/fasta/fasta/format.doc /construction/biology/fasta/fasta/readme.* /construction/biology/fasta/stage/usr/local/share/doc/fasta ====> Compressing man pages (compress-man) -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for fasta-21.1.1 file sizes/checksums [34]: . done packing files [34]: . done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Wednesday, 18 APR 2018 at 02:04:43 UTC Duration: 00:00:15