=> Building biology/mapm3 Started : Thursday, 30 AUG 2018 at 13:02:55 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/mapm3 XDG_CONFIG_HOME=/construction/biology/mapm3 HOME=/construction/biology/mapm3 TMPDIR="/tmp" PATH=/construction/biology/mapm3/.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/mapm3 XDG_CONFIG_HOME=/construction/biology/mapm3 HOME=/construction/biology/mapm3 TMPDIR="/tmp" PATH=/construction/biology/mapm3/.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 -Wno-return-type -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -std=gnu89" CPP="cpp" CPPFLAGS="" LDFLAGS=" -L/usr/local/lib -Wl,-rpath=/usr/local/lib" LIBS="" CXX="c++" CXXFLAGS=" -pipe -Wno-return-type -I/usr/local/include -I/usr/local/include/ncurses -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 -------------------------------------------------- SYS_LIBS=" -L/usr/local/lib -Wl,-rpath=/usr/local/lib -lm -lncurses" DESTDIR=/construction/biology/mapm3/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- PORTDOCS="" PORTEXAMPLES="" OSREL=5.3 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/mapm3" EXAMPLESDIR="share/examples/mapm3" DATADIR="share/mapm3" WWWDIR="www/mapm3" ETCDIR="etc/mapm3" -------------------------------------------------- -- SUB_LIST -------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/mapm3 DOCSDIR=/usr/local/share/doc/mapm3 EXAMPLESDIR=/usr/local/share/examples/mapm3 WWWDIR=/usr/local/www/mapm3 ETCDIR=/usr/local/etc/mapm3 -------------------------------------------------- -- /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 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> mapm3-3.0 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 ===> mapm3-3.0 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of mapm3-3.0 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> Fetching all distfiles required by mapm3-3.0 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> Fetching all distfiles required by mapm3-3.0 for building => SHA256 Checksum OK for mapm3-source.tar.Z. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> Fetching all distfiles required by mapm3-3.0 for building ===> Extracting for mapm3-3.0 => SHA256 Checksum OK for mapm3-source.tar.Z. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for mapm3-3.0 ===> Applying ports patches for mapm3-3.0 /bin/cp /construction/biology/mapm3/mapm3-3.0/sun/* /construction/biology/mapm3/mapm3-3.0 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> mapm3-3.0 depends on file: /usr/local/lib/libncurses.so.6 - not found ===> Installing existing package /packages/All/ncurses-6.0.0s20171223_1.txz Installing ncurses-6.0.0s20171223_1... Extracting ncurses-6.0.0s20171223_1: .......... done ===> mapm3-3.0 depends on file: /usr/local/lib/libncurses.so.6 - found ===> Returning to build of mapm3-3.0 -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for mapm3-3.0 -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for mapm3-3.0 cc -pipe -Wno-return-type -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -std=gnu89 -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./lib/memlib.c -o ./lib/memlib.o cc -pipe -Wno-return-type -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -std=gnu89 -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./lib/mathlib.c -o ./lib/mathlib.o cc -pipe -Wno-return-type -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -std=gnu89 -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./lib/iolib.c -o ./lib/iolib.o cc -pipe -Wno-return-type -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -std=gnu89 -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./lib/msglib.c -o ./lib/msglib.o cc -pipe -Wno-return-type -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -std=gnu89 -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./lib/strlib.c -o ./lib/strlib.o cc -pipe -Wno-return-type -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -std=gnu89 -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./lib/shell.c -o ./lib/shell.o cc -pipe -Wno-return-type -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -std=gnu89 -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./lib/table.c -o ./lib/table.o cc -pipe -Wno-return-type -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -std=gnu89 -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./lib/eqn.c -o ./lib/eqn.o cc -pipe -Wno-return-type -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -std=gnu89 -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./lib/stats.c -o ./lib/stats.o cc -pipe -Wno-return-type -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -std=gnu89 -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./lib/syscode.c -o ./lib/syscode.o ./lib/syscode.c: In function 'untrapped_msg': ./lib/syscode.c:234:47: warning: trigraph ??) ignored, use -trigraphs to enable [-Wtrigraphs] { fprintf(stderr, "Untrapped error %d (???)\n",msg); exit(1); } ^ ./lib/syscode.c: In function 'trapped_msg': ./lib/syscode.c:243:36: warning: trigraph ??) ignored, use -trigraphs to enable [-Wtrigraphs] { fprintf(stderr,"Error %d (???)\n",msg); exit(1); } ^ ./lib/syscode.c: In function 'verbose_untrapped_msg': ./lib/syscode.c:255:56: warning: trigraph ??) ignored, use -trigraphs to enable [-Wtrigraphs] if (msg<1 || msg>MSGS) { fprintf(stderr,"error #%d (???)\n",msg); exit(1); } ^ ld -r ./lib/memlib.o ./lib/mathlib.o ./lib/iolib.o ./lib/msglib.o ./lib/strlib.o ./lib/shell.o ./lib/table.o ./lib/eqn.o ./lib/stats.o ./lib/syscode.o -o lib.o cc -pipe -Wno-return-type -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -std=gnu89 -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./mapm/state.c -o ./mapm/state.o cc -pipe -Wno-return-type -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -std=gnu89 -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./mapm/reader.c -o ./mapm/reader.o cc -pipe -Wno-return-type -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -std=gnu89 -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./mapm/ctm.c -o ./mapm/ctm.o cc -pipe -Wno-return-type -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -std=gnu89 -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./mapm/print.c -o ./mapm/print.o cc -pipe -Wno-return-type -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -std=gnu89 -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./mapm/sequence.c -o ./mapm/sequence.o cc -pipe -Wno-return-type -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -std=gnu89 -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./mapm/main.c -o ./mapm/main.o cc -pipe -Wno-return-type -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -std=gnu89 -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./mapm/quick23.c -o ./mapm/quick23.o cc -pipe -Wno-return-type -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -std=gnu89 -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./mapm/maps.c -o ./mapm/maps.o cc -pipe -Wno-return-type -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -std=gnu89 -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./mapm/info.c -o ./mapm/info.o cc -pipe -Wno-return-type -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -std=gnu89 -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./mapm/chroms.c -o ./mapm/chroms.o cc -pipe -Wno-return-type -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -std=gnu89 -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./mapm/orders.c -o ./mapm/orders.o cc -pipe -Wno-return-type -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -std=gnu89 -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./mapm/sys_cmds.c -o ./mapm/sys_cmds.o cc -pipe -Wno-return-type -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -std=gnu89 -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./mapm/two_cmds.c -o ./mapm/two_cmds.o cc -pipe -Wno-return-type -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -std=gnu89 -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./mapm/npt_cmds.c -o ./mapm/npt_cmds.o cc -pipe -Wno-return-type -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -std=gnu89 -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./mapm/auto_cmd.c -o ./mapm/auto_cmd.o cc -pipe -Wno-return-type -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -std=gnu89 -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./lib/makehelp.c -o ./lib/makehelp.o cc ./lib/makehelp.o lib.o -L/usr/local/lib -Wl,-rpath=/usr/local/lib -lm -lncurses -o ./lib/makehelp ./lib/makehelp ./mapm/mapmhelp.src ./mapm/mapmhelp.c mapmaker.help mapmaker.ps General Information... About MAPMAKER... Release Notes... Starting MAPMAKER... Tutorial... entering commands... abbreviating commands... keyboard editing... PostScript Output... Basic Commands... help... photo... prepare data... load data... save data... quit... Sequences... sequence... history... expand sequence... insert... append... delete... edit sequence... let... names... forget named sequence... translate... Two-Point Analysis... two point... lod table... big lods... near... links... pairwise... group... default linkage criteria... suggest subset... informativeness criteria... Multipoint Analysis... map... draw map... compare... try... ripple... order... build... multipoint criteria... Genome Analysis... make chromosome... assign... attach... unassign... anchor... framework... place... together... list loci... list status... list chromosomes... list assignments... draw chromosome... draw all chromosomes... age... class... make class... Error Detection... error detection... error probability... error thresholds... genotypes... Three Point... use three point... three point... triple linkage criteria... triple exclusion criteria... triple error detection... forget three point... Joining Haplotypes... join haplotypes... list haplotypes... restore haplotypes... Parameters and Options... print names... print maps... tolerance... auto save data... units... centimorgan function... more mode... Miscellaneous Commands... previous commands... review output... change directory... run... time... comment... remark... system... import data... export data... wizard mode... ./lib/makehelp done cc -pipe -Wno-return-type -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -std=gnu89 -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./mapm/mapmhelp.c -o ./mapm/mapmhelp.o cc -pipe -Wno-return-type -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -std=gnu89 -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./mapm/database.c -o ./mapm/database.o cc -pipe -Wno-return-type -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -std=gnu89 -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./mapm/ps_maps.c -o ./mapm/ps_maps.o cc ./mapm/state.o ./mapm/reader.o ./mapm/ctm.o ./mapm/print.o ./mapm/sequence.o ./mapm/main.o ./mapm/quick23.o ./mapm/maps.o ./mapm/info.o ./mapm/chroms.o ./mapm/orders.o ./mapm/sys_cmds.o ./mapm/two_cmds.o ./mapm/npt_cmds.o ./mapm/auto_cmd.o ./mapm/mapmhelp.o ./mapm/database.o ./mapm/ps_maps.o lib.o -L/usr/local/lib -Wl,-rpath=/usr/local/lib -lm -lncurses -o mapmaker cc -pipe -Wno-return-type -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -std=gnu89 -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./quant/qcmds.c -o ./quant/qcmds.o cc -pipe -Wno-return-type -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -std=gnu89 -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./quant/qctm.c -o ./quant/qctm.o cc -pipe -Wno-return-type -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -std=gnu89 -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./quant/qdata.c -o ./quant/qdata.o cc -pipe -Wno-return-type -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -std=gnu89 -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./quant/qseq.c -o ./quant/qseq.o cc -pipe -Wno-return-type -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -std=gnu89 -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./quant/qtop.c -o ./quant/qtop.o cc -pipe -Wno-return-type -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -std=gnu89 -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./quant/qraw.c -o ./quant/qraw.o cc -pipe -Wno-return-type -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -std=gnu89 -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./quant/qprint.c -o ./quant/qprint.o cc -pipe -Wno-return-type -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -std=gnu89 -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./quant/qcontext.c -o ./quant/qcontext.o cc -pipe -Wno-return-type -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -std=gnu89 -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./quant/qwiggle.c -o ./quant/qwiggle.o cc -pipe -Wno-return-type -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -std=gnu89 -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./quant/qps_scan.c -o ./quant/qps_scan.o ./lib/makehelp ./quant/qtlhelp.src ./quant/qtlhelp.c qtl.help qtl.ps General Information... About MAPMAKER/QTL... Release Notes... Starting MAPMAKER/QTL... Tutorial... entering commands... abbreviating commands... keyboard editing... PostScript Output... Basic Commands... help... photo... load data... save data... quit... Sequences... sequence... history... list loci... edit sequence... let... names... forget named sequence... Traits... trait... make trait... show trait... list traits... forget trait... Mapping Commands... map... scan... list scans... show scan... draw scan... forget scan... forget all scans... show peaks... show trys... compare... list compares... show compare... forget compare... forget all compares... show best maps... show linkage map... Parameters and Options... print names... units... auto save data... more mode... Miscellaneous Commands... run... change directory... system... previous commands... review output... time... comment... wizard mode... ./lib/makehelp done cc -pipe -Wno-return-type -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -std=gnu89 -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./quant/qtlhelp.c -o ./quant/qtlhelp.o cc ./quant/qcmds.o ./quant/qctm.o ./quant/qdata.o ./quant/qseq.o ./quant/qtop.o ./quant/qraw.o ./quant/qprint.o ./quant/qcontext.o ./quant/qwiggle.o ./quant/qps_scan.o ./quant/qtlhelp.o lib.o -L/usr/local/lib -Wl,-rpath=/usr/local/lib -lm -lncurses -o qtl -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- ===> mapm3-3.0 depends on file: /usr/local/lib/libncurses.so.6 - found -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for mapm3-3.0 ===> Generating temporary packing list cp mapmaker mapmaker.help xmapmaker /construction/biology/mapm3/stage/usr/local/bin cp qtl qtl.help xqtl /construction/biology/mapm3/stage/usr/local/bin ====> Compressing man pages (compress-man) -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for mapm3-3.0 file sizes/checksums [6]: . done packing files [6]: . done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Thursday, 30 AUG 2018 at 13:03:41 UTC Duration: 00:00:46