=> Building biology/mapm3 build started at Tue Oct 4 17:46:19 PDT 2016 port directory: /usr/ports/biology/mapm3 building for: DragonFly pkgbox64.dragonflybsd.org 4.7-DEVELOPMENT DragonFly v4.7.0.78.g7d868-DEVELOPMENT #7: Mon Aug 1 22:25:32 PDT 2016 root@pkgbox64.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 maintained by: tphilipp@potion-studios.com ident warning: no id keywords in /build/boomdata/data/.m/bleeding-edge-default/ref/../08//usr/ports/biology/mapm3/Makefile Makefile ident: Poudriere version: 3.1-pre Host OSVERSION: 400700 Jail OSVERSION: 400702 !!! Jail is newer than host. (Jail: 400702, Host: 400700) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- STATUS=1 SAVED_TERM=screen MASTERMNT=/build/boomdata/data/.m/bleeding-edge-default/ref PATH=/usr/local/libexec/poudriere:/sbin:/bin:/usr/sbin:/usr/bin:/usr/pkg/bin:/usr/pkg/sbin:/usr/games:/usr/local/sbin:/usr/local/bin:/usr/pkg/xorg/bin:/usr/X11R6/bin:/root/bin:/sbin:/usr/sbin POUDRIERE_BUILD_TYPE=bulk PKGNAME=mapm3-3.0 OLDPWD=/root/boom PWD=/build/boomdata/data/.m/bleeding-edge-default/ref/.p/pool MASTERNAME=bleeding-edge-default TERM=cons25 USER=root HOME=/root POUDRIERE_VERSION=3.1-pre LOCALBASE=/usr/local PACKAGE_BUILDING=yes ---End Environment--- ---Begin OPTIONS List--- ---End OPTIONS List--- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- XDG_DATA_HOME=/wrkdirs/biology/mapm3 XDG_CONFIG_HOME=/wrkdirs/biology/mapm3 HOME=/wrkdirs/biology/mapm3 TMPDIR="/tmp" SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc50 --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/biology/mapm3 XDG_CONFIG_HOME=/wrkdirs/biology/mapm3 HOME=/wrkdirs/biology/mapm3 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 -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 444" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- OSREL=4.7 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local PORTDOCS="" PORTEXAMPLES="" LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/mapm3" EXAMPLESDIR="share/examples/mapm3" DATADIR="share/mapm3" WWWDIR="www/mapm3" ETCDIR="etc/mapm3" --End PLIST_SUB-- --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 --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs NO_BACKUP=yes USE_PACKAGE_DEPENDS=yes PKG_CREATE_VERBOSE=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORT_DBDIR=/options PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles MAKE_JOBS_NUMBER=5 ---End make.conf--- =================================================== =========================================================================== =================================================== ===> mapm3-3.0 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.8.7_3.txz Installing pkg-1.8.7_3... Extracting pkg-1.8.7_3: .......... done ===> mapm3-3.0 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of mapm3-3.0 =========================================================================== =================================================== =========================================================================== =================================================== ===> Fetching all distfiles required by mapm3-3.0 for building =========================================================================== =================================================== ===> Fetching all distfiles required by mapm3-3.0 for building => SHA256 Checksum OK for mapm3-source.tar.Z. =========================================================================== =================================================== =========================================================================== =================================================== ===> Fetching all distfiles required by mapm3-3.0 for building ===> Extracting for mapm3-3.0 => SHA256 Checksum OK for mapm3-source.tar.Z. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for mapm3-3.0 ===> Applying ports patches for mapm3-3.0 /bin/cp /wrkdirs/biology/mapm3/mapm3-3.0/sun/* /wrkdirs/biology/mapm3/mapm3-3.0 =========================================================================== =================================================== ===> mapm3-3.0 depends on file: /usr/local/lib/libncurses.so.6 - not found ===> Installing existing package /packages/All/ncurses-6.0_5.txz Installing ncurses-6.0_5... Extracting ncurses-6.0_5: .......... done Message from ncurses-6.0_5: ===> NOTICE: The ncurses 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 ===> mapm3-3.0 depends on file: /usr/local/lib/libncurses.so.6 - found ===> Returning to build of mapm3-3.0 =========================================================================== =================================================== =========================================================================== =================================================== ===> Configuring for mapm3-3.0 =========================================================================== =================================================== ===> 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 =========================================================================== =================================================== ===> mapm3-3.0 depends on file: /usr/local/lib/libncurses.so.6 - found =========================================================================== =================================================== ===> Staging for mapm3-3.0 ===> Generating temporary packing list cp mapmaker mapmaker.help xmapmaker /wrkdirs/biology/mapm3/stage/usr/local/bin cp qtl qtl.help xqtl /wrkdirs/biology/mapm3/stage/usr/local/bin ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===> Building package for mapm3-3.0 file sizes/checksums [6]: . done packing files [6]: . done packing directories [0]: . done =========================================================================== => Cleaning up wrkdir ===> Cleaning for mapm3-3.0 build of biology/mapm3 ended at Tue Oct 4 17:47:01 PDT 2016 build time: 00:00:42