------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/ncurses-6.2.20200831.txz SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> mapm3-3.0_1 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> mapm3-3.0_1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by mapm3-3.0_1 for building SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> mapm3-3.0_1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by mapm3-3.0_1 for building => SHA256 Checksum OK for mapm3-source.tar.Z. SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> mapm3-3.0_1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by mapm3-3.0_1 for building ===> Extracting for mapm3-3.0_1 => SHA256 Checksum OK for mapm3-source.tar.Z. Extracted Memory Use: 3.01M SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for mapm3-3.0_1 ===> Applying ports patches for mapm3-3.0_1 from /xports/biology/mapm3/files /bin/cp /construction/biology/mapm3/mapm3-3.0_1/sun/* /construction/biology/mapm3/mapm3-3.0_1 SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> mapm3-3.0_1 depends on file: /usr/local/lib/libncurses.so.6 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> mapm3-3.0_1 depends on file: /usr/local/lib/libncurses.so.6 - found ===> Configuring for mapm3-3.0_1 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for mapm3-3.0_1 cc -pipe -fcommon -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 -fcommon -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 -fcommon -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 -fcommon -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 -fcommon -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 -fcommon -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 -fcommon -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 -fcommon -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 -fcommon -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 -fcommon -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 -fcommon -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 -fcommon -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 -fcommon -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 -fcommon -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 -fcommon -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 -fcommon -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 -fcommon -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 -fcommon -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 -fcommon -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 -fcommon -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 -fcommon -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 -fcommon -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 -fcommon -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 -fcommon -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 -fcommon -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 -fcommon -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 -fcommon -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 -fcommon -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 -fcommon -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 -fcommon -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 -fcommon -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 -fcommon -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 -fcommon -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 -fcommon -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 -fcommon -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 -fcommon -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 -fcommon -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 -fcommon -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 -fcommon -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 -fcommon -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 SUCCEEDED 00:00:39 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- ===> mapm3-3.0_1 depends on file: /usr/local/lib/libncurses.so.6 - found SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- ===> Staging for mapm3-3.0_1 ===> mapm3-3.0_1 depends on file: /usr/local/lib/libncurses.so.6 - found ===> 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 /usr/bin/strip /construction/biology/mapm3/stage/usr/local/bin/mapmaker /usr/bin/strip /construction/biology/mapm3/stage/usr/local/bin/qtl ====> Compressing man pages (compress-man) ====> Running Q/A tests (stage-qa) Warning: You have disabled the licenses framework with DISABLE_LICENSES, unable to run checks SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: check-plist ------------------------------------------------------------------------------- ====> Checking for pkg-plist issues (check-plist) ===> Parsing plist ===> Checking for items in STAGEDIR missing from pkg-plist ===> Checking for items in pkg-plist which are not in STAGEDIR ===> No pkg-plist issues found (check-plist) SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: package ------------------------------------------------------------------------------- ===> Building package for mapm3-3.0_1 file sizes/checksums [6]: 0% file sizes/checksums [6]: 100% packing files [6]: 0% packing files [6]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:00:01 TOTAL TIME 00:00:45