------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/indexinfo-0.3.1.txz Installing /packages/All/gettext-runtime-0.21.txz Installing /packages/All/gmake-4.3_2.txz SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> mafft-7.266 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> mafft-7.266 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by mafft-7.266 for building SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> mafft-7.266 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by mafft-7.266 for building => SHA256 Checksum OK for mafft-7.266-without-extensions-src.tgz. SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> mafft-7.266 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by mafft-7.266 for building ===> Extracting for mafft-7.266 => SHA256 Checksum OK for mafft-7.266-without-extensions-src.tgz. Extracted Memory Use: 2.65M SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for mafft-7.266 ===> Applying ports patches for mafft-7.266 from /xports/biology/mafft/files SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> mafft-7.266 depends on package: gmake>=4.3 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> mafft-7.266 depends on package: gmake>=4.3 - found ===> Configuring for mafft-7.266 SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for mafft-7.266 gmake[1]: Entering directory '/construction/biology/mafft/mafft-7.266-without-extensions/core' cp mafftash_premafft.tmpl mafftash_premafft.pl cp seekquencer_premafft.tmpl seekquencer_premafft.pl cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c mtxutl.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c io.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c mltaln9.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c tddis.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c constants.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c nj.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c partSalignmm.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c Lalignmm.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c rna.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c Salignmm.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c Dalignmm.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c Falign.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c Falign_localhom.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c Galign11.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c MSalignmm.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c fftFunctions.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c fft.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c tditeration.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c dvtditr.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c defs.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c SAalignmm.c -o SAalignmm.o cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c treeOperation.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c addfunctions.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c dndfast7.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c dndblast.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c sextet5.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c mafft-distance.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c MSalign11.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c suboptalign11.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c genalign11.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c Lalign11.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c pairlocalalign.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c pair2hat3s.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c multi2hat3s.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c pairash.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c addsingle.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c splittbfast.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c disttbfast.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c tbfast.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c mafft-profile.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c f2cl.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c mccaskillwrap.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c contrafoldwrap.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c countlen.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c seq2regtable.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c regtable2seq.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c score.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c getlag.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c dndpre.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c setcore.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c replaceu.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c restoreu.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c setdirection.c cc -Denablemultithread -pipe -O2 -fno-strict-aliasing -c makedirectionlist.c cc -o version version.c -Denablemultithread -pipe -O2 -fno-strict-aliasing sed "s:_LIBDIR:/usr/local/libexec/mafft:" mafft.tmpl > mafft sed "s:_BINDIR:/usr/local/bin:" mafft-homologs.tmpl > mafft-homologs.rb cc -o f2cl mtxutl.o io.o f2cl.o constants.o defs.o -Denablemultithread -pipe -O2 -fno-strict-aliasing -lm -pthread cc -o countlen mtxutl.o io.o countlen.o defs.o -Denablemultithread -pipe -O2 -fno-strict-aliasing -lm -pthread cc -o seq2regtable mtxutl.o io.o seq2regtable.o defs.o -Denablemultithread -pipe -O2 -fno-strict-aliasing -lm -pthread cc -o dvtditr mtxutl.o io.o mltaln9.o tddis.o constants.o nj.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o MSalignmm.o fftFunctions.o fft.o tditeration.o dvtditr.o defs.o SAalignmm.o treeOperation.o addfunctions.o -Denablemultithread -pipe -O2 -fno-strict-aliasing -lm -pthread cc -o dndfast7 dndfast7.o io.o constants.o mtxutl.o mltaln9.o tddis.o defs.o -Denablemultithread -pipe -O2 -fno-strict-aliasing -lm -pthread cc -o dndblast dndblast.o io.o constants.o mtxutl.o mltaln9.o tddis.o defs.o -Denablemultithread -pipe -O2 -fno-strict-aliasing -lm -pthread cc -o sextet5 io.o constants.o mtxutl.o mltaln9.o tddis.o sextet5.o defs.o -Denablemultithread -pipe -O2 -fno-strict-aliasing -lm -pthread cc -o mafft-distance io.o constants.o mtxutl.o mltaln9.o tddis.o mafft-distance.o defs.o -Denablemultithread -pipe -O2 -fno-strict-aliasing -lm -pthread cc -o pairlocalalign mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o MSalignmm.o Galign11.o MSalign11.o suboptalign11.o genalign11.o Lalign11.o SAalignmm.o pairlocalalign.o defs.o fft.o fftFunctions.o -Denablemultithread -pipe -O2 -fno-strict-aliasing -lm -pthread cc -o pair2hat3s mtxutl.o io.o mltaln9.o tddis.o constants.o pair2hat3s.o defs.o fft.o fftFunctions.o -Denablemultithread -pipe -O2 -fno-strict-aliasing -lm -pthread cc -o multi2hat3s mtxutl.o io.o mltaln9.o tddis.o constants.o multi2hat3s.o defs.o fft.o fftFunctions.o -Denablemultithread -pipe -O2 -fno-strict-aliasing -lm -pthread cc -o pairash mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o MSalignmm.o Galign11.o MSalign11.o suboptalign11.o genalign11.o Lalign11.o SAalignmm.o pairash.o defs.o fft.o fftFunctions.o -Denablemultithread -pipe -O2 -fno-strict-aliasing -lm -pthread cc -o addsingle mtxutl.o io.o mltaln9.o tddis.o constants.o MSalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o SAalignmm.o addsingle.o defs.o fft.o fftFunctions.o addfunctions.o -Denablemultithread -pipe -O2 -fno-strict-aliasing -lm -pthread cc -o splittbfast mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o SAalignmm.o MSalignmm.o Lalign11.o splittbfast.o defs.o fft.o fftFunctions.o -Denablemultithread -pipe -O2 -fno-strict-aliasing -lm -pthread cc -o disttbfast mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o SAalignmm.o MSalignmm.o disttbfast.o defs.o fft.o fftFunctions.o addfunctions.o -Denablemultithread -pipe -O2 -fno-strict-aliasing -lm -pthread cc -o tbfast mtxutl.o io.o mltaln9.o tddis.o constants.o MSalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o SAalignmm.o tbfast.o defs.o fft.o fftFunctions.o addfunctions.o -Denablemultithread -pipe -O2 -fno-strict-aliasing -lm -pthread cc -o mafft-profile io.o mtxutl.o mltaln9.o tddis.o constants.o partSalignmm.o MSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o SAalignmm.o Galign11.o Falign.o Falign_localhom.o fftFunctions.o fft.o mafft-profile.o defs.o -Denablemultithread -pipe -O2 -fno-strict-aliasing -lm -pthread cc -o mccaskillwrap mtxutl.o io.o mccaskillwrap.o constants.o defs.o mltaln9.o -Denablemultithread -pipe -O2 -fno-strict-aliasing -lm -pthread cc -o contrafoldwrap mtxutl.o io.o contrafoldwrap.o constants.o defs.o mltaln9.o -Denablemultithread -pipe -O2 -fno-strict-aliasing -lm -pthread cc -o regtable2seq mtxutl.o io.o regtable2seq.o defs.o mltaln9.o -Denablemultithread -pipe -O2 -fno-strict-aliasing -lm -pthread cc -o score io.o mtxutl.o mltaln9.o score.o constants.o defs.o -Denablemultithread -pipe -O2 -fno-strict-aliasing -lm -pthread cc -o getlag mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Falign.o Falign_localhom.o Galign11.o SAalignmm.o MSalignmm.o Dalignmm.o getlag.o defs.o fft.o fftFunctions.o -Denablemultithread -pipe -O2 -fno-strict-aliasing -lm -pthread cc -o dndpre dndpre.o io.o constants.o mtxutl.o mltaln9.o defs.o -Denablemultithread -pipe -O2 -fno-strict-aliasing -lm -pthread cc -o setcore mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o SAalignmm.o MSalignmm.o setcore.o defs.o fft.o fftFunctions.o -Denablemultithread -pipe -O2 -fno-strict-aliasing -lm -pthread cc -o replaceu mtxutl.o io.o replaceu.o defs.o mltaln9.o -Denablemultithread -pipe -O2 -fno-strict-aliasing -lm -pthread cc -o restoreu mtxutl.o io.o restoreu.o defs.o mltaln9.o -Denablemultithread -pipe -O2 -fno-strict-aliasing -lm -pthread cc -o setdirection mtxutl.o io.o setdirection.o defs.o mltaln9.o -Denablemultithread -pipe -O2 -fno-strict-aliasing -lm -pthread cc -o makedirectionlist mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o SAalignmm.o MSalignmm.o Lalign11.o makedirectionlist.o defs.o fft.o fftFunctions.o addfunctions.o -Denablemultithread -pipe -O2 -fno-strict-aliasing -lm -pthread gmake[1]: Leaving directory '/construction/biology/mafft/mafft-7.266-without-extensions/core' SUCCEEDED 00:00:11 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- ===> Staging for mafft-7.266 ===> Generating temporary packing list gmake[1]: Entering directory '/construction/biology/mafft/mafft-7.266-without-extensions/core' /bin/mkdir -p /construction/biology/mafft/stage/usr/local/libexec/mafft /construction/biology/mafft/stage/usr/local/bin /construction/biology/mafft/stage/usr/local/man/man1 install -m 555 mafft mafft-homologs.rb /construction/biology/mafft/stage/usr/local/bin install -s -m 555 dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign pair2hat3s multi2hat3s pairash addsingle splittbfast disttbfast tbfast mafft-profile f2cl mccaskillwrap contrafoldwrap countlen seq2regtable regtable2seq score getlag dndpre setcore replaceu restoreu setdirection makedirectionlist version /construction/biology/mafft/stage/usr/local/libexec/mafft install -m 555 mafftash_premafft.pl seekquencer_premafft.pl /construction/biology/mafft/stage/usr/local/libexec/mafft install -m 0644 mafft.1 mafft-homologs.1 /construction/biology/mafft/stage/usr/local/man/man1 ln -s mafft /construction/biology/mafft/stage/usr/local/bin/linsi; ln -s mafft /construction/biology/mafft/stage/usr/local/bin/ginsi; ln -s mafft /construction/biology/mafft/stage/usr/local/bin/fftns; ln -s mafft /construction/biology/mafft/stage/usr/local/bin/fftnsi; ln -s mafft /construction/biology/mafft/stage/usr/local/bin/nwns; ln -s mafft /construction/biology/mafft/stage/usr/local/bin/nwnsi; ln -s mafft /construction/biology/mafft/stage/usr/local/bin/einsi; ln -s mafft /construction/biology/mafft/stage/usr/local/bin/mafft-linsi; ln -s mafft /construction/biology/mafft/stage/usr/local/bin/mafft-ginsi; ln -s mafft /construction/biology/mafft/stage/usr/local/bin/mafft-fftns; ln -s mafft /construction/biology/mafft/stage/usr/local/bin/mafft-fftnsi; ln -s mafft /construction/biology/mafft/stage/usr/local/bin/mafft-nwns; ln -s mafft /construction/biology/mafft/stage/usr/local/bin/mafft-nwnsi; ln -s mafft /construction/biology/mafft/stage/usr/local/bin/mafft-einsi; ln -s mafft /construction/biology/mafft/stage/usr/local/bin/mafft-xinsi; ln -s mafft /construction/biology/mafft/stage/usr/local/bin/mafft-qinsi; ln -s ../libexec/mafft/mafft-profile /construction/biology/mafft/stage/usr/local/bin/mafft-profile ln -s ../libexec/mafft/mafft-distance /construction/biology/mafft/stage/usr/local/bin/mafft-distance gmake[1]: Leaving directory '/construction/biology/mafft/mafft-7.266-without-extensions/core' install -m 0644 /construction/biology/mafft/mafft-7.266-without-extensions/test/* /construction/biology/mafft/stage/usr/local/share/examples/mafft install -m 0644 /construction/biology/mafft/mafft-7.266-without-extensions/readme /construction/biology/mafft/stage/usr/local/share/doc/mafft ====> 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 00:00:02 ------------------------------------------------------------------------------- -- 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 mafft-7.266 file sizes/checksums [67]: 0% file sizes/checksums [67]: 100% packing files [67]: 0% packing files [67]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:00:13 TOTAL TIME 00:00:30