------------------------------------------------------------------------------- -- 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 ------------------------------------------------------------------------------- ===> muscle-3.8.1551 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> muscle-3.8.1551 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by muscle-3.8.1551 for building SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> muscle-3.8.1551 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by muscle-3.8.1551 for building => SHA256 Checksum OK for muscle_src_3.8.1551.tar.gz. SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> muscle-3.8.1551 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by muscle-3.8.1551 for building ===> Extracting for muscle-3.8.1551 => SHA256 Checksum OK for muscle_src_3.8.1551.tar.gz. Extracted Memory Use: 1.23M SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for muscle-3.8.1551 ===> Converting DOS text files to UNIX text files ===> Applying ports patches for muscle-3.8.1551 from /xports/biology/muscle/files /bin/mv /construction/biology/muscle/muscle-3.8.1551/subfams.cpp /construction/biology/muscle/muscle-3.8.1551/subfams.cpp.not_to_be_compiled SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> muscle-3.8.1551 depends on package: gmake>=4.3 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> muscle-3.8.1551 depends on package: gmake>=4.3 - found ===> Configuring for muscle-3.8.1551 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for muscle-3.8.1551 gmake[1]: Entering directory '/construction/biology/muscle/muscle-3.8.1551' c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 aligngivenpath.cpp -o aligngivenpath.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 aligngivenpathsw.cpp -o aligngivenpathsw.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 aligntwomsas.cpp -o aligntwomsas.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 aligntwoprofs.cpp -o aligntwoprofs.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 aln.cpp -o aln.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 alpha.cpp -o alpha.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 anchors.cpp -o anchors.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 bittraceback.cpp -o bittraceback.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 blosum62.cpp -o blosum62.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 blosumla.cpp -o blosumla.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 clust.cpp -o clust.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 cluster.cpp -o cluster.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 clwwt.cpp -o clwwt.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 color.cpp -o color.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 cons.cpp -o cons.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 diaglist.cpp -o diaglist.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 diffobjscore.cpp -o diffobjscore.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 diffpaths.cpp -o diffpaths.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 difftrees.cpp -o difftrees.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 difftreese.cpp -o difftreese.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 distcalc.cpp -o distcalc.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 distfunc.cpp -o distfunc.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 distpwkimura.cpp -o distpwkimura.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 domuscle.cpp -o domuscle.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 dosp.cpp -o dosp.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 dpreglist.cpp -o dpreglist.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 drawtree.cpp -o drawtree.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 edgelist.cpp -o edgelist.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 enumopts.cpp -o enumopts.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 enumtostr.cpp -o enumtostr.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 estring.cpp -o estring.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 fasta.cpp -o fasta.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 fasta2.cpp -o fasta2.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 fastclust.cpp -o fastclust.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 fastdist.cpp -o fastdist.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 fastdistjones.cpp -o fastdistjones.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 fastdistkbit.cpp -o fastdistkbit.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 fastdistkmer.cpp -o fastdistkmer.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 fastdistmafft.cpp -o fastdistmafft.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 fastdistnuc.cpp -o fastdistnuc.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 fastscorepath2.cpp -o fastscorepath2.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 finddiags.cpp -o finddiags.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 finddiagsn.cpp -o finddiagsn.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 glbalign.cpp -o glbalign.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 glbalign352.cpp -o glbalign352.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 glbaligndiag.cpp -o glbaligndiag.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 glbalignle.cpp -o glbalignle.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 glbalignsimple.cpp -o glbalignsimple.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 glbalignsp.cpp -o glbalignsp.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 glbalignspn.cpp -o glbalignspn.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 glbalignss.cpp -o glbalignss.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 glbalndimer.cpp -o glbalndimer.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 globals.cpp -o globals.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 globalslinux.cpp -o globalslinux.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 globalsosx.cpp -o globalsosx.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 globalsother.cpp -o globalsother.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 globalswin32.cpp -o globalswin32.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 gonnet.cpp -o gonnet.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 henikoffweight.cpp -o henikoffweight.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 henikoffweightpb.cpp -o henikoffweightpb.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 html.cpp -o html.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 hydro.cpp -o hydro.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 intmath.cpp -o intmath.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 local.cpp -o local.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 main.cpp -o main.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 makerootmsa.cpp -o makerootmsa.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 makerootmsab.cpp -o makerootmsab.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 maketree.cpp -o maketree.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 mhack.cpp -o mhack.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 mpam200.cpp -o mpam200.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 msa.cpp -o msa.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 msa2.cpp -o msa2.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 msadistkimura.cpp -o msadistkimura.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 msf.cpp -o msf.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 muscle.cpp -o muscle.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 muscleout.cpp -o muscleout.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 nucmx.cpp -o nucmx.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 nwdasimple.cpp -o nwdasimple.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 nwdasimple2.cpp -o nwdasimple2.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 nwdasmall.cpp -o nwdasmall.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 nwrec.cpp -o nwrec.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 nwsmall.cpp -o nwsmall.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 objscore.cpp -o objscore.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 objscore2.cpp -o objscore2.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 objscoreda.cpp -o objscoreda.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 onexception.cpp -o onexception.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 options.cpp -o options.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 outweights.cpp -o outweights.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 pam200mafft.cpp -o pam200mafft.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 params.cpp -o params.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 phy.cpp -o phy.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 phy2.cpp -o phy2.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 phy3.cpp -o phy3.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 phy4.cpp -o phy4.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 phyfromclust.cpp -o phyfromclust.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 phyfromfile.cpp -o phyfromfile.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 physeq.cpp -o physeq.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 phytofile.cpp -o phytofile.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 posgap.cpp -o posgap.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 ppscore.cpp -o ppscore.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 profdb.cpp -o profdb.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 profile.cpp -o profile.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 profilefrommsa.cpp -o profilefrommsa.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 progalign.cpp -o progalign.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 progress.cpp -o progress.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 progressivealign.cpp -o progressivealign.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 pwpath.cpp -o pwpath.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 readmx.cpp -o readmx.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 realigndiffs.cpp -o realigndiffs.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 realigndiffse.cpp -o realigndiffse.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 refine.cpp -o refine.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 refinehoriz.cpp -o refinehoriz.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 refinesubfams.cpp -o refinesubfams.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 refinetree.cpp -o refinetree.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 refinetreee.cpp -o refinetreee.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 refinevert.cpp -o refinevert.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 refinew.cpp -o refinew.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 savebest.cpp -o savebest.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 scoredist.cpp -o scoredist.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 scoregaps.cpp -o scoregaps.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 scorehistory.cpp -o scorehistory.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 scorepp.cpp -o scorepp.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 seq.cpp -o seq.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 seqvect.cpp -o seqvect.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 setblosumweights.cpp -o setblosumweights.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 setgscweights.cpp -o setgscweights.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 setnewhandler.cpp -o setnewhandler.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 spfast.cpp -o spfast.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 sptest.cpp -o sptest.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 stabilize.cpp -o stabilize.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 subfam.cpp -o subfam.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 sw.cpp -o sw.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 termgaps.cpp -o termgaps.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 textfile.cpp -o textfile.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 threewaywt.cpp -o threewaywt.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 tomhydro.cpp -o tomhydro.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 traceback.cpp -o traceback.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 tracebackopt.cpp -o tracebackopt.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 tracebacksw.cpp -o tracebacksw.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 treefrommsa.cpp -o treefrommsa.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 typetostr.cpp -o typetostr.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 upgma2.cpp -o upgma2.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 usage.cpp -o usage.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 validateids.cpp -o validateids.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 vtml2.cpp -o vtml2.o c++ -c -O3 -funroll-loops -Winline -DNDEBUG=1 writescorefile.cpp -o writescorefile.o c++ -O3 -funroll-loops -Winline -DNDEBUG=1 -o muscle aligngivenpath.o aligngivenpathsw.o aligntwomsas.o aligntwoprofs.o aln.o alpha.o anchors.o bittraceback.o blosum62.o blosumla.o clust.o cluster.o clwwt.o color.o cons.o diaglist.o diffobjscore.o diffpaths.o difftrees.o difftreese.o distcalc.o distfunc.o distpwkimura.o domuscle.o dosp.o dpreglist.o drawtree.o edgelist.o enumopts.o enumtostr.o estring.o fasta.o fasta2.o fastclust.o fastdist.o fastdistjones.o fastdistkbit.o fastdistkmer.o fastdistmafft.o fastdistnuc.o fastscorepath2.o finddiags.o finddiagsn.o glbalign.o glbalign352.o glbaligndiag.o glbalignle.o glbalignsimple.o glbalignsp.o glbalignspn.o glbalignss.o glbalndimer.o globals.o globalslinux.o globalsosx.o globalsother.o globalswin32.o gonnet.o henikoffweight.o henikoffweightpb.o html.o hydro.o intmath.o local.o main.o makerootmsa.o makerootmsab.o maketree.o mhack.o mpam200.o msa.o msa2.o msadistkimura.o msf.o muscle.o muscleout.o nucmx.o nwdasimple.o nwdasimple2.o nwdasmall.o nwrec.o nwsmall.o objscore.o objscore2.o objscoreda.o onexception.o options.o outweights.o pam200mafft.o params.o phy.o phy2.o phy3.o phy4.o phyfromclust.o phyfromfile.o physeq.o phytofile.o posgap.o ppscore.o profdb.o profile.o profilefrommsa.o progalign.o progress.o progressivealign.o pwpath.o readmx.o realigndiffs.o realigndiffse.o refine.o refinehoriz.o refinesubfams.o refinetree.o refinetreee.o refinevert.o refinew.o savebest.o scoredist.o scoregaps.o scorehistory.o scorepp.o seq.o seqvect.o setblosumweights.o setgscweights.o setnewhandler.o spfast.o sptest.o stabilize.o subfam.o sw.o termgaps.o textfile.o threewaywt.o tomhydro.o traceback.o tracebackopt.o tracebacksw.o treefrommsa.o typetostr.o upgma2.o usage.o validateids.o vtml2.o writescorefile.o -lm gmake[1]: Leaving directory '/construction/biology/muscle/muscle-3.8.1551' SUCCEEDED 00:00:10 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- ===> Staging for muscle-3.8.1551 ===> Generating temporary packing list install -s -m 555 /construction/biology/muscle/muscle-3.8.1551/muscle /construction/biology/muscle/stage/usr/local/bin ====> 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 muscle-3.8.1551 file sizes/checksums [1]: 0% file sizes/checksums [1]: 100% packing files [1]: 0% packing files [1]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:00:01 TOTAL TIME 00:00:14