------------------------------------------------------------------------------- -- Phase: Environment ------------------------------------------------------------------------------- NO_DEPENDS=1 UNAME_r=6.1 UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=unknown UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 LANG=C HOME=/root USER=root TERM=dumb SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: showconfig ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ENV ------------------------------------------------------------------------------- MAKE=gmake XDG_DATA_HOME=/construction/biology/muscle XDG_CONFIG_HOME=/construction/biology/muscle HOME=/construction/biology/muscle TMPDIR="/tmp" PATH=/construction/biology/muscle/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc80 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ARGS ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: MAKE_ENV ------------------------------------------------------------------------------- XDG_DATA_HOME=/construction/biology/muscle XDG_CONFIG_HOME=/construction/biology/muscle HOME=/construction/biology/muscle TMPDIR="/tmp" PATH=/construction/biology/muscle/.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=gcc80 PREFIX=/usr/local LOCALBASE=/usr/local NOPROFILE=1 CC="cc" CFLAGS="-pipe -O2 -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="c++" CXXFLAGS=" -pipe -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" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: MAKE_ARGS ------------------------------------------------------------------------------- DESTDIR=/construction/biology/muscle/stage SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: PLIST_SUB ------------------------------------------------------------------------------- OSREL=6.1 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/muscle" EXAMPLESDIR="share/examples/muscle" DATADIR="share/muscle" WWWDIR="www/muscle" ETCDIR="etc/muscle" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: SUB_LIST ------------------------------------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/muscle DOCSDIR=/usr/local/share/doc/muscle EXAMPLESDIR=/usr/local/share/examples/muscle WWWDIR=/usr/local/www/muscle ETCDIR=/usr/local/etc/muscle SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: /etc/make.conf ------------------------------------------------------------------------------- DPORTS_BUILDER=yes DISABLE_LICENSES=yes DEFAULT_VERSIONS=ssl=openssl FORCE_PACKAGE=yes DEVELOPER=yes USE_PACKAGE_DEPENDS_ONLY=yes PORTSDIR=/xports PORT_DBDIR=/options PKG_DBDIR=/var/db/pkg PKG_CACHEDIR=/var/cache/pkg PKG_SUFX=.txz DEVELOPER=1 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=600102 OSVERSION=9999999 OSREL=6.1 _OSRELEASE=6.1-SYNTH DISTDIR=/distfiles WRKDIRPREFIX=/construction BATCH=yes PACKAGE_BUILDING=yes PKG_CREATE_VERBOSE=yes MAKE_JOBS_NUMBER=10 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- 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 00:00:01 ------------------------------------------------------------------------------- -- 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 00:00:00 ------------------------------------------------------------------------------- -- 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 00:00:00 ------------------------------------------------------------------------------- -- 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 00:00:13