=> Building biology/muscle Started : Sunday, 7 JUL 2019 at 04:25:55 UTC Platform: 5.7-DEVELOPMENT DragonFly v5.7.0.83.g49866-DEVELOPMENT #40: Sun Jun 30 03:00:04 PDT 2019 root@pkgbox64.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 -------------------------------------------------- -- Environment -------------------------------------------------- UNAME_r=5.4-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.4-SYNTH UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 TERM=dumb PKG_CACHEDIR=/var/cache/pkg8 PKG_DBDIR=/var/db/pkg8 PORTSDIR=/xports LANG=C HOME=/root USER=root -------------------------------------------------- -- Options -------------------------------------------------- -------------------------------------------------- -- CONFIGURE_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 SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc80 -------------------------------------------------- -- CONFIGURE_ARGS -------------------------------------------------- -------------------------------------------------- -- 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" -------------------------------------------------- -- MAKE_ARGS -------------------------------------------------- DESTDIR=/construction/biology/muscle/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- OSREL=5.4 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" -------------------------------------------------- -- 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 -------------------------------------------------- -- /etc/make.conf -------------------------------------------------- SYNTHPROFILE=Release-5.4 USE_PACKAGE_DEPENDS_ONLY=yes PACKAGE_BUILDING=yes BATCH=yes PKG_CREATE_VERBOSE=yes PORTSDIR=/xports DISTDIR=/distfiles WRKDIRPREFIX=/construction PORT_DBDIR=/options PACKAGES=/packages MAKE_JOBS_NUMBER_LIMIT=5 HAVE_COMPAT_IA32_KERN= CONFIGURE_MAX_CMD_LEN=262144 _PERL5_FROM_BIN=5.28.1 _ALTCCVERSION_921dbbb2=none _OBJC_ALTCCVERSION_921dbbb2=none _SMP_CPUS=8 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500400 OSVERSION=9999999 OSREL=5.4 _OSRELEASE=5.4-SYNTH PYTHONBASE=/usr/local _PKG_CHECKED=1 -------------------------------------------------------------------------------- -- Phase: check-sanity -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> muscle-3.8.31 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.11.1.txz Installing pkg-1.11.1... Extracting pkg-1.11.1: .......... done ===> muscle-3.8.31 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of muscle-3.8.31 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> Fetching all distfiles required by muscle-3.8.31 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> Fetching all distfiles required by muscle-3.8.31 for building => SHA256 Checksum OK for muscle3.8.31_src.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> Fetching all distfiles required by muscle-3.8.31 for building ===> Extracting for muscle-3.8.31 => SHA256 Checksum OK for muscle3.8.31_src.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for muscle-3.8.31 ===> Converting DOS text files to UNIX text files ===> Applying ports patches for muscle-3.8.31 ===> Applying dragonfly patches for muscle-3.8.31 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for muscle-3.8.31 -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for muscle-3.8.31 --- muscle --- chmod +x ./mk ./mk + CPPNames='aligngivenpath aligngivenpathsw aligntwomsas aligntwoprofs aln alpha anchors bittraceback blosum62 blosumla clust cluster clwwt color cons diaglist diffobjscore diffpaths difftrees difftreese distcalc distfunc distpwkimura domuscle dosp dpreglist drawtree edgelist enumopts enumtostr estring fasta fasta2 fastclust fastdist fastdistjones fastdistkbit fastdistkmer fastdistmafft fastdistnuc fastscorepath2 finddiags finddiagsn glbalign glbalign352 glbaligndiag glbalignle glbalignsimple glbalignsp glbalignspn glbalignss glbalndimer globals globalslinux globalsosx globalsother globalswin32 gonnet henikoffweight henikoffweightpb html hydro intmath local main makerootmsa makerootmsab maketree mhack mpam200 msa msa2 msadistkimura msf muscle muscleout nucmx nwdasimple nwdasimple2 nwdasmall nwrec nwsmall objscore objscore2 objscoreda onexception options outweights pam200mafft params phy phy2 phy3 phy4 phyfromclust phyfromfile physeq phytofile posgap ppscore profdb profile profilefrommsa progalign progress progressivealign pwpath readmx realigndiffs realigndiffse refine refinehoriz refinesubfams refinetree refinetreee refinevert refinew savebest scoredist scoregaps scorehistory scorepp seq seqvect setblosumweights setgscweights setnewhandler spfast sptest stabilize subfam subfams sw termgaps textfile threewaywt tomhydro traceback tracebackopt tracebacksw treefrommsa typetostr upgma2 usage validateids vtml2 writescorefile' + ObjNames='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 subfams.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' + rm -f '*.o' muscle.make.stdout.txt muscle.make.stderr.txt + echo aligngivenpath aligngivenpath + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' aligngivenpath.cpp -o aligngivenpath.o + echo aligngivenpathsw aligngivenpathsw + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' aligngivenpathsw.cpp -o aligngivenpathsw.o + echo aligntwomsas aligntwomsas + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' aligntwomsas.cpp -o aligntwomsas.o + echo aligntwoprofs aligntwoprofs + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' aligntwoprofs.cpp -o aligntwoprofs.o + echo aln aln + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' aln.cpp -o aln.o + echo alpha alpha + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' alpha.cpp -o alpha.o + echo anchors anchors + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' anchors.cpp -o anchors.o + echo bittraceback bittraceback + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' bittraceback.cpp -o bittraceback.o + echo blosum62 blosum62 + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' blosum62.cpp -o blosum62.o + echo blosumla blosumla + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' blosumla.cpp -o blosumla.o + echo clust clust + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' clust.cpp -o clust.o + echo cluster cluster + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' cluster.cpp -o cluster.o + echo clwwt clwwt + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' clwwt.cpp -o clwwt.o + echo color color + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' color.cpp -o color.o + echo cons cons + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' cons.cpp -o cons.o + echo diaglist diaglist + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' diaglist.cpp -o diaglist.o + echo diffobjscore diffobjscore + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' diffobjscore.cpp -o diffobjscore.o + echo diffpaths diffpaths + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' diffpaths.cpp -o diffpaths.o + echo difftrees difftrees + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' difftrees.cpp -o difftrees.o + echo difftreese difftreese + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' difftreese.cpp -o difftreese.o + echo distcalc distcalc + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' distcalc.cpp -o distcalc.o + echo distfunc distfunc + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' distfunc.cpp -o distfunc.o + echo distpwkimura distpwkimura + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' distpwkimura.cpp -o distpwkimura.o + echo domuscle domuscle + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' domuscle.cpp -o domuscle.o + echo dosp dosp + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' dosp.cpp -o dosp.o + echo dpreglist dpreglist + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' dpreglist.cpp -o dpreglist.o + echo drawtree drawtree + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' drawtree.cpp -o drawtree.o + echo edgelist edgelist + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' edgelist.cpp -o edgelist.o + echo enumopts enumopts + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' enumopts.cpp -o enumopts.o + echo enumtostr enumtostr + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' enumtostr.cpp -o enumtostr.o + echo estring estring + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' estring.cpp -o estring.o + echo fasta fasta + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' fasta.cpp -o fasta.o + echo fasta2 fasta2 + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' fasta2.cpp -o fasta2.o + echo fastclust fastclust + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' fastclust.cpp -o fastclust.o + echo fastdist fastdist + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' fastdist.cpp -o fastdist.o + echo fastdistjones fastdistjones + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' fastdistjones.cpp -o fastdistjones.o + echo fastdistkbit fastdistkbit + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' fastdistkbit.cpp -o fastdistkbit.o + echo fastdistkmer fastdistkmer + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' fastdistkmer.cpp -o fastdistkmer.o + echo fastdistmafft fastdistmafft + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' fastdistmafft.cpp -o fastdistmafft.o + echo fastdistnuc fastdistnuc + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' fastdistnuc.cpp -o fastdistnuc.o + echo fastscorepath2 fastscorepath2 + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' fastscorepath2.cpp -o fastscorepath2.o + echo finddiags finddiags + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' finddiags.cpp -o finddiags.o + echo finddiagsn finddiagsn + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' finddiagsn.cpp -o finddiagsn.o + echo glbalign glbalign + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' glbalign.cpp -o glbalign.o + echo glbalign352 glbalign352 + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' glbalign352.cpp -o glbalign352.o + echo glbaligndiag glbaligndiag + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' glbaligndiag.cpp -o glbaligndiag.o + echo glbalignle glbalignle + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' glbalignle.cpp -o glbalignle.o + echo glbalignsimple glbalignsimple + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' glbalignsimple.cpp -o glbalignsimple.o + echo glbalignsp glbalignsp + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' glbalignsp.cpp -o glbalignsp.o + echo glbalignspn glbalignspn + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' glbalignspn.cpp -o glbalignspn.o + echo glbalignss glbalignss + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' glbalignss.cpp -o glbalignss.o + echo glbalndimer glbalndimer + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' glbalndimer.cpp -o glbalndimer.o + echo globals globals + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' globals.cpp -o globals.o + echo globalslinux globalslinux + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' globalslinux.cpp -o globalslinux.o + echo globalsosx globalsosx + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' globalsosx.cpp -o globalsosx.o + echo globalsother globalsother + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' globalsother.cpp -o globalsother.o + echo globalswin32 globalswin32 + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' globalswin32.cpp -o globalswin32.o + echo gonnet gonnet + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' gonnet.cpp -o gonnet.o + echo henikoffweight henikoffweight + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' henikoffweight.cpp -o henikoffweight.o + echo henikoffweightpb henikoffweightpb + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' henikoffweightpb.cpp -o henikoffweightpb.o + echo html html + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' html.cpp -o html.o + echo hydro hydro + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' hydro.cpp -o hydro.o + echo intmath intmath + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' intmath.cpp -o intmath.o + echo local local + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' local.cpp -o local.o + echo main main + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' main.cpp -o main.o + echo makerootmsa makerootmsa + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' makerootmsa.cpp -o makerootmsa.o + echo makerootmsab makerootmsab + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' makerootmsab.cpp -o makerootmsab.o + echo maketree maketree + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' maketree.cpp -o maketree.o + echo mhack mhack + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' mhack.cpp -o mhack.o + echo mpam200 mpam200 + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' mpam200.cpp -o mpam200.o + echo msa msa + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' msa.cpp -o msa.o + echo msa2 msa2 + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' msa2.cpp -o msa2.o + echo msadistkimura msadistkimura + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' msadistkimura.cpp -o msadistkimura.o + echo msf msf + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' msf.cpp -o msf.o + echo muscle muscle + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' muscle.cpp -o muscle.o + echo muscleout muscleout + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' muscleout.cpp -o muscleout.o + echo nucmx nucmx + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' nucmx.cpp -o nucmx.o + echo nwdasimple nwdasimple + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' nwdasimple.cpp -o nwdasimple.o + echo nwdasimple2 nwdasimple2 + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' nwdasimple2.cpp -o nwdasimple2.o + echo nwdasmall nwdasmall + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' nwdasmall.cpp -o nwdasmall.o + echo nwrec nwrec + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' nwrec.cpp -o nwrec.o + echo nwsmall nwsmall + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' nwsmall.cpp -o nwsmall.o + echo objscore objscore + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' objscore.cpp -o objscore.o + echo objscore2 objscore2 + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' objscore2.cpp -o objscore2.o + echo objscoreda objscoreda + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' objscoreda.cpp -o objscoreda.o + echo onexception onexception + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' onexception.cpp -o onexception.o + echo options options + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' options.cpp -o options.o + echo outweights outweights + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' outweights.cpp -o outweights.o + echo pam200mafft pam200mafft + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' pam200mafft.cpp -o pam200mafft.o + echo params params + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' params.cpp -o params.o + echo phy phy + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' phy.cpp -o phy.o + echo phy2 phy2 + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' phy2.cpp -o phy2.o + echo phy3 phy3 + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' phy3.cpp -o phy3.o + echo phy4 phy4 + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' phy4.cpp -o phy4.o + echo phyfromclust phyfromclust + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' phyfromclust.cpp -o phyfromclust.o + echo phyfromfile phyfromfile + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' phyfromfile.cpp -o phyfromfile.o + echo physeq physeq + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' physeq.cpp -o physeq.o + echo phytofile phytofile + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' phytofile.cpp -o phytofile.o + echo posgap posgap + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' posgap.cpp -o posgap.o + echo ppscore ppscore + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' ppscore.cpp -o ppscore.o + echo profdb profdb + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' profdb.cpp -o profdb.o + echo profile profile + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' profile.cpp -o profile.o + echo profilefrommsa profilefrommsa + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' profilefrommsa.cpp -o profilefrommsa.o + echo progalign progalign + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' progalign.cpp -o progalign.o + echo progress progress + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' progress.cpp -o progress.o + echo progressivealign progressivealign + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' progressivealign.cpp -o progressivealign.o + echo pwpath pwpath + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' pwpath.cpp -o pwpath.o + echo readmx readmx + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' readmx.cpp -o readmx.o + echo realigndiffs realigndiffs + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' realigndiffs.cpp -o realigndiffs.o + echo realigndiffse realigndiffse + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' realigndiffse.cpp -o realigndiffse.o + echo refine refine + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' refine.cpp -o refine.o + echo refinehoriz refinehoriz + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' refinehoriz.cpp -o refinehoriz.o + echo refinesubfams refinesubfams + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' refinesubfams.cpp -o refinesubfams.o + echo refinetree refinetree + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' refinetree.cpp -o refinetree.o + echo refinetreee refinetreee + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' refinetreee.cpp -o refinetreee.o + echo refinevert refinevert + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' refinevert.cpp -o refinevert.o + echo refinew refinew + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' refinew.cpp -o refinew.o + echo savebest savebest + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' savebest.cpp -o savebest.o + echo scoredist scoredist + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' scoredist.cpp -o scoredist.o + echo scoregaps scoregaps + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' scoregaps.cpp -o scoregaps.o + echo scorehistory scorehistory + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' scorehistory.cpp -o scorehistory.o + echo scorepp scorepp + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' scorepp.cpp -o scorepp.o + echo seq seq + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' seq.cpp -o seq.o + echo seqvect seqvect + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' seqvect.cpp -o seqvect.o + echo setblosumweights setblosumweights + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' setblosumweights.cpp -o setblosumweights.o + echo setgscweights setgscweights + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' setgscweights.cpp -o setgscweights.o + echo setnewhandler setnewhandler + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' setnewhandler.cpp -o setnewhandler.o + echo spfast spfast + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' spfast.cpp -o spfast.o + echo sptest sptest + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' sptest.cpp -o sptest.o + echo stabilize stabilize + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' stabilize.cpp -o stabilize.o + echo subfam subfam + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' subfam.cpp -o subfam.o + echo subfams subfams + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' subfams.cpp -o subfams.o + echo sw sw + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' sw.cpp -o sw.o + echo termgaps termgaps + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' termgaps.cpp -o termgaps.o + echo textfile textfile + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' textfile.cpp -o textfile.o + echo threewaywt threewaywt + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' threewaywt.cpp -o threewaywt.o + echo tomhydro tomhydro + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' tomhydro.cpp -o tomhydro.o + echo traceback traceback + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' traceback.cpp -o traceback.o + echo tracebackopt tracebackopt + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' tracebackopt.cpp -o tracebackopt.o + echo tracebacksw tracebacksw + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' tracebacksw.cpp -o tracebacksw.o + echo treefrommsa treefrommsa + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' treefrommsa.cpp -o treefrommsa.o + echo typetostr typetostr + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' typetostr.cpp -o typetostr.o + echo upgma2 upgma2 + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' upgma2.cpp -o upgma2.o + echo usage usage + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' usage.cpp -o usage.o + echo validateids validateids + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' validateids.cpp -o validateids.o + echo vtml2 vtml2 + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' vtml2.cpp -o vtml2.o + echo writescorefile writescorefile + c++ -c -O3 -msse2 '-mfpmath=sse' '-D_FILE_OFFSET_BITS=64' '-DNDEBUG=1' writescorefile.cpp -o writescorefile.o + LINK_OPTS='' + uname -s + [ DragonFly '==' Linux ] + c++ -g -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 subfams.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 + cat muscle.make.stderr.txt + ls -lh muscle -rwxr-xr-x 1 root wheel 468K Jul 8 04:26 muscle + sum muscle 35783 468 muscle -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for muscle-3.8.31 ===> Generating temporary packing list install -s -m 555 /construction/biology/muscle/muscle3.8.31/src/muscle /construction/biology/muscle/stage/usr/local/bin ====> Compressing man pages (compress-man) -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for muscle-3.8.31 file sizes/checksums [1]: . done packing files [1]: . done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Sunday, 7 JUL 2019 at 04:26:34 UTC Duration: 00:00:39