* Package:    sci-biology/muscle-5.1.0:0
 * Repository: gentoo
 * Maintainer: sci-biology@gentoo.org
 * USE:        abi_x86_64 amd64 elibc_glibc kernel_linux
 * FEATURES:   network-sandbox preserve-libs sandbox userpriv usersandbox

>>> Unpacking source...
>>> Unpacking muscle-5.1.0.tar.gz to /var/tmp/portage/sci-biology/muscle-5.1.0/work
>>> Source unpacked in /var/tmp/portage/sci-biology/muscle-5.1.0/work
>>> Preparing source in /var/tmp/portage/sci-biology/muscle-5.1.0/work/muscle-5.1.0/src ...
 * Applying 0001-Makefile-fix-horribleness-so-that-it-respects-build-.patch ...
 [ ok ]
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-biology/muscle-5.1.0/work/muscle-5.1.0/src ...
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-biology/muscle-5.1.0/work/muscle-5.1.0/src ...
make -j4 
mkdir -p Linux/
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/addconfseq.o addconfseq.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/align.o align.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/alignpairflat.o alignpairflat.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/allocflat.o allocflat.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/alnalnsflat.o alnalnsflat.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/alnmsasflat.o alnmsasflat.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/alnmsasflat3.o alnmsasflat3.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/alpha.o alpha.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/alpha3.o alpha3.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/assertsameseqs.o assertsameseqs.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/buildposterior3flat.o buildposterior3flat.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/buildpostflat.o buildpostflat.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/bwdflat3.o bwdflat3.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/calcalnflat.o calcalnflat.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/calcalnscoreflat.o calcalnscoreflat.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/calcalnscoresparse.o calcalnscoresparse.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/calcposteriorflat.o calcposteriorflat.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/colscoreefa.o colscoreefa.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/consflat.o consflat.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/conspairflat.o conspairflat.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/defaulthmmparams.o defaulthmmparams.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/derep.o derep.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/diagbox.o diagbox.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/disperse.o disperse.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/dividetree.o dividetree.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/eacluster.o eacluster.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/eadistmx.o eadistmx.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/eadistmxmsas.o eadistmxmsas.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/eesort.o eesort.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/efabestcols.o efabestcols.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/efabestconf.o efabestconf.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/efaexplode.o efaexplode.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/efastats.o efastats.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/ensemble.o ensemble.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/fa2efa.o fa2efa.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/fasta.o fasta.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/fasta2.o fasta2.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/fwdflat3.o fwdflat3.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/getconsseq.o getconsseq.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/getpairs.o getpairs.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/getpostpairsalignedflat.o getpostpairsalignedflat.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/globalinputms.o globalinputms.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/guidetreejoinorder.o guidetreejoinorder.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/heatmapcolors.o heatmapcolors.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/help.o help.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/hmmdump.o hmmdump.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/hmmparams.o hmmparams.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/jalview.o jalview.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/jointrees.o jointrees.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/letterconf.o letterconf.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/letterconfhtml.o letterconfhtml.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/logaln.o logaln.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/logdistmx.o logdistmx.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/logmx.o logmx.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/main.o main.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/make_a2m.o make_a2m.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/maxcc.o maxcc.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/mpcflat.o mpcflat.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/msa.o msa.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/msa2.o msa2.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/msastats.o msastats.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/multisequence.o multisequence.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/mysparsemx.o mysparsemx.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/myutils.o myutils.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/pairhmm.o pairhmm.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/permutetree.o permutetree.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/perturbhmm.o perturbhmm.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/pprog.o pprog.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/pprog2.o pprog2.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/pprogt.o pprogt.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/probcons.o probcons.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/progalnflat.o progalnflat.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/project.o project.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/qscore.o qscore.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/qscore2.o qscore2.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/qscoreefa.o qscoreefa.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/qscorer.o qscorer.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/quarts.o quarts.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/randomchaintree.o randomchaintree.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/refineflat.o refineflat.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/relabel.o relabel.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/relaxflat.o relaxflat.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/resample.o resample.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/seb8.o seb8.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/seq.o seq.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/sequence.o sequence.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/setprobconsparams.o setprobconsparams.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/stripgappycols.o stripgappycols.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/stripgappyrows.o stripgappyrows.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/super4.o super4.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/super5.o super5.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/testfb.o testfb.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/testlog.o testlog.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/testscoretype.o testscoretype.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/textfile.o textfile.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/totalprobflat.o totalprobflat.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/tracebackflat.o tracebackflat.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/transaln.o transaln.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/transq.o transq.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/tree.o tree.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/tree2.o tree2.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/tree4.o tree4.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/treefromfile.o treefromfile.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/treeperm.o treeperm.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/treesplitter.o treesplitter.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/treesubsetnodes.o treesubsetnodes.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/treetofile.o treetofile.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/trimtoref.o trimtoref.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/trimtorefefa.o trimtorefefa.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/uclust.o uclust.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/upgma5.o upgma5.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/usage.o usage.cpp
x86_64-pc-linux-gnu-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/usorter.o usorter.cpp
x86_64-pc-linux-gnu-g++ -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -fopenmp -pthread -lpthread  Linux/addconfseq.o Linux/align.o Linux/alignpairflat.o Linux/allocflat.o Linux/alnalnsflat.o Linux/alnmsasflat.o Linux/alnmsasflat3.o Linux/alpha.o Linux/alpha3.o Linux/assertsameseqs.o Linux/buildposterior3flat.o Linux/buildpostflat.o Linux/bwdflat3.o Linux/calcalnflat.o Linux/calcalnscoreflat.o Linux/calcalnscoresparse.o Linux/calcposteriorflat.o Linux/colscoreefa.o Linux/consflat.o Linux/conspairflat.o Linux/defaulthmmparams.o Linux/derep.o Linux/diagbox.o Linux/disperse.o Linux/dividetree.o Linux/eacluster.o Linux/eadistmx.o Linux/eadistmxmsas.o Linux/eesort.o Linux/efabestcols.o Linux/efabestconf.o Linux/efaexplode.o Linux/efastats.o Linux/ensemble.o Linux/fa2efa.o Linux/fasta.o Linux/fasta2.o Linux/fwdflat3.o Linux/getconsseq.o Linux/getpairs.o Linux/getpostpairsalignedflat.o Linux/globalinputms.o Linux/guidetreejoinorder.o Linux/heatmapcolors.o Linux/help.o Linux/hmmdump.o Linux/hmmparams.o Linux/jalview.o Linux/jointrees.o Linux/letterconf.o Linux/letterconfhtml.o Linux/logaln.o Linux/logdistmx.o Linux/logmx.o Linux/main.o Linux/make_a2m.o Linux/maxcc.o Linux/mpcflat.o Linux/msa.o Linux/msa2.o Linux/msastats.o Linux/multisequence.o Linux/mysparsemx.o Linux/myutils.o Linux/pairhmm.o Linux/permutetree.o Linux/perturbhmm.o Linux/pprog.o Linux/pprog2.o Linux/pprogt.o Linux/probcons.o Linux/progalnflat.o Linux/project.o Linux/qscore.o Linux/qscore2.o Linux/qscoreefa.o Linux/qscorer.o Linux/quarts.o Linux/randomchaintree.o Linux/refineflat.o Linux/relabel.o Linux/relaxflat.o Linux/resample.o Linux/seb8.o Linux/seq.o Linux/sequence.o Linux/setprobconsparams.o Linux/stripgappycols.o Linux/stripgappyrows.o Linux/super4.o Linux/super5.o Linux/testfb.o Linux/testlog.o Linux/testscoretype.o Linux/textfile.o Linux/totalprobflat.o Linux/tracebackflat.o Linux/transaln.o Linux/transq.o Linux/tree.o Linux/tree2.o Linux/tree4.o Linux/treefromfile.o Linux/treeperm.o Linux/treesplitter.o Linux/treesubsetnodes.o Linux/treetofile.o Linux/trimtoref.o Linux/trimtorefefa.o Linux/uclust.o Linux/upgma5.o Linux/usage.o Linux/usorter.o -o Linux/muscle
x86_64-pc-linux-gnu-g++: fatal error: cannot read spec file ‘libgomp.spec’: No such file or directory
compilation terminated.
make: *** [Makefile:34: Linux/muscle] Error 1
 * ERROR: sci-biology/muscle-5.1.0::gentoo failed (compile phase):
 *   emake failed
 * 
 * If you need support, post the output of `emerge --info '=sci-biology/muscle-5.1.0::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sci-biology/muscle-5.1.0::gentoo'`.
 * The complete build log is located at '/var/log/portage/sci-biology:muscle-5.1.0:20240320-135228.log'.
 * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/muscle-5.1.0/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-biology/muscle-5.1.0/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-biology/muscle-5.1.0/work/muscle-5.1.0/src'
 * S: '/var/tmp/portage/sci-biology/muscle-5.1.0/work/muscle-5.1.0/src'