The following packages will be installed:
 mafft 
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mafft-7.475-with-extensions/
mafft-7.475-with-extensions/MPI/
mafft-7.475-with-extensions/MPI/nodepair_mpi.c
mafft-7.475-with-extensions/MPI/pairlocalalign_mpi.c
mafft-7.475-with-extensions/MPI/mpiscript.tmpl
mafft-7.475-with-extensions/MPI/mltaln9_mpi.c
mafft-7.475-with-extensions/MPI/Makefile
mafft-7.475-with-extensions/license
mafft-7.475-with-extensions/test/
mafft-7.475-with-extensions/test/sample.ginsi.allowshift
mafft-7.475-with-extensions/test/sample.fftnsi
mafft-7.475-with-extensions/test/samplerna
mafft-7.475-with-extensions/test/sample.lins1
mafft-7.475-with-extensions/test/sample.parttree
mafft-7.475-with-extensions/test/sample.linsi
mafft-7.475-with-extensions/test/samplerna.qinsi
mafft-7.475-with-extensions/test/sample.fftns2
mafft-7.475-with-extensions/test/sample.gins1
mafft-7.475-with-extensions/test/samplerna.xinsi
mafft-7.475-with-extensions/test/sample
mafft-7.475-with-extensions/test/sample.dpparttree
mafft-7.475-with-extensions/test/script
mafft-7.475-with-extensions/test/sample.ginsi
mafft-7.475-with-extensions/extensions/
mafft-7.475-with-extensions/extensions/mxscarna_src/
mafft-7.475-with-extensions/extensions/mxscarna_src/Main.cc
mafft-7.475-with-extensions/extensions/mxscarna_src/ScoreType.hpp
mafft-7.475-with-extensions/extensions/mxscarna_src/Globaldp.cpp
mafft-7.475-with-extensions/extensions/mxscarna_src/McCaskill.cpp
mafft-7.475-with-extensions/extensions/mxscarna_src/GlobalParameters.cpp
mafft-7.475-with-extensions/extensions/mxscarna_src/scarna.hpp
mafft-7.475-with-extensions/extensions/mxscarna_src/AlifoldMEA.h
mafft-7.475-with-extensions/extensions/mxscarna_src/config.h
mafft-7.475-with-extensions/extensions/mxscarna_src/BPPMatrix.hpp
mafft-7.475-with-extensions/extensions/mxscarna_src/Makefile
mafft-7.475-with-extensions/extensions/mxscarna_src/README
mafft-7.475-with-extensions/extensions/mxscarna_src/AlifoldMEA.cpp
mafft-7.475-with-extensions/extensions/mxscarna_src/vienna/
mafft-7.475-with-extensions/extensions/mxscarna_src/vienna/params.h
mafft-7.475-with-extensions/extensions/mxscarna_src/vienna/energy_param.hpp
mafft-7.475-with-extensions/extensions/mxscarna_src/vienna/COPYING
mafft-7.475-with-extensions/extensions/mxscarna_src/vienna/energy_param.cpp
mafft-7.475-with-extensions/extensions/mxscarna_src/vienna/energy_const.h
mafft-7.475-with-extensions/extensions/mxscarna_src/vienna/energy_par.h
mafft-7.475-with-extensions/extensions/mxscarna_src/postProcessings.cpp
mafft-7.475-with-extensions/extensions/mxscarna_src/nrutil.h
mafft-7.475-with-extensions/extensions/mxscarna_src/seq2scs.cpp
mafft-7.475-with-extensions/extensions/mxscarna_src/Globaldp.hpp
mafft-7.475-with-extensions/extensions/mxscarna_src/StemCandidate.hpp
mafft-7.475-with-extensions/extensions/mxscarna_src/McCaskill.hpp
mafft-7.475-with-extensions/extensions/mxscarna_src/params-weird
mafft-7.475-with-extensions/extensions/mxscarna_src/Util.hpp
mafft-7.475-with-extensions/extensions/mxscarna_src/Beta.hpp
mafft-7.475-with-extensions/extensions/mxscarna_src/probconsRNA/
mafft-7.475-with-extensions/extensions/mxscarna_src/probconsRNA/Main.cc
mafft-7.475-with-extensions/extensions/mxscarna_src/probconsRNA/SparseMatrix.h
mafft-7.475-with-extensions/extensions/mxscarna_src/probconsRNA/FixRef.cc
mafft-7.475-with-extensions/extensions/mxscarna_src/probconsRNA/ProbabilisticModel.h
mafft-7.475-with-extensions/extensions/mxscarna_src/probconsRNA/SafeVector.h
mafft-7.475-with-extensions/extensions/mxscarna_src/probconsRNA/MakeGnuPlot.cc
mafft-7.475-with-extensions/extensions/mxscarna_src/probconsRNA/Defaults.h_backup
mafft-7.475-with-extensions/extensions/mxscarna_src/probconsRNA/FileBuffer.h
mafft-7.475-with-extensions/extensions/mxscarna_src/probconsRNA/Makefile
mafft-7.475-with-extensions/extensions/mxscarna_src/probconsRNA/ScoreType.h
mafft-7.475-with-extensions/extensions/mxscarna_src/probconsRNA/train-script
mafft-7.475-with-extensions/extensions/mxscarna_src/probconsRNA/ProjectPairwise.cc
mafft-7.475-with-extensions/extensions/mxscarna_src/probconsRNA/mlparams0
mafft-7.475-with-extensions/extensions/mxscarna_src/probconsRNA/README
mafft-7.475-with-extensions/extensions/mxscarna_src/probconsRNA/Sequence.h
mafft-7.475-with-extensions/extensions/mxscarna_src/probconsRNA/MultiSequence.h
mafft-7.475-with-extensions/extensions/mxscarna_src/probconsRNA/CompareToRef.cc
mafft-7.475-with-extensions/extensions/mxscarna_src/probconsRNA/Defaults.h
mafft-7.475-with-extensions/extensions/mxscarna_src/probconsRNA/EMtrainingALL.txt
mafft-7.475-with-extensions/extensions/mxscarna_src/probconsRNA/EvolutionaryTree.h
mafft-7.475-with-extensions/extensions/Makefile
mafft-7.475-with-extensions/extensions/univscript.tmpl
mafft-7.475-with-extensions/extensions/compileoncygwin
mafft-7.475-with-extensions/binaries/
mafft-7.475-with-extensions/binaries/.gitkeep
mafft-7.475-with-extensions/scripts/
mafft-7.475-with-extensions/scripts/.gitkeep
mafft-7.475-with-extensions/core/
mafft-7.475-with-extensions/core/setcore.c
mafft-7.475-with-extensions/core/mafft-profile.c
mafft-7.475-with-extensions/core/mafft-homologs.1
mafft-7.475-with-extensions/core/pairash.c
mafft-7.475-with-extensions/core/setdirection.c
mafft-7.475-with-extensions/core/fft.h
mafft-7.475-with-extensions/core/Falign_localhom.c
mafft-7.475-with-extensions/core/nj.c
mafft-7.475-with-extensions/core/dndfast7.c
mafft-7.475-with-extensions/core/constants.c
mafft-7.475-with-extensions/core/sextet5.c
mafft-7.475-with-extensions/core/dndblast.c
mafft-7.475-with-extensions/core/MSalign11.c
mafft-7.475-with-extensions/core/regtable2seq.c
mafft-7.475-with-extensions/core/dndpre.c
mafft-7.475-with-extensions/core/mafft-distance.c
mafft-7.475-with-extensions/core/serial.c
mafft-7.475-with-extensions/core/interface.c
mafft-7.475-with-extensions/core/JTT.c
mafft-7.475-with-extensions/core/mtxutl.h
mafft-7.475-with-extensions/core/rna.c
mafft-7.475-with-extensions/core/miyata5.h
mafft-7.475-with-extensions/core/pairlocalalignmain.c
mafft-7.475-with-extensions/core/blosum.c
mafft-7.475-with-extensions/core/mafft.bat.win10
mafft-7.475-with-extensions/core/rnatest.c
mafft-7.475-with-extensions/core/Lalignmm.c
mafft-7.475-with-extensions/core/makemergetable.rb
mafft-7.475-with-extensions/core/dndfast4.c
mafft-7.475-with-extensions/core/multi2hat3s.c
mafft-7.475-with-extensions/core/seekquencer_premafft.tmpl
mafft-7.475-with-extensions/core/countlen.c
mafft-7.475-with-extensions/core/univscript.tmpl
mafft-7.475-with-extensions/core/Salignmm.c
mafft-7.475-with-extensions/core/dp.h
mafft-7.475-with-extensions/core/miyata.h
mafft-7.475-with-extensions/core/compileoncygwin
mafft-7.475-with-extensions/core/regionalrealignment.rb
mafft-7.475-with-extensions/core/Makefile.sos
mafft-7.475-with-extensions/core/Lalign11.c
mafft-7.475-with-extensions/core/mafftash_premafft.tmpl
mafft-7.475-with-extensions/core/Galign11.c
mafft-7.475-with-extensions/core/fft.c
mafft-7.475-with-extensions/core/maffttext2hex.c
mafft-7.475-with-extensions/core/restoreu.c
mafft-7.475-with-extensions/core/share.h
mafft-7.475-with-extensions/core/compileonmsys
mafft-7.475-with-extensions/core/score.c
mafft-7.475-with-extensions/core/dndpre_score.c
mafft-7.475-with-extensions/core/contrafoldwrap.c
mafft-7.475-with-extensions/core/mtxutl.c
mafft-7.475-with-extensions/core/tddis.c
mafft-7.475-with-extensions/core/getlag.c
mafft-7.475-with-extensions/core/iteration.c
mafft-7.475-with-extensions/core/nodepair.c
mafft-7.475-with-extensions/core/mafft.1
mafft-7.475-with-extensions/core/treeOperation.c
mafft-7.475-with-extensions/core/SAalignmm.c
mafft-7.475-with-extensions/core/replaceu.c
mafft-7.475-with-extensions/core/version.c
mafft-7.475-with-extensions/core/mafft.h
mafft-7.475-with-extensions/core/MSalignmm.c
mafft-7.475-with-extensions/core/fftFunctions.c
mafft-7.475-with-extensions/core/tditeration.c
mafft-7.475-with-extensions/core/pairlocalalign.c
mafft-7.475-with-extensions/core/dvtditr.c
mafft-7.475-with-extensions/core/newick2mafft.rb
mafft-7.475-with-extensions/core/hex2maffttext.c
mafft-7.475-with-extensions/core/blosum.h
mafft-7.475-with-extensions/core/suboptalign11.c
mafft-7.475-with-extensions/core/genalign11.c
mafft-7.475-with-extensions/core/mccaskillwrap.c
mafft-7.475-with-extensions/core/mafft-sparsecore.tmpl
mafft-7.475-with-extensions/core/seq2regtable.c
mafft-7.475-with-extensions/core/DNA.h
mafft-7.475-with-extensions/core/partSalignmm.c
mafft-7.475-with-extensions/core/Dalignmm.c
mafft-7.475-with-extensions/core/addfunctions.c
mafft-7.475-with-extensions/core/mingw64mingw32dll
mafft-7.475-with-extensions/core/splittbfast.c
mafft-7.475-with-extensions/core/makedirectionlist.c
mafft-7.475-with-extensions/core/mafft-homologs.tmpl
mafft-7.475-with-extensions/core/io.c
mafft-7.475-with-extensions/core/f2cl.c
mafft-7.475-with-extensions/core/mafft.ps1
mafft-7.475-with-extensions/core/mafft.bat
mafft-7.475-with-extensions/core/functions.h
mafft-7.475-with-extensions/core/dash_client.go
mafft-7.475-with-extensions/core/Falign.c
mafft-7.475-with-extensions/core/tbfast.c
mafft-7.475-with-extensions/core/mltaln9.c
mafft-7.475-with-extensions/core/mltaln.h
mafft-7.475-with-extensions/core/defs.c
mafft-7.475-with-extensions/core/disttbfast.c
mafft-7.475-with-extensions/core/addsingle.c
mafft-7.475-with-extensions/core/filter.c
mafft-7.475-with-extensions/core/mafft.tmpl
mafft-7.475-with-extensions/core/Makefile
mafft-7.475-with-extensions/readme
rm -f *.o *.a *.exe *~ mafftash_premafft.pl seekquencer_premafft.pl dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign multi2hat3s pairash addsingle maffttext2hex hex2maffttext splittbfast disttbfast tbfast nodepair mafft-profile f2cl mccaskillwrap contrafoldwrap countlen seq2regtable regtable2seq score getlag dndpre setcore filter replaceu restoreu setdirection makedirectionlist version  mafft mafft-homologs.rb mafft-sparsecore.rb libdisttbfast.so libdisttbfast.dylib libdisttbfast.dll *.gcda *.gcno 
cp mafftash_premafft.tmpl mafftash_premafft.pl
cp seekquencer_premafft.tmpl seekquencer_premafft.pl
gcc  -Denablemultithread  -std=c99 -O2 -fPIC -c mtxutl.c
gcc  -Denablemultithread  -std=c99 -O2 -fPIC -c io.c
gcc  -Denablemultithread  -std=c99 -O2 -fPIC -c mltaln9.c
mltaln9.c: In function ‘check_guidetreefile’:
mltaln9.c:2850:9: warning: ‘fgets’ writing 999 bytes into a region of size 100 overflows the destination [-Wstringop-overflow=]
 2850 |         fgets( string, 999, fp );
      |         ^~~~~~~~~~~~~~~~~~~~~~~~
mltaln9.c:2834:14: note: destination object ‘string’ of size 100
 2834 |         char string[100];
      |              ^~~~~~
In file included from mltaln.h:12,
                 from mltaln9.c:1:
/usr/include/stdio.h:568:14: note: in a call to function ‘fgets’ declared with attribute ‘access (write_only, 1, 2)’
  568 | extern char *fgets (char *__restrict __s, int __n, FILE *__restrict __stream)
      |              ^~~~~
gcc  -Denablemultithread  -std=c99 -O2 -fPIC -c tddis.c
gcc  -Denablemultithread  -std=c99 -O2 -fPIC -c constants.c
gcc  -Denablemultithread  -std=c99 -O2 -fPIC -c nj.c
gcc  -Denablemultithread  -std=c99 -O2 -fPIC -c partSalignmm.c  
gcc  -Denablemultithread  -std=c99 -O2 -fPIC -c Lalignmm.c 
gcc  -Denablemultithread  -std=c99 -O2 -fPIC -c rna.c 
gcc  -Denablemultithread  -std=c99 -O2 -fPIC -c Salignmm.c 
gcc  -Denablemultithread  -std=c99 -O2 -fPIC -c Dalignmm.c 
gcc  -Denablemultithread  -std=c99 -O2 -fPIC -c Falign.c
gcc  -Denablemultithread  -std=c99 -O2 -fPIC -c Falign_localhom.c
gcc  -Denablemultithread  -std=c99 -O2 -fPIC -c Galign11.c 
gcc  -Denablemultithread  -std=c99 -O2 -fPIC -c Lalign11.c 
gcc  -Denablemultithread  -std=c99 -O2 -fPIC -c genalign11.c 
gcc  -Denablemultithread  -std=c99 -O2 -fPIC -c MSalignmm.c 
gcc  -Denablemultithread  -std=c99 -O2 -fPIC -c fftFunctions.c
gcc  -Denablemultithread  -std=c99 -O2 -fPIC -c fft.c 
gcc  -Denablemultithread  -std=c99 -O2 -fPIC -c tditeration.c
gcc  -Denablemultithread  -std=c99 -O2 -fPIC -c dvtditr.c
gcc  -Denablemultithread  -std=c99 -O2 -fPIC -c defs.c
gcc  -Denablemultithread  -std=c99 -O2 -fPIC -c SAalignmm.c -o SAalignmm.o
gcc  -Denablemultithread  -std=c99 -O2 -fPIC -c treeOperation.c
gcc  -Denablemultithread  -std=c99 -O2 -fPIC -c addfunctions.c
gcc -o dvtditr mtxutl.o io.o mltaln9.o tddis.o constants.o nj.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o MSalignmm.o fftFunctions.o fft.o tditeration.o dvtditr.o defs.o SAalignmm.o treeOperation.o addfunctions.o   -Denablemultithread  -std=c99 -O2 -fPIC  -lm  -lpthread
gcc  -Denablemultithread  -std=c99 -O2 -fPIC -c dndfast7.c
gcc -o dndfast7 dndfast7.o io.o constants.o mtxutl.o mltaln9.o tddis.o defs.o Galign11.o Lalign11.o genalign11.o  -Denablemultithread  -std=c99 -O2 -fPIC  -lm  -lpthread
gcc  -Denablemultithread  -std=c99 -O2 -fPIC -c dndblast.c
gcc -o dndblast dndblast.o io.o constants.o mtxutl.o mltaln9.o tddis.o defs.o Galign11.o Lalign11.o genalign11.o  -Denablemultithread  -std=c99 -O2 -fPIC  -lm  -lpthread
gcc  -Denablemultithread  -std=c99 -O2 -fPIC -c sextet5.c
gcc -o sextet5 io.o constants.o mtxutl.o mltaln9.o tddis.o sextet5.o defs.o Galign11.o Lalign11.o genalign11.o  -Denablemultithread  -std=c99 -O2 -fPIC  -lm  -lpthread
gcc  -Denablemultithread  -std=c99 -O2 -fPIC -c mafft-distance.c
gcc -o mafft-distance io.o constants.o mtxutl.o mltaln9.o tddis.o mafft-distance.o defs.o Galign11.o Lalign11.o genalign11.o  -Denablemultithread  -std=c99 -O2 -fPIC  -lm  -lpthread
gcc  -Denablemultithread  -std=c99 -O2 -fPIC -c MSalign11.c 
gcc  -Denablemultithread  -std=c99 -O2 -fPIC -c suboptalign11.c 
gcc  -Denablemultithread  -std=c99 -O2 -fPIC -c pairlocalalignmain.c
gcc  -Denablemultithread  -std=c99 -O2 -fPIC -c pairlocalalign.c
gcc -o pairlocalalign mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o MSalignmm.o Galign11.o Lalign11.o genalign11.o MSalign11.o suboptalign11.o SAalignmm.o pairlocalalignmain.o pairlocalalign.o defs.o fft.o fftFunctions.o  -Denablemultithread  -std=c99 -O2 -fPIC  -lm  -lpthread
gcc  -Denablemultithread  -std=c99 -O2 -fPIC -c multi2hat3s.c
gcc -o multi2hat3s mtxutl.o io.o mltaln9.o tddis.o constants.o multi2hat3s.o defs.o fft.o fftFunctions.o Galign11.o Lalign11.o genalign11.o  -Denablemultithread  -std=c99 -O2 -fPIC  -lm  -lpthread
gcc  -Denablemultithread  -std=c99 -O2 -fPIC -c pairash.c
gcc -o pairash mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o MSalignmm.o Galign11.o Lalign11.o genalign11.o MSalign11.o suboptalign11.o SAalignmm.o pairash.o defs.o fft.o fftFunctions.o  -Denablemultithread  -std=c99 -O2 -fPIC  -lm  -lpthread
gcc  -Denablemultithread  -std=c99 -O2 -fPIC -c addsingle.c
gcc -o addsingle mtxutl.o io.o mltaln9.o tddis.o constants.o MSalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o addsingle.o defs.o fft.o fftFunctions.o addfunctions.o  -Denablemultithread  -std=c99 -O2 -fPIC  -lm  -lpthread
gcc -o maffttext2hex maffttext2hex.c  -Denablemultithread  -std=c99 -O2 -fPIC  -lm  -lpthread
gcc -o hex2maffttext hex2maffttext.c  -Denablemultithread  -std=c99 -O2 -fPIC  -lm  -lpthread
gcc  -Denablemultithread  -std=c99 -O2 -fPIC -c splittbfast.c
gcc -o splittbfast mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o  Dalignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o MSalignmm.o splittbfast.o defs.o fft.o fftFunctions.o   -Denablemultithread  -std=c99 -O2 -fPIC  -lm  -lpthread
gcc  -Denablemultithread  -std=c99 -O2 -fPIC -c disttbfast.c
gcc -o disttbfast mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o MSalignmm.o disttbfast.o defs.o fft.o fftFunctions.o addfunctions.o  -Denablemultithread  -std=c99 -O2 -fPIC  -lm  -lpthread
gcc  -Denablemultithread  -std=c99 -O2 -fPIC -c tbfast.c
gcc -o tbfast mtxutl.o io.o mltaln9.o tddis.o constants.o MSalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o tbfast.o defs.o fft.o fftFunctions.o addfunctions.o pairlocalalign.o MSalign11.o   -Denablemultithread  -std=c99 -O2 -fPIC  -lm  -lpthread
gcc  -Denablemultithread  -std=c99 -O2 -fPIC -c nodepair.c
gcc -o nodepair mtxutl.o io.o mltaln9.o tddis.o constants.o MSalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o nodepair.o defs.o fft.o fftFunctions.o addfunctions.o pairlocalalign.o MSalign11.o  -Denablemultithread  -std=c99 -O2 -fPIC  -lm  -lpthread
gcc  -Denablemultithread  -std=c99 -O2 -fPIC -c mafft-profile.c
gcc -o mafft-profile io.o mtxutl.o mltaln9.o tddis.o constants.o partSalignmm.o MSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o SAalignmm.o Galign11.o Lalign11.o genalign11.o Falign.o Falign_localhom.o fftFunctions.o fft.o mafft-profile.o defs.o  -Denablemultithread  -std=c99 -O2 -fPIC  -lm  -lpthread
gcc  -Denablemultithread  -std=c99 -O2 -fPIC -c f2cl.c
gcc -o f2cl mtxutl.o io.o f2cl.o constants.o defs.o  -Denablemultithread  -std=c99 -O2 -fPIC  -lm  -lpthread
gcc  -Denablemultithread  -std=c99 -O2 -fPIC -c mccaskillwrap.c
gcc -o mccaskillwrap mtxutl.o io.o mccaskillwrap.o constants.o defs.o mltaln9.o Galign11.o Lalign11.o genalign11.o  -Denablemultithread  -std=c99 -O2 -fPIC  -lm  -lpthread
gcc  -Denablemultithread  -std=c99 -O2 -fPIC -c contrafoldwrap.c
gcc -o contrafoldwrap mtxutl.o io.o contrafoldwrap.o constants.o defs.o mltaln9.o Galign11.o Lalign11.o genalign11.o  -Denablemultithread  -std=c99 -O2 -fPIC  -lm  -lpthread
gcc  -Denablemultithread  -std=c99 -O2 -fPIC -c countlen.c
gcc -o countlen mtxutl.o io.o countlen.o defs.o  -Denablemultithread  -std=c99 -O2 -fPIC  -lm  -lpthread
gcc  -Denablemultithread  -std=c99 -O2 -fPIC -c seq2regtable.c
gcc -o seq2regtable mtxutl.o io.o seq2regtable.o defs.o  -Denablemultithread  -std=c99 -O2 -fPIC  -lm  -lpthread
gcc  -Denablemultithread  -std=c99 -O2 -fPIC -c regtable2seq.c
gcc -o regtable2seq mtxutl.o io.o regtable2seq.o defs.o mltaln9.o Galign11.o Lalign11.o genalign11.o  -Denablemultithread  -std=c99 -O2 -fPIC  -lm  -lpthread
gcc  -Denablemultithread  -std=c99 -O2 -fPIC -c score.c
gcc -o score io.o mtxutl.o mltaln9.o score.o constants.o defs.o Galign11.o Lalign11.o genalign11.o  -Denablemultithread  -std=c99 -O2 -fPIC  -lm  -lpthread
gcc  -Denablemultithread  -std=c99 -O2 -fPIC -c getlag.c
gcc -o getlag mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o MSalignmm.o Dalignmm.o getlag.o defs.o fft.o fftFunctions.o  -Denablemultithread  -std=c99 -O2 -fPIC  -lm  -lpthread
gcc  -Denablemultithread  -std=c99 -O2 -fPIC -c dndpre.c
gcc -o dndpre dndpre.o io.o constants.o mtxutl.o mltaln9.o defs.o Galign11.o Lalign11.o genalign11.o  -Denablemultithread  -std=c99 -O2 -fPIC  -lm  -lpthread
gcc  -Denablemultithread  -std=c99 -O2 -fPIC -c setcore.c
gcc -o setcore mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o MSalignmm.o setcore.o defs.o fft.o fftFunctions.o  -Denablemultithread  -std=c99 -O2 -fPIC  -lm  -lpthread
gcc -O2 -fPIC   -c -o filter.o filter.c
gcc -o filter mtxutl.o io.o filter.o defs.o mltaln9.o Galign11.o Lalign11.o genalign11.o  -Denablemultithread  -std=c99 -O2 -fPIC  -lm  -lpthread
gcc  -Denablemultithread  -std=c99 -O2 -fPIC -c replaceu.c
gcc -o replaceu mtxutl.o io.o replaceu.o defs.o mltaln9.o Galign11.o Lalign11.o genalign11.o  -Denablemultithread  -std=c99 -O2 -fPIC  -lm  -lpthread
gcc  -Denablemultithread  -std=c99 -O2 -fPIC -c restoreu.c
gcc -o restoreu mtxutl.o io.o restoreu.o defs.o mltaln9.o Galign11.o Lalign11.o genalign11.o  -Denablemultithread  -std=c99 -O2 -fPIC  -lm  -lpthread
gcc  -Denablemultithread  -std=c99 -O2 -fPIC -c setdirection.c
gcc -o setdirection mtxutl.o io.o setdirection.o defs.o mltaln9.o Galign11.o Lalign11.o genalign11.o  -Denablemultithread  -std=c99 -O2 -fPIC  -lm  -lpthread
gcc  -Denablemultithread  -std=c99 -O2 -fPIC -c makedirectionlist.c
gcc -o makedirectionlist mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o  Dalignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o MSalignmm.o makedirectionlist.o defs.o fft.o fftFunctions.o addfunctions.o  -Denablemultithread  -std=c99 -O2 -fPIC  -lm  -lpthread
gcc -o version version.c  -Denablemultithread  -std=c99 -O2 -fPIC  -lm  -lpthread 
sed "s:_LIBDIR:/usr/libexec/mafft:" mafft.tmpl  > mafft
sed "s:_BINDIR:/usr/bin:" mafft-homologs.tmpl  > mafft-homologs.rb
sed "s:_BINDIR:/usr/bin:" mafft-sparsecore.tmpl  > mafft-sparsecore.rb
cp mafft mafft-homologs.rb mafft-sparsecore.rb ../scripts
chmod 755 ../scripts/*
cp mafftash_premafft.pl seekquencer_premafft.pl dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign multi2hat3s pairash addsingle maffttext2hex hex2maffttext splittbfast disttbfast tbfast nodepair mafft-profile f2cl mccaskillwrap contrafoldwrap countlen seq2regtable regtable2seq score getlag dndpre setcore filter replaceu restoreu setdirection makedirectionlist version  ../binaries
chmod 755 ../binaries/*
cp mafft.1 mafft-homologs.1 ../binaries
done.
rm -f *.o *.a *.exe *~ mxscarnamod
make clean -C mxscarna_src
make[1]: Entering directory '/usr/src/slapt-src/academic/mafft/mafft-7.475-with-extensions/extensions/mxscarna_src'
rm -f mxscarna  *.o *.h~ *.hpp~ *.cpp~ *.cc~ ./vienna/*.o 
make -C ./probconsRNA clean
make[2]: Entering directory '/usr/src/slapt-src/academic/mafft/mafft-7.475-with-extensions/extensions/mxscarna_src/probconsRNA'
rm -f probcons 
make[2]: Leaving directory '/usr/src/slapt-src/academic/mafft/mafft-7.475-with-extensions/extensions/mxscarna_src/probconsRNA'
make[1]: Leaving directory '/usr/src/slapt-src/academic/mafft/mafft-7.475-with-extensions/extensions/mxscarna_src'
make CFLAGS1="" -C mxscarna_src
make[1]: Entering directory '/usr/src/slapt-src/academic/mafft/mafft-7.475-with-extensions/extensions/mxscarna_src'
g++ -I./probconsRNA -I./vienna -I./ -DNDEBUG -DNumInsertStates=1 -DVERSION="2.0" -O2 -fPIC  -std=c++98 -c Main.cc -o Main.o
g++ -I./probconsRNA -I./vienna -I./ -DNDEBUG -DNumInsertStates=1 -DVERSION="2.0" -O2 -fPIC  -std=c++98 -c McCaskill.cpp -o McCaskill.o
g++ -I./probconsRNA -I./vienna -I./ -DNDEBUG -DNumInsertStates=1 -DVERSION="2.0" -O2 -fPIC  -std=c++98 -c ./vienna/energy_param.cpp -o ./vienna/energy_param.o
g++ -I./probconsRNA -I./vienna -I./ -DNDEBUG -DNumInsertStates=1 -DVERSION="2.0" -O2 -fPIC  -std=c++98 -c seq2scs.cpp -o seq2scs.o
g++ -I./probconsRNA -I./vienna -I./ -DNDEBUG -DNumInsertStates=1 -DVERSION="2.0" -O2 -fPIC  -std=c++98 -c Globaldp.cpp -o Globaldp.o
g++ -I./probconsRNA -I./vienna -I./ -DNDEBUG -DNumInsertStates=1 -DVERSION="2.0" -O2 -fPIC  -std=c++98 -c postProcessings.cpp -o postProcessings.o
g++ -I./probconsRNA -I./vienna -I./ -DNDEBUG -DNumInsertStates=1 -DVERSION="2.0" -O2 -fPIC  -std=c++98 -c AlifoldMEA.cpp -o AlifoldMEA.o
g++ -L./probconsRNA  -L./ -DNDEBUG -DNumInsertStates=1 -DVERSION="2.0" -O2 -fPIC  -std=c++98 -lm -o mxscarna Main.o McCaskill.o vienna/energy_param.o seq2scs.o Globaldp.o postProcessings.o AlifoldMEA.o
make[1]: Leaving directory '/usr/src/slapt-src/academic/mafft/mafft-7.475-with-extensions/extensions/mxscarna_src'
mv mxscarna_src/mxscarna mxscarnamod
cp mxscarnamod ../binaries
chmod 755 ../binaries/*
done.
cp mafft mafft-homologs.rb mafft-sparsecore.rb ../scripts
chmod 755 ../scripts/*
cp mafftash_premafft.pl seekquencer_premafft.pl dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign multi2hat3s pairash addsingle maffttext2hex hex2maffttext splittbfast disttbfast tbfast nodepair mafft-profile f2cl mccaskillwrap contrafoldwrap countlen seq2regtable regtable2seq score getlag dndpre setcore filter replaceu restoreu setdirection makedirectionlist version  ../binaries
chmod 755 ../binaries/*
cp mafft.1 mafft-homologs.1 ../binaries
done.
mkdir -p /usr/src/slapt-src/academic/mafft/package-mafft/usr/libexec/mafft
chmod 755 /usr/src/slapt-src/academic/mafft/package-mafft/usr/libexec/mafft
mkdir -p /usr/src/slapt-src/academic/mafft/package-mafft/usr/bin
chmod 755 /usr/src/slapt-src/academic/mafft/package-mafft/usr/bin
chmod 755 mafft mafft-homologs.rb mafft-sparsecore.rb
install mafft mafft-homologs.rb mafft-sparsecore.rb  /usr/src/slapt-src/academic/mafft/package-mafft/usr/bin
chmod 755 dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign multi2hat3s pairash addsingle maffttext2hex hex2maffttext splittbfast disttbfast tbfast nodepair mafft-profile f2cl mccaskillwrap contrafoldwrap countlen seq2regtable regtable2seq score getlag dndpre setcore filter replaceu restoreu setdirection makedirectionlist version  ||:     # in MinGW, it's ok if this fails
strip dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign multi2hat3s pairash addsingle maffttext2hex hex2maffttext splittbfast disttbfast tbfast nodepair mafft-profile f2cl mccaskillwrap contrafoldwrap countlen seq2regtable regtable2seq score getlag dndpre setcore filter replaceu restoreu setdirection makedirectionlist version  ||: # may fail for dash_client on mac.
install dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign multi2hat3s pairash addsingle maffttext2hex hex2maffttext splittbfast disttbfast tbfast nodepair mafft-profile f2cl mccaskillwrap contrafoldwrap countlen seq2regtable regtable2seq score getlag dndpre setcore filter replaceu restoreu setdirection makedirectionlist version  /usr/src/slapt-src/academic/mafft/package-mafft/usr/libexec/mafft
install mafftash_premafft.pl seekquencer_premafft.pl /usr/src/slapt-src/academic/mafft/package-mafft/usr/libexec/mafft
install -m 644 mafft.1 mafft-homologs.1 /usr/src/slapt-src/academic/mafft/package-mafft/usr/libexec/mafft
( cd /usr/src/slapt-src/academic/mafft/package-mafft/usr/bin; \
rm -f linsi ginsi einsi fftns fftnsi nwns nwnsi xinsi qinsi; \
rm -f mafft-linsi mafft-ginsi mafft-einsi mafft-fftns mafft-fftnsi mafft-nwns mafft-nwnsi mafft-xinsi mafft-qinsi mafft-randomcore.rb ; \
ln -s mafft linsi; ln -s mafft ginsi; ln -s mafft fftns; \
ln -s mafft fftnsi; ln -s mafft nwns; ln -s mafft nwnsi; \
ln -s mafft einsi; \
ln -s mafft mafft-linsi; ln -s mafft mafft-ginsi; ln -s mafft mafft-fftns; \
ln -s mafft mafft-fftnsi; ln -s mafft mafft-nwns; ln -s mafft mafft-nwnsi; \
ln -s mafft mafft-einsi; ln -s mafft mafft-xinsi; ln -s mafft mafft-qinsi;\
rm -f mafft-profile mafft-profile.exe; ln -s /usr/src/slapt-src/academic/mafft/package-mafft/usr/libexec/mafft/mafft-profile .; \
rm -f mafft-distance mafft-distance.exe; ln -s /usr/src/slapt-src/academic/mafft/package-mafft/usr/libexec/mafft/mafft-distance . )
mkdir -p /usr/src/slapt-src/academic/mafft/package-mafft/usr/man/man1
chmod 755 /usr/src/slapt-src/academic/mafft/package-mafft/usr/man/man1
install -m 644 mafft.1 mafft-homologs.1 /usr/src/slapt-src/academic/mafft/package-mafft/usr/man/man1
cp mxscarnamod ../binaries
chmod 755 ../binaries/*
done.
mkdir -p /usr/src/slapt-src/academic/mafft/package-mafft/usr/libexec/mafft
chmod 755 /usr/src/slapt-src/academic/mafft/package-mafft/usr/libexec/mafft
chmod 755 mxscarnamod
install mxscarnamod /usr/src/slapt-src/academic/mafft/package-mafft/usr/libexec/mafft

Slackware package maker, version 3.14159265.

Searching for symbolic links:
usr/bin/einsi	mafft
usr/bin/fftns	mafft
usr/bin/fftnsi	mafft
usr/bin/ginsi	mafft
usr/bin/linsi	mafft
usr/bin/mafft-distance	/usr/libexec/mafft/mafft-distance
usr/bin/mafft-einsi	mafft
usr/bin/mafft-fftns	mafft
usr/bin/mafft-fftnsi	mafft
usr/bin/mafft-ginsi	mafft
usr/bin/mafft-linsi	mafft
usr/bin/mafft-nwns	mafft
usr/bin/mafft-nwnsi	mafft
usr/bin/mafft-profile	/usr/libexec/mafft/mafft-profile
usr/bin/mafft-qinsi	mafft
usr/bin/mafft-xinsi	mafft
usr/bin/nwns	mafft
usr/bin/nwnsi	mafft

Making symbolic link creation script:
( cd usr/bin ; rm -rf einsi )
( cd usr/bin ; ln -sf mafft einsi )
( cd usr/bin ; rm -rf fftns )
( cd usr/bin ; ln -sf mafft fftns )
( cd usr/bin ; rm -rf fftnsi )
( cd usr/bin ; ln -sf mafft fftnsi )
( cd usr/bin ; rm -rf ginsi )
( cd usr/bin ; ln -sf mafft ginsi )
( cd usr/bin ; rm -rf linsi )
( cd usr/bin ; ln -sf mafft linsi )
( cd usr/bin ; rm -rf mafft-distance )
( cd usr/bin ; ln -sf /usr/libexec/mafft/mafft-distance mafft-distance )
( cd usr/bin ; rm -rf mafft-einsi )
( cd usr/bin ; ln -sf mafft mafft-einsi )
( cd usr/bin ; rm -rf mafft-fftns )
( cd usr/bin ; ln -sf mafft mafft-fftns )
( cd usr/bin ; rm -rf mafft-fftnsi )
( cd usr/bin ; ln -sf mafft mafft-fftnsi )
( cd usr/bin ; rm -rf mafft-ginsi )
( cd usr/bin ; ln -sf mafft mafft-ginsi )
( cd usr/bin ; rm -rf mafft-linsi )
( cd usr/bin ; ln -sf mafft mafft-linsi )
( cd usr/bin ; rm -rf mafft-nwns )
( cd usr/bin ; ln -sf mafft mafft-nwns )
( cd usr/bin ; rm -rf mafft-nwnsi )
( cd usr/bin ; ln -sf mafft mafft-nwnsi )
( cd usr/bin ; rm -rf mafft-profile )
( cd usr/bin ; ln -sf /usr/libexec/mafft/mafft-profile mafft-profile )
( cd usr/bin ; rm -rf mafft-qinsi )
( cd usr/bin ; ln -sf mafft mafft-qinsi )
( cd usr/bin ; rm -rf mafft-xinsi )
( cd usr/bin ; ln -sf mafft mafft-xinsi )
( cd usr/bin ; rm -rf nwns )
( cd usr/bin ; ln -sf mafft nwns )
( cd usr/bin ; rm -rf nwnsi )
( cd usr/bin ; ln -sf mafft nwnsi )

It is recommended that you make these lines your new installation script.

Would you like to make this stuff the install script for this package
and remove the symbolic links ([y]es, [n]o)? y


Removing symbolic links:
removed './usr/bin/linsi'
removed './usr/bin/ginsi'
removed './usr/bin/fftns'
removed './usr/bin/fftnsi'
removed './usr/bin/nwns'
removed './usr/bin/nwnsi'
removed './usr/bin/einsi'
removed './usr/bin/mafft-linsi'
removed './usr/bin/mafft-ginsi'
removed './usr/bin/mafft-fftns'
removed './usr/bin/mafft-fftnsi'
removed './usr/bin/mafft-nwns'
removed './usr/bin/mafft-nwnsi'
removed './usr/bin/mafft-einsi'
removed './usr/bin/mafft-xinsi'
removed './usr/bin/mafft-qinsi'
removed './usr/bin/mafft-distance'
removed './usr/bin/mafft-profile'

Creating your new ./install/doinst.sh...

This next step is optional - you can set the directories in your package
to some sane permissions. If any of the directories in your package have
special permissions, then DO NOT reset them here!

Would you like to reset all directory permissions to 755 (drwxr-xr-x) and
directory ownerships to root.root ([y]es, [n]o)? n

Creating Slackware package:  /usr/src/slapt-src/academic/mafft/mafft-7.475-x86_64-1salix15.0.txz

./
install/
install/doinst.sh
install/slack-desc
usr/
usr/bin/
usr/bin/mafft
usr/bin/mafft-homologs.rb
usr/bin/mafft-sparsecore.rb
usr/doc/
usr/doc/mafft-7.475/
usr/doc/mafft-7.475/References
usr/doc/mafft-7.475/license
usr/doc/mafft-7.475/mafft.SlackBuild
usr/doc/mafft-7.475/readme
usr/libexec/
usr/libexec/mafft/
usr/libexec/mafft/addsingle
usr/libexec/mafft/contrafoldwrap
usr/libexec/mafft/countlen
usr/libexec/mafft/disttbfast
usr/libexec/mafft/dndblast
usr/libexec/mafft/dndfast7
usr/libexec/mafft/dndpre
usr/libexec/mafft/dvtditr
usr/libexec/mafft/f2cl
usr/libexec/mafft/filter
usr/libexec/mafft/getlag
usr/libexec/mafft/hex2maffttext
usr/libexec/mafft/mafft-distance
usr/libexec/mafft/mafft-profile
usr/libexec/mafft/mafftash_premafft.pl
usr/libexec/mafft/maffttext2hex
usr/libexec/mafft/makedirectionlist
usr/libexec/mafft/mccaskillwrap
usr/libexec/mafft/multi2hat3s
usr/libexec/mafft/mxscarnamod
usr/libexec/mafft/nodepair
usr/libexec/mafft/pairash
usr/libexec/mafft/pairlocalalign
usr/libexec/mafft/regtable2seq
usr/libexec/mafft/replaceu
usr/libexec/mafft/restoreu
usr/libexec/mafft/score
usr/libexec/mafft/seekquencer_premafft.pl
usr/libexec/mafft/seq2regtable
usr/libexec/mafft/setcore
usr/libexec/mafft/setdirection
usr/libexec/mafft/sextet5
usr/libexec/mafft/splittbfast
usr/libexec/mafft/tbfast
usr/libexec/mafft/version
usr/man/
usr/man/man1/
usr/man/man1/mafft-homologs.1.gz
usr/man/man1/mafft.1.gz
usr/share/
usr/share/mafft/
usr/share/mafft/test/
usr/share/mafft/test/sample
usr/share/mafft/test/sample.dpparttree
usr/share/mafft/test/sample.fftns2
usr/share/mafft/test/sample.fftnsi
usr/share/mafft/test/sample.gins1
usr/share/mafft/test/sample.ginsi
usr/share/mafft/test/sample.ginsi.allowshift
usr/share/mafft/test/sample.lins1
usr/share/mafft/test/sample.linsi
usr/share/mafft/test/sample.parttree
usr/share/mafft/test/samplerna
usr/share/mafft/test/samplerna.qinsi
usr/share/mafft/test/samplerna.xinsi
usr/share/mafft/test/script

Slackware package /usr/src/slapt-src/academic/mafft/mafft-7.475-x86_64-1salix15.0.txz created.

Installing package mafft-7.475-with-extensions-src...