The following packages will be installed: mafft Fetching README... 0%100%100%100%100%100%Done Fetching References... 0%100%100%100%100%100%Done Fetching mafft.SlackBuild... 0%100%100%100%100%100%Done Fetching mafft.info... 0%100%100%100%100%100%Done Fetching slack-desc... 0%100%100%100%100%100%Done 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...