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Packages/mafft/mafft-7.487-2-x86_64-build.log
starsareintherose eeb4358381 add mafft
2021-08-10 22:21:03 +08:00

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make: Entering directory '/build/mafft/src/mafft-7.487-with-extensions/core'
cp mafftash_premafft.tmpl mafftash_premafft.pl
cp seekquencer_premafft.tmpl seekquencer_premafft.pl
gcc -Denablemultithread -std=c99 -O3 -c mtxutl.c
gcc -Denablemultithread -std=c99 -O3 -c io.c
gcc -Denablemultithread -std=c99 -O3 -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 -O3 -c tddis.c
gcc -Denablemultithread -std=c99 -O3 -c constants.c
gcc -Denablemultithread -std=c99 -O3 -c nj.c
gcc -Denablemultithread -std=c99 -O3 -c partSalignmm.c
gcc -Denablemultithread -std=c99 -O3 -c Lalignmm.c
gcc -Denablemultithread -std=c99 -O3 -c rna.c
gcc -Denablemultithread -std=c99 -O3 -c Salignmm.c
gcc -Denablemultithread -std=c99 -O3 -c Dalignmm.c
gcc -Denablemultithread -std=c99 -O3 -c Falign.c
gcc -Denablemultithread -std=c99 -O3 -c Falign_localhom.c
gcc -Denablemultithread -std=c99 -O3 -c Galign11.c
gcc -Denablemultithread -std=c99 -O3 -c Lalign11.c
gcc -Denablemultithread -std=c99 -O3 -c genalign11.c
gcc -Denablemultithread -std=c99 -O3 -c MSalignmm.c
gcc -Denablemultithread -std=c99 -O3 -c fftFunctions.c
gcc -Denablemultithread -std=c99 -O3 -c fft.c
gcc -Denablemultithread -std=c99 -O3 -c tditeration.c
gcc -Denablemultithread -std=c99 -O3 -c dvtditr.c
gcc -Denablemultithread -std=c99 -O3 -c defs.c
gcc -Denablemultithread -std=c99 -O3 -c SAalignmm.c -o SAalignmm.o
gcc -Denablemultithread -std=c99 -O3 -c treeOperation.c
gcc -Denablemultithread -std=c99 -O3 -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 -O3 -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -lm -lpthread
gcc -Denablemultithread -std=c99 -O3 -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 -O3 -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -lm -lpthread
gcc -Denablemultithread -std=c99 -O3 -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 -O3 -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -lm -lpthread
gcc -Denablemultithread -std=c99 -O3 -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 -O3 -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -lm -lpthread
gcc -Denablemultithread -std=c99 -O3 -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 -O3 -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -lm -lpthread
gcc -Denablemultithread -std=c99 -O3 -c MSalign11.c
gcc -Denablemultithread -std=c99 -O3 -c suboptalign11.c
gcc -Denablemultithread -std=c99 -O3 -c pairlocalalignmain.c
gcc -Denablemultithread -std=c99 -O3 -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 -O3 -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -lm -lpthread
gcc -Denablemultithread -std=c99 -O3 -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 -O3 -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -lm -lpthread
gcc -Denablemultithread -std=c99 -O3 -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 -O3 -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -lm -lpthread
gcc -Denablemultithread -std=c99 -O3 -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 -O3 -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -lm -lpthread
gcc -o maffttext2hex maffttext2hex.c -Denablemultithread -std=c99 -O3 -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -lm -lpthread
gcc -o hex2maffttext hex2maffttext.c -Denablemultithread -std=c99 -O3 -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -lm -lpthread
gcc -Denablemultithread -std=c99 -O3 -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 -O3 -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -lm -lpthread
gcc -Denablemultithread -std=c99 -O3 -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 -O3 -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -lm -lpthread
gcc -Denablemultithread -std=c99 -O3 -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 -O3 -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -lm -lpthread
gcc -Denablemultithread -std=c99 -O3 -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 -O3 -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -lm -lpthread
gcc -Denablemultithread -std=c99 -O3 -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 -O3 -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -lm -lpthread
gcc -Denablemultithread -std=c99 -O3 -c f2cl.c
gcc -o f2cl mtxutl.o io.o f2cl.o constants.o defs.o -Denablemultithread -std=c99 -O3 -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -lm -lpthread
gcc -Denablemultithread -std=c99 -O3 -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 -O3 -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -lm -lpthread
gcc -Denablemultithread -std=c99 -O3 -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 -O3 -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -lm -lpthread
gcc -Denablemultithread -std=c99 -O3 -c countlen.c
gcc -o countlen mtxutl.o io.o countlen.o defs.o -Denablemultithread -std=c99 -O3 -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -lm -lpthread
gcc -Denablemultithread -std=c99 -O3 -c seq2regtable.c
gcc -o seq2regtable mtxutl.o io.o seq2regtable.o defs.o -Denablemultithread -std=c99 -O3 -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -lm -lpthread
gcc -Denablemultithread -std=c99 -O3 -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 -O3 -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -lm -lpthread
gcc -Denablemultithread -std=c99 -O3 -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 -O3 -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -lm -lpthread
gcc -Denablemultithread -std=c99 -O3 -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 -O3 -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -lm -lpthread
gcc -Denablemultithread -std=c99 -O3 -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 -O3 -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -lm -lpthread
gcc -Denablemultithread -std=c99 -O3 -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 -O3 -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -lm -lpthread
gcc -O3 -D_FORTIFY_SOURCE=2 -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 -O3 -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -lm -lpthread
gcc -Denablemultithread -std=c99 -O3 -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 -O3 -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -lm -lpthread
gcc -Denablemultithread -std=c99 -O3 -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 -O3 -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -lm -lpthread
gcc -Denablemultithread -std=c99 -O3 -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 -O3 -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -lm -lpthread
gcc -Denablemultithread -std=c99 -O3 -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 -O3 -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -lm -lpthread
gcc -o version version.c -Denablemultithread -std=c99 -O3 -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -lm -lpthread
sed "s:_LIBDIR:/usr/lib/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.
make: Leaving directory '/build/mafft/src/mafft-7.487-with-extensions/core'
make: Entering directory '/build/mafft/src/mafft-7.487-with-extensions/extensions'
make CFLAGS1="" -C mxscarna_src
make[1]: Entering directory '/build/mafft/src/mafft-7.487-with-extensions/extensions/mxscarna_src'
g++ -I./probconsRNA -I./vienna -I./ -DNDEBUG -DNumInsertStates=1 -DVERSION="2.0" -O3 -std=c++98 -c Main.cc -o Main.o
g++ -I./probconsRNA -I./vienna -I./ -DNDEBUG -DNumInsertStates=1 -DVERSION="2.0" -O3 -std=c++98 -c McCaskill.cpp -o McCaskill.o
g++ -I./probconsRNA -I./vienna -I./ -DNDEBUG -DNumInsertStates=1 -DVERSION="2.0" -O3 -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" -O3 -std=c++98 -c seq2scs.cpp -o seq2scs.o
g++ -I./probconsRNA -I./vienna -I./ -DNDEBUG -DNumInsertStates=1 -DVERSION="2.0" -O3 -std=c++98 -c Globaldp.cpp -o Globaldp.o
g++ -I./probconsRNA -I./vienna -I./ -DNDEBUG -DNumInsertStates=1 -DVERSION="2.0" -O3 -std=c++98 -c postProcessings.cpp -o postProcessings.o
g++ -I./probconsRNA -I./vienna -I./ -DNDEBUG -DNumInsertStates=1 -DVERSION="2.0" -O3 -std=c++98 -c AlifoldMEA.cpp -o AlifoldMEA.o
g++ -L./probconsRNA -L./ -DNDEBUG -DNumInsertStates=1 -DVERSION="2.0" -O3 -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 '/build/mafft/src/mafft-7.487-with-extensions/extensions/mxscarna_src'
mv mxscarna_src/mxscarna mxscarnamod
cp mxscarnamod ../binaries
chmod 755 ../binaries/*
done.
make: Leaving directory '/build/mafft/src/mafft-7.487-with-extensions/extensions'
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