config.hは以下のようになっている。
# Edit the configuration variables below to match your system. The default # values given here should work on GNU/Linux systems. CC= gcc CFLAGS= -O2 -Wall # Notes: clang can replace gcc above; # for icc (version 13.0.1) you need to use -O1 in cflags. # The yacc compiler is typically "yacc" (for the *real* yacc), "byacc" # (for the Berkeley equivalent) or "bison -y" (to get yacc compatible output # from bison). Note that /bin/yacc is sometimes a symlink to bison; on # such systems you need the -y flag. # Note that you need to get version 1.875 or later of bison. Since this # was released in 2003, that should not be much of a problem.... # Go to http://www.gnu.org/software/bison/bison.html for more information. YACC = bison -y # The GNU version of lex is called flex. So the following variable is # either "lex" or "flex", depending upon your system. LEX = flex # Uncomment & use these 3 lines to use Genbank in addition to FASTN: # GBHOME=/home/macke/gensearch # GBLIB=$(GBHOME)/libgb.a # CFLAGS=-O2 -DUSE_GENBANK
you may need to locate the C-compiler, lex or yacc, and set compiler
flags.
と説明があったのでbisonをインストールしておく。
$ brew install bison ・・・ bison is keg-only, which means it was not symlinked into /usr/local, because macOS already provides this software and installing another version in parallel can cause all kinds of trouble. If you need to have bison first in your PATH run: echo 'export PATH="/usr/local/opt/bison/bin:$PATH"' >> ~/.bash_profile For compilers to find bison you may need to set: export LDFLAGS="-L/usr/local/opt/bison/lib"
言われたとおりPATHを通しておく。
lexもいるようなので
$ brew install flex ・・・ flex is keg-only, which means it was not symlinked into /usr/local, because macOS already provides this software and installing another version in parallel can cause all kinds of trouble. If you need to have flex first in your PATH run: echo 'export PATH="/usr/local/opt/flex/bin:$PATH"' >> ~/.bash_profile For compilers to find flex you may need to set: export LDFLAGS="-L/usr/local/opt/flex/lib" export CPPFLAGS="-I/usr/local/opt/flex/include"
これまたPATHを通しておく。
さてmakeしてみる。
$ make
cd src; make
gcc -O2 -Wall -c -o rnamot.o rnamot.c
flex rmlex.l
bison -y -d -v -t rmgrm.y
rmgrm.y: warning: 1 shift/reduce conflict [-Wconflicts-sr]
gcc -O2 -Wall -c -o compile.o compile.c
gcc -O2 -Wall -c -o dbutil.o dbutil.c
gcc -O2 -Wall -c -o dump.o dump.c
gcc -O2 -Wall -c -o efn.o efn.c
gcc -O2 -Wall -c -o efn2.o efn2.c
gcc -O2 -Wall -c -o errormsg.o errormsg.c
gcc -O2 -Wall -c -o find_motif.o find_motif.c
gcc -O2 -Wall -c -o getargs.o getargs.c
gcc -O2 -Wall -c -o log.o log.c
gcc -O2 -Wall -c -o mm_regexp.o mm_regexp.c
./mk_dumpnode.h.sh y.tab.h > dumpnode.h
gcc -O2 -Wall -c -o node.o node.c
gcc -O2 -Wall -c -o preprocessor.o preprocessor.c
gcc -O2 -Wall -c -o regexp.o regexp.c
regexp.c:344:15: warning: implicit conversion from 'int' to 'char' changes value from 255
to -1 [-Wconstant-conversion]
*ep++ = 255;
~ ^~~
1 warning generated.
gcc -O2 -Wall -c -o score.o score.c
gcc -O2 -Wall -c -o split.o split.c
gcc -O2 -Wall -c -o y.tab.o y.tab.c
y.tab.c:1601:16: warning: implicit declaration of function 'yylex' is invalid in C99
[-Wimplicit-function-declaration]
yychar = yylex ();
^
y.tab.c:2631:7: warning: implicit declaration of function 'yyerror' is invalid in C99
[-Wimplicit-function-declaration]
yyerror (YY_("syntax error"));
^
y.tab.c:2742:3: warning: implicit declaration of function 'yyerror' is invalid in C99
[-Wimplicit-function-declaration]
yyerror (YY_("memory exhausted"));
^
In file included from rmgrm.y:545:
lex.yy.c:1691:17: warning: unused function 'yyunput' [-Wunused-function]
static void yyunput (int c, char * yy_bp )
^
4 warnings generated.
gcc -O2 -Wall -o rnamotif rnamot.o compile.o dbutil.o dump.o efn.o efn2.o errormsg.o find_motif.o getargs.o log.o mm_regexp.o node.o preprocessor.o regexp.o score.o split.o y.tab.o -lm
gcc -O2 -Wall -c -o rmprune.o rmprune.c
gcc -O2 -Wall -o rmprune rmprune.o split.o log.o
gcc -O2 -Wall -c -o rm2ct.o rm2ct.c
gcc -O2 -Wall -o rm2ct rm2ct.o split.o log.o
gcc -O2 -Wall -c -o rmfmt.o rmfmt.c
gcc -O2 -Wall -o rmfmt rmfmt.o split.o log.o
gcc -O2 -Wall -c -o efn_drv.o efn_drv.c
gcc -O2 -Wall -o efn_drv efn_drv.o efn.o split.o log.o -lm
gcc -O2 -Wall -c -o efn2_drv.o efn2_drv.c
gcc -O2 -Wall -o efn2_drv efn2_drv.o efn2.o split.o log.o -lm warningはでたものの、makeはできたらしく、srcディレクトリに色々できている。
testを走らせてみる。
$ make test cd test; make ===================================================== Running nanlin test: nanlin.descr: complete descr length: min/max = 54/58 PASSED ===================================================== Running pk1 test: pk1.descr: complete descr length: min/max = 22/46 PASSED ===================================================== Running pk_j1+2 test: pk_j1+2.descr: complete descr length: min/max = 66/118 PASSED ===================================================== Running qu+tr test: qu+tr.descr: complete descr length: min/max = 45/101 PASSED ===================================================== Running score.1 test: score.1.descr: complete descr length: min/max = 18/24 PASSED ===================================================== Running score.2 test: score.2.descr: complete descr length: min/max = 25/40 PASSED ===================================================== Running trna test: trna.descr: complete descr length: min/max = 63/95 PASSED ===================================================== Running mp.ends test: mp.ends.descr: complete descr length: min/max = 20/24 PASSED ===================================================== Running efn test: ・・・ < SEU28SRRNA -21.400 0 152 28 tcaac cgg . ggcg g actg tcct cagt g cgcc . ccg cccgc < TTERRDA -21.700 0 59 27 cgagt cgc . gcgc . ccgg ggcg ccgg . gcgc g gcg cacgg < MEPMETH -22.100 0 1234 32 acaat ggga . tcc ga cccc gaaa gggg ga gga aa tccc ctaaa < MVORR16SY -22.700 0 1201 32 acaat ggga . cgc ga cccc gaaa gggg ga gcg aa tccc ctaaa < THCLRRNA -23.200 0 261 22 ctgaa cc . ctc . cggg gaaa cccg . gag . gg gatgt < HRTSSRRNA -24.400 0 667 31 tcttt agtg gt ccgc . ccc ttcg ggg a gcgg gt cact ggcct FAILED (possibly; see if diffs above look OK)
FAILEDで終わった。なにかまずいのか。
echo 'export EFNDATA="/Users/kuro/local/bin/rnamotif-master/efndata"' >> ~/.bash_profile
これでヨシ。
