Problems compiling Fasta and Blast under Linux

Les Grivell les at amc.uva.nl
Tue Jul 5 07:12:41 EST 1994


Has anyone successfully compiled Fasta and or Blast under Linux?
If so, I would be grateful fo any advice: attempts so far have resulted
in the following output.

Fasta
cc -g -DUNIX -DBIGMEM -DHZ=100 -c time.c
time.c:19: conflicting types for `stime'
/usr/include/time.h:53: previous declaration of `stime'
make: *** [time.o] Error 1
cc  -g -DUNIX -DBIGMEM -c -DMAXSAV=10 urdf.c
urdf.c: In function `main':
urdf.c:152: too few arguments to function `exit'
urdf.c:157: too few arguments to function `exit'
urdf.c:216: too few arguments to function `exit'
urdf.c:239: too few arguments to function `exit'
urdf.c: In function `allocdiag':
urdf.c:962: too few arguments to function `exit'
make: *** [urdfn.o] Error 1
cc -g -DUNIX -DBIGMEM -c bestscor.c
bestscor.c: In function `main':
bestscor.c:55: too few arguments to function `exit'
bestscor.c:60: too few arguments to function `exit'
make: *** [bestscor.o] Error 1
cc -g -DUNIX -DBIGMEM -c lalign.c
lalign.c: In function `initseq':
lalign.c:351: too few arguments to function `exit'
make: *** [lalign.o] Error 1
cc -g -DUNIX -DBIGMEM -DTPLOT -c lalign.c
lalign.c: In function `initseq':
lalign.c:351: too few arguments to function `exit'
make: *** [plalign.o] Error 1
cc  -g -DUNIX -DBIGMEM -c -DMAXSAV=10 urss.c
urss.c: In function `main':
urss.c:96: too few arguments to function `exit'
urss.c:101: too few arguments to function `exit'
urss.c:153: too few arguments to function `exit'
urss.c:174: too few arguments to function `exit'
make: *** [urss.o] Error 1
cc -g -DUNIX -DBIGMEM -c align.c
align.c: In function `initseq':
align.c:291: too few arguments to function `exit'
make: *** [align.o] Error 1
make: Target `all' not remade because of errors.
 
Blast
cd lib; make   CC="gcc" CCOPT="-g" OPTIONS="  -DREFINED_STATS "
make[1]: Entering directory `/home/les/blaststuff/blast/lib'
gcc -g -I../include -I../ncbi/include -I../gish/include -I../dfa -DREFINED_STATS
    -c banner.c -o banner.o
In file included from banner.c:4:
../include/blast.h:169: warning: `NCHUNKS' redefined
../gish/include/gish.h:96: warning: this is the location of the previous definit
ion
In file included from banner.c:2:
../gish/include/gish.h:129: parse error before `key_t'
../gish/include/gish.h:129: warning: no semicolon at end of struct or union
../gish/include/gish.h:133: parse error before `}'
../gish/include/gish.h:133: warning: data definition has no type or storage clas
s
../gish/include/gish.h:152: parse error before `shm_dat'
../gish/include/gish.h:152: warning: no semicolon at end of struct or union
../gish/include/gish.h:153: warning: data definition has no type or storage clas
s
In file included from banner.c:3:
../gish/include/gishlib.h:134: parse error before `*'
../gish/include/gishlib.h:134: warning: data definition has no type or storage c
lass
../gish/include/gishlib.h:135: parse error before `shm_mkkey'
../gish/include/gishlib.h:135: warning: data definition has no type or storage c
lass
../gish/include/gishlib.h:136: parse error before `*'
../gish/include/gishlib.h:137: parse error before `*'
../gish/include/gishlib.h:137: warning: data definition has no type or storage c
lass
../gish/include/gishlib.h:140: parse error before `key'
../gish/include/gishlib.h:143: parse error before `*'
../gish/include/gishlib.h:143: warning: data definition has no type or storage c
lass
../gish/include/gishlib.h:144: parse error before `*'
../gish/include/gishlib.h:145: parse error before `*'
../gish/include/gishlib.h:146: parse error before `*'
../gish/include/gishlib.h:147: parse error before `MFILE'
../gish/include/gishlib.h:148: parse error before `MFILE'
../gish/include/gishlib.h:149: parse error before `*'
../gish/include/gishlib.h:150: parse error before `*'
../gish/include/gishlib.h:153: parse error before `*'
../gish/include/gishlib.h:154: parse error before `*'
../gish/include/gishlib.h:155: parse error before `*'
../gish/include/gishlib.h:156: parse error before `*'
../gish/include/gishlib.h:157: parse error before `*'
In file included from ../include/blast.h:187,
                 from banner.c:4:
../include/shmutil.h:14: `shm_dat' redeclared as different kind of symbol
../gish/include/gish.h:133: previous declaration of `shm_dat'
../include/shmutil.h:14: warning: `shm_dat' was declared `extern' and later `sta
tic'
../include/shmutil.h:19: conflicting types for `shm_attfile'
../gish/include/gishlib.h:134: previous declaration of `shm_attfile'
../include/shmutil.h:21: conflicting types for `shm_loadfile'
../gish/include/gishlib.h:137: previous declaration of `shm_loadfile'
../include/shmutil.h:23: parse error before `key'
In file included from banner.c:4:
../include/blast.h:362: `MFILE' redeclared as different kind of symbol
../gish/include/gish.h:153: previous declaration of `MFILE'
../include/blast.h:362: warning: `MFILE' was declared `extern' and later `static
'
../include/blast.h:364: conflicting types for `mfil_open'
../gish/include/gishlib.h:143: previous declaration of `mfil_open'
../include/blast.h:490: conflicting types for `fatal'
../gish/include/gishlib.h:110: previous declaration of `fatal'
make[1]: *** [banner.o] Error 1
make[1]: Leaving directory `/home/les/blaststuff/blast/lib'
make: *** [always] Error 1








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