Help with blast compilation on Linux (gish)

David Pincus enzyme at athena.mit.edu
Fri Oct 27 08:48:03 EST 1995


Hi there... I'm trying to get the Blast package up and running 
on my Linux machine and am running into difficulties compiling
the gish package.

I was able to get the ncbi toolkit to compile with only one warning message.
but gish won't compile. The error is as follows:

biodrive:/usr/GDE/gish% make all
cd mem; make  CC="cc" CCOPT="-O" INCLUDE="-I../include -I../ncbi/include" GISHLIB="../lib/libgish.a" ARFLAGS="cru"
make[1]: Entering directory `/usr/GDE/gish/mem'
cc -O -I../include -I../ncbi/include -c   -c mem_allo.c -o mem_allo.o
In file included from mem_allo.c:2:
../include/gishlib.h:89: conflicting types for `basename'
/usr/local/include/unistd.h:644: previous declaration of `basename'
make[1]: *** [mem_allo.o] Error 1
make[1]: Leaving directory `/usr/GDE/gish/mem'
make: *** [comp/mem] Error 2


now line 2 of mem_allo.c includes gishlib.h... whose line 89 is:

CharPtr LIBCALL basename PROTO((CharPtr fname, CharPtr extension));

and line 644 of unistd.h is:

extern char     *basename __P((__const char *__name));

now i am fairly familiar with unix but my C is severely lacking, 
Any help resolving this would be much appreciated.  I'm using the current
release of gish (fresh from ncbi) and gish's makefile I left untouched.

Much thanx

David Pincus




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