need help from a C programmer

Fernan Aguero fernan at iib.unsam.edu.ar
Thu Dec 15 11:11:29 PST 2005


Hi!

I need help from someone with experience in C programming,
and knowledge of FreeBSD specifics.

I'm trying to build Jim Kent´s BLAT on FreeBSD
http://www.soe.ucsc.edu/~kent/src/blat33Src.zip

I've already got some progress, and a few patches, with help
from the author and UCSC staff. But I've come to an obstacle
that I (no C knowledge) can't fix. 

[ ... ]
cd hg/pslPretty && gmake
gmake[1]: Entering directory `/scratch/fernan/ports/blat/work/blatSrc/hg/pslPret
ty'
gcc34 -ggdb -o ../../bin/i386/pslPretty pslPretty.o ../../lib/i386/jkweb.a -lm
pslPretty.o: In function `prettyOutString':
pslPretty.o(.text+0x668): undefined reference to `__ctype_b_loc'
pslPretty.o: In function `pslPretty':
pslPretty.o(.text+0x116d): undefined reference to `stdout'
collect2: ld returned 1 exit status
gmake[1]: *** [pslPretty] Error 1

The authors also are intrigued: "stdout at least is about as
basic and common of a C symbol as you can get. It looks
like pslPretty isn't using ctype directly, but through
isalpha() which is nearly as common as stdout"

I, can't help much, but perhaps someone in the list has some
clue as to what might be going on?

My draft port is here
http://genoma.unsam.edu.ar/~fernan/freebsd/blat/blat.shar.gz

And the complete output here
http://genoma.unsam.edu.ar/~fernan/freebsd/blat/blat.out.gz

Thanks in advance,

Fernan


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