ports/51709: Port update (maintainer): biology/ncbi-toolkit

[Tony Maher]

Hello,

thanks for looking at this.

> gcc -pipe -pthread -O -c  -I../include -I/usr/X11R6/include -L/usr/X11R6/lib -DWIN_MOTIF ncbimsg.c
> ncbimsg.c: In function `GetOneChar':
> ncbimsg.c:498: syntax error before "rfds"
> ncbimsg.c:500: `rfds' undeclared (first use in this function)
> ncbimsg.c:500: (Each undeclared identifier is reported only once
> ncbimsg.c:500: for each function it appears in.)
> *** Error code 1

This error messages is very familiar!  Did the patches apply correctly?
The patch file "files/patch-ncbilcl.fbd" fixes this bug by adding 

#define _XOPEN_SOURCE 600  /* req. for 5.0 */
#include <sys/select.h>    /* req. for 5.0.  fd_set def. moved from types.h */

(and it does not affect building on 4.8-stable).

I have just reapplied the patch I sent in on the original copy of ncbi-toolkit
and scp ncbi-toolkit to the 5.0 machine. I have just rebuilt on both my
stable and current machines without any problems.
And to be extra sure I have downloaded patch of web page and compared it to
my copy - they are identical.

thanks
--
tonym