ports/67735: biology/ncbi-toolkit does not build bl2seq

[Fernan Aguero]

The following reply was made to PR ports/67735; it has been noted by GNATS.

From: Fernan Aguero <fernan at iib.unsam.edu.ar>
To: Volker Stolz <vs at FreeBSD.org>
Cc: FreeBSD GNATS PR Submission <freebsd-gnats-submit at FreeBSD.org>
Subject: Re: ports/67735: biology/ncbi-toolkit does not build bl2seq
Date: Thu, 17 Mar 2005 18:35:04 -0300

 +----[ Volker Stolz <vs at FreeBSD.org> (25.Jun.2004 16:43):
 |
 | Synopsis: biology/ncbi-toolkit does not build bl2seq
 | 
 | State-Changed-From-To: feedback->analyzed
 | State-Changed-By: vs
 | State-Changed-When: Fri Jun 25 13:42:40 GMT 2004
 | State-Changed-Why: 
 | Submitter is working on a fix.
 | 
 | http://www.freebsd.org/cgi/query-pr.cgi?pr=67735
 |
 +----]
 
 Hi Volker, here I am again. I'm sorry for taking so long.
 I'm sure you have already forgotten everything about this
 PR, so I'm including a reminder of what we talked about.
 It's mostly all in this thread:
 http://lists.freebsd.org/pipermail/freebsd-ports-bugs/2004-June/034653.html
 
 As discussed before I'm taking maintainership of the port.
 The changes I've made are detailed below:
 
 The previous port accumulated changes in the form of patches
 that were stored under files/. Some of them are no longer
 needed (patch-bl2seq, patch-ncbilcl.fbd). And for the
 remaining patches (patch-aa, Makefile) I decided that it was
 clearer to have them rewritten into the port's Makefile.
 Below is a summary of what has changed and what has just
 been moved into the Makefile:
 
 o the port has been updated to the latest release which includes BLAST
   2.2.10 from Oct 20th, 2004 (20041020). See
   http://www.ncbi.nih.gov/blast/blast_whatsnew.shtml
   
 o the list of executables has been updated. See ports/67735 which
   complains about bl2seq not being installed. This also makes
   files/patch-bl2seq obsolete. Moreover the executables
   have now been separated into categories, which make sense (we follow
   Aaron Ucko the Debian package maintainer who also happens to work at the
   NCBI, and thus has a more complete vision of the toolkit). Perhaps in
   the future we can let the user choose between installation of a full
   toolkit or just some parts of it.
 
 o a list of man pages and mlinks have been added (not present in the
   previous port versions.
 
 o the do-build and do-install targets were previously introduced in the
   form of patches: files/Makefile and files/patch-aa. They are now
   reproduced within the port's Makefile
 
 o files/patch-ncbilcl.fbd is failing to apply.
   The file ncbilcl.fbd is a system dependent header version for FreeBSD
   The current revision of ${WRKSRC}/corelib/ncbilcl.fbd now includes the
   last change previously applied by the patch (select.h) but not the first one
   (define _XOPEN_SOURCE). The two changes included in the patch were
   labeled as 'req. for 5.0'. However, I'm unable to test these changes,
   as the toolkit is building fine for me under i386, 4.10-RELEASE-p5
   I've ommitted the patch and will see what happens in the build cluster
   on FreeBSD-5. If necessary will reroll the patch again.
 
 o blastcl3?
   On my box, blasctl3 is built fine, but drops the
   connections against the NCBI servers. I don't know if this
   is FreeBSD specific. The ncbi staff is already aware of
   this but we'll need more testers to reproduce it.
 
 o set DIST_SUBDIR to the distribution date (PORTVERSION) in order to
   distinguish the different distfiles