Date: Thu, 17 Mar 2005 21:40:06 GMT From: Fernan Aguero <fernan@iib.unsam.edu.ar> To: freebsd-ports-bugs@FreeBSD.org Subject: Re: ports/67735: biology/ncbi-toolkit does not build bl2seq Message-ID: <200503172140.j2HLe6wp005826@freefall.freebsd.org>
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The following reply was made to PR ports/67735; it has been noted by GNATS. From: Fernan Aguero <fernan@iib.unsam.edu.ar> To: Volker Stolz <vs@FreeBSD.org> Cc: FreeBSD GNATS PR Submission <freebsd-gnats-submit@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@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
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