Date: Thu, 24 Jun 2004 09:57:16 -0300 From: Fernan Aguero <fernan@iib.unsam.edu.ar> To: Volker Stolz <vs@freebsd.org> Cc: tonym@biolateral.com.au Subject: Re: ports/67735: biology/ncbi-toolkit does not build bl2seq Message-ID: <20040624125716.GB1310@iib.unsam.edu.ar> In-Reply-To: <200406142133.i5ELXjYK046396@freefall.freebsd.org> References: <200406142133.i5ELXjYK046396@freefall.freebsd.org>
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+----[ Volker Stolz <vs@freebsd.org> (14.Jun.2004 18:35): | | Synopsis: biology/ncbi-toolkit does not build bl2seq | | State-Changed-From-To: open->feedback | State-Changed-By: vs | State-Changed-When: Mon Jun 14 21:33:16 GMT 2004 | State-Changed-Why: | Requested patches. | | http://www.freebsd.org/cgi/query-pr.cgi?pr=67735 | +----] Hi Volker, I guess that I've narrowed the problem and will test it now. I've also taken the opportunity to update the port to the latest version (2004.06.16). However, to finish and send the patches, I need to get something clear (because I'm not the maintainer) and any change that I propose will have to be approved by him. The ncbi-toolkit basically doesn't need to be 'ported' because it builds fine without using the ports system. However, it does not have any install target, so the FreeBSD port is just essentially providing this missing functionality. The patch-aa in the port contains an addition to the ncbi-toolkit makefile (actually called makeall.unx), that provides three install targets: one for binaries, one for include files and one for libraries. The two latter targets install files by using globs (*.h, *.a), however the install target for binaries only installs some of the binaries that are built (only those listed in the patch itself (see $EXE). bl2seq was not listed in EXE (and thus not installed) even though it is built by default (i.e. appears in ${WRKSRC}/bin together with all other executables). Searching the list, showed that bl2seq was once listed in EXE, and so perhaps was inadvertently removed: http://lists.freebsd.org/pipermail/freebsd-ports-bugs/2003-May/002610.html My question is (an so I'm CCing the maintainer): what was the reason for creating such a list and not just installing all the executables under ${WRKSRC}/bin? May I just fix the port by installing everything under ${WRKSRC}/bin? This would have the added benefit of absorb any future changes in the toolkit. We install what was built. For instance, the updated port does not build fmerge, however fmerge is listed in EXE, and thus the installation step chokes on this and aborts. This would not happen if we take the approach mentioned above. (BTW I'm trying to see why it was not build ... I don't see anything that looks like an error, will check if it was retired by the NCBI). I will test the updated port and finish checking things for submission. Fernan -- F e r n a n A g u e r o http://genoma.unsam.edu.ar/~fernan
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