The standard build of ncbi-toolkit does not produce the executable bl2seq, which is part of the toolkit. The source bl2seq.c is present under ncbi/build/, it is not compiled, and obviously it is not installed (bin/bl2seq is not listed in pkg-plist). However, I do remember using bl2seq about a year ago, and can see it in an old pkg-plist. The ncbi-toolkit has been updated, so perhaps this is already fixed in the new version?. I'm downloading the tarball now, but will not have time to work on it until late next week. How-To-Repeat: cd /usr/ports/biology/ncbi-toolkit make ls work/ncbi/build/bl2seq* you'll see just bl2seq.c (not bl2seq.o, not bl2seq)
Please submit patches :) Volker
State Changed From-To: open->feedback Requested patches.
State Changed From-To: feedback->analyzed Submitter is working on a fix.
+----[ 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
+----[ Volker Stolz <vs@FreeBSD.org> (25.Jun.2004 16:43): | | Synopsis: biology/ncbi-toolkit does not build bl2seq | +----] Grrr, I forgot to add the patch. Here it is, Fernan
State Changed From-To: analyzed->open Feedback received
Dear maintainer of FreeBSD port biology/ncbi-toolkit, please disregard my previous message and instead take a look at patch in http://www.freebsd.org/cgi/query-pr.cgi?q=67735 Do you approve this update? -- Pav Lucistnik <pav@oook.cz> <pav@FreeBSD.org> The number you dialed is imaginary. Please turn your phone by 90 degrees and try again.
State Changed From-To: open->feedback Asked for maintainer's approval
Responsible Changed From-To: freebsd-ports-bugs->pav Handle
+----[ Pav Lucistnik <pav@FreeBSD.org> (19.Mar.2005 15:15): | | Synopsis: biology/ncbi-toolkit does not build bl2seq | | State-Changed-From-To: open->feedback | State-Changed-By: pav | State-Changed-When: Sat Mar 19 18:13:17 GMT 2005 | State-Changed-Why: | Asked for maintainer's approval | +----] Hi Pav, the current maintainer has already stated that he is no longer working in the field and agrees on having the port maintained by me: http://lists.freebsd.org/pipermail/freebsd-ports-bugs/2004-June/035351.html Fernan
State Changed From-To: feedback->closed Patch committed, thanks!