Bug 74331 - update biology/hmmer and take maintainership
Summary: update biology/hmmer and take maintainership
Status: Closed FIXED
Alias: None
Product: Ports & Packages
Classification: Unclassified
Component: Individual Port(s) (show other bugs)
Version: Latest
Hardware: Any Any
: Normal Affects Only Me
Assignee: freebsd-ports-bugs (Nobody)
Depends on:
Reported: 2004-11-24 20:00 UTC by Fernan Aguero
Modified: 2004-11-25 22:37 UTC (History)
1 user (show)

See Also:

hmmer.diff (5.29 KB, patch)
2004-11-24 20:00 UTC, Fernan Aguero
no flags Details | Diff

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Description Fernan Aguero 2004-11-24 20:00:45 UTC

	Update HMMER to the latest available version.
	While here, add an option (WITH_PVM) so that cluster users can build
	hmmer with pvm support.

	CONFIGURE_ARGS have been set to the defaults used by the software
	authors (see http://hmmer.wustl.edu/#download). This includes enabling
	threads by default. On my FreeBSD-4.10 builds do fine. 
	I have not tested this under 5.x myself. However, it appears that the
	thread checks in ${WRKSRC}/configure have been rewritten. 
	I cannot judge if this will work in 5.x, though, due to my limited
	knowledge of this issue and my lack of experience with 5.x

	But I'm sure that any fellow committer reading this can do better than
	me at it :)  (look for 'FreeBSD' within the file)
Comment 1 Fernan Aguero 2004-11-25 12:23:35 UTC
I just wanted to add something to the comments made before
by me on the threads issue. Perhaps this serves to see if
the port will build and run fine on 5.x.

I contacted the software author asking for clarification on
the threads issue and he thus replied:

"Note that they were not patching HMMER per se here [talking
about the patch-configure in 2.2.g], but a copy of the
ACX_PTHREAD macro from the autoconf macro archive, which I
include in my configure.ac. (so they oughtto've notified the
ACX_PTHREAD author?) HMMER's relying on autoconf to get it
the pthreads configuration right on all platforms. If any
more problems arise here, check against the latest version
of ACX_PTHREAD in the archive; if I need to update my copy
of the macro in HMMER, let me know. That is, it would be
best *not* to patch HMMER's copy of ACX_PTHREAD; better to
patch ACX_PTHREAD itself, in the autoconf macro archive,
then update HMMER's copy."


Fernán Agüero | Instituto de Investigaciones Biotecnológicas
email         | fernan at { iib.unsam.edu.ar , mail.retina.ar }
wwww          | http://genoma.unsam.edu.ar/~fernan
phone, fax    | +54 11 { 4580-7255 ext 310, 4752-9639 }
Comment 2 Sergey Matveychuk freebsd_committer 2004-11-25 22:36:21 UTC
State Changed
From-To: open->closed

Committed, thanks! 
pkg-plist fixed