The p5-bioperl port is currently at v0.7.2 in the ports tree. However several releases have been made since then. The latest bioperl release is v1.2 This PR addresses the update to this latest release. Since there are some substantial changes I preferred to re-submit the whole port instead of diffs. The pkg-comment and pkg-descr, however, haven't changed since the original submission of the port. Note that this new port just handles the installation of bioperl and not of additional extra stuff (bioperl-gui, bioperl-corba-server, bioperl-corba-client). This is unlike the behaviour of the current port. The extra stuff, though still functional, had very little adoption among users, and does not appear to be currently supported/maintained. Also, I am requesting maintainership of the port. I have talked about this with Johann and he agrees with me taking maintainership of this port. How-To-Repeat: uudecode bioperl-1.2.shar.gz.uu gzip -d bioperl-1.2.shar.gz sh bioperl-1.2.shar
Lately Fernan Aguero told: > Since there are some substantial changes I preferred to re-submit the > whole port instead of diffs. The pkg-comment and pkg-descr, however, > haven't changed since the original submission of the port. i think committers would like to see diffs anyways. if they are too large put them on a webpage cheers simon -- /"\ http://corecode.ath.cx/#donate \ / \ ASCII Ribbon Campaign / \ Against HTML Mail and News
I'm now submitting recursive unified diffs as requested. I know, it was in the porter's handbook. It's just that it makes no sense to me to diff two different files. As i said, it's not that I've changed a thing here or there, I actually rewrote the Makefile. Anyway, here are the diffs, Fernan +----[ FreeBSD-gnats-submit@FreeBSD.org <FreeBSD-gnats-submit@FreeBSD.org> (21.Jan.2003 14:13): | | Thank you very much for your problem report. | It has the internal identification `ports/47303'. | The individual assigned to look at your | report is: freebsd-ports-bugs. | | You can access the state of your problem report at any time | via this link: | | http://www.freebsd.org/cgi/query-pr.cgi?pr=47303 | | >Category: ports | >Responsible: freebsd-ports-bugs | >Synopsis: Update biology/p5-bioperl to latest release | >Arrival-Date: Tue Jan 21 09:10:02 PST 2003 | | +----] -- F e r n a n A g u e r o http://genoma.unsam.edu.ar/~fernan
Lately Fernan Aguero told: > diff -ruN p5-bioperl.new/Makefile p5-bioperl/Makefile > --- p5-bioperl.new/Makefile Wed Jan 22 10:01:22 2003 > +++ p5-bioperl/Makefile Fri Jan 25 08:46:09 2002 woo! reverse diff is hard to read, but here we go: [...] > -MASTER_SITES= ftp://bioperl.org/pub/DIST/ \ > - http://bioperl.org/DIST \ ^ add / [...] > -DISTFILES= ${DISTNAME}${EXTRACT_SUFX} is that needed? [...] > # These are all run-time dependencies, but listing them in ${BUILD_DEPENDS} > # prevents a flood of build-time warnings. > -# > -# Text::Shellwords does not appear to be in the ports tree > -# and is required by Bio::Graphics:FeatureFile.pm > -# > -# DB_File is required to access Berkeley DB > -# by Bio::DB::Flat and Bio::SeqFeature::Collection > -# but is not in the ports tree > -# > -# perhaps they're included with perl? > -# let me know if they are is this optional or mandatory? if so they need to be ported [...] > -.for doc in AUTHORS BUGS Changes DEPRECATED FAQ INSTALL LICENSE PLATFORMS README > - ${INSTALL_MAN} ${WRKSRC}/${doc} ${DOCSDIR} better use ${INSTALL_DATA}? cheers simon -- /"\ http://corecode.ath.cx/#donate \ / \ ASCII Ribbon Campaign / \ Against HTML Mail and News
+----[ Simon 'corecode' Schubert <corecode@corecode.ath.cx> (22.Jan.2003 11:14): | | Lately Fernan Aguero told: | | > diff -ruN p5-bioperl.new/Makefile p5-bioperl/Makefile | > --- p5-bioperl.new/Makefile Wed Jan 22 10:01:22 2003 | > +++ p5-bioperl/Makefile Fri Jan 25 08:46:09 2002 | | woo! reverse diff is hard to read, but here we go: I just followed the porter's handbook ... is it 'reverse' or 'recursive'? If you ask about --- for the new files and +++ for the old ones ... I can change the order, but again a clear example was in the handbook and this time I did want to follow it precisely :) | [...] | > -MASTER_SITES= ftp://bioperl.org/pub/DIST/ \ | > - http://bioperl.org/DIST \ | ^ add / OK | [...] | > -DISTFILES= ${DISTNAME}${EXTRACT_SUFX} | | is that needed? perhaps this got over from the old Makefile. not needed anymore. | [...] | > # These are all run-time dependencies, but listing them in ${BUILD_DEPENDS} | > # prevents a flood of build-time warnings. | > -# | > -# Text::Shellwords does not appear to be in the ports tree | > -# and is required by Bio::Graphics:FeatureFile.pm | > -# | > -# DB_File is required to access Berkeley DB | > -# by Bio::DB::Flat and Bio::SeqFeature::Collection | > -# but is not in the ports tree | > -# | > -# perhaps they're included with perl? | > -# let me know if they are | | is this optional or mandatory? if so they need to be ported Let me explain. bioperl is not just a module it is a whole-bunch of modules with complex inter-dependencies. So, the answer to the question of them being optional is, yes, they don't prevent the installation, there is no build-time warnings (at least in my system, I'd like to see other people testing). I just copied what the bioperl release says about its dependencies (it would not be surprising, either, that some dependency from an older release was not removed from the README). However, even if there are no build-time warnings, perhaps some issues may arise later. For example, if you plan to use, say, Bio::Graphics::FeatureFile.pm, then perhaps you do need it. I put this in question marks in the Makefile, because I don't know if these modules are 'basic' or part of the standard perl installation. Even though there are no ports for them, I had them installed in my system (again perhaps as a result of some now forgotten manual installation, that's why I'd like someone else to test it). If, after all, they need to be ported, I can try port them. | [...] | > -.for doc in AUTHORS BUGS Changes DEPRECATED FAQ INSTALL LICENSE PLATFORMS README | > - ${INSTALL_MAN} ${WRKSRC}/${doc} ${DOCSDIR} | | better use ${INSTALL_DATA}? I'm not an experienced porter, perhaps ${INSTALL_DATA} is OK. Should I resubmit everything? Or is this post enough to commit the port? Fernan | | cheers | simon | | -- | /"\ http://corecode.ath.cx/#donate | \ / | \ ASCII Ribbon Campaign | / \ Against HTML Mail and News | +----] -- F e r n a n A g u e r o http://genoma.unsam.edu.ar/~fernan
Lately Fernan Aguero told: > Should I resubmit everything? Or is this post enough to > commit the port? depends :) i'd either add the final diff (for that, change order of old/new) as followup to the audit trail or just wait for a nice committer to contact you... cheers simon -- /"\ http://corecode.ath.cx/#donate \ / \ ASCII Ribbon Campaign / \ Against HTML Mail and News
Here we go, recursive diff but now reversing the order and correcting a few things. Thanks, Fernan +----[ FreeBSD-gnats-submit@FreeBSD.org <FreeBSD-gnats-submit@FreeBSD.org> (21.Jan.2003 14:13): | | Thank you very much for your problem report. | It has the internal identification `ports/47303'. | The individual assigned to look at your | report is: freebsd-ports-bugs. | | You can access the state of your problem report at any time | via this link: | | http://www.freebsd.org/cgi/query-pr.cgi?pr=47303 | | >Category: ports | >Responsible: freebsd-ports-bugs | >Synopsis: Update biology/p5-bioperl to latest release | >Arrival-Date: Tue Jan 21 09:10:02 PST 2003 | | +----] -- F e r n a n A g u e r o http://genoma.unsam.edu.ar/~fernan
Responsible Changed From-To: freebsd-ports-bugs->wjv Over to maintainer.
Fernan, are you still interested in taking over this port? Is this still the current version? The last time I email wjv@ he said that real life was taking priority over FreeBSD work right now, so I'm going to try to pitch in here.
State Changed From-To: open->feedback Set to feedback to note that I'm going to try to track the state of this PR.
Responsible Changed From-To: wjv->linimon I've heard rumours that linimon@ is busy with these ones.
State Changed From-To: feedback->closed Committed, thanks for being so patient, and volunteering to take over this port.