Date: Wed, 22 Jan 2003 07:00:17 -0800 (PST) From: Fernan Aguero <fernan@iib.unsam.edu.ar> To: freebsd-ports-bugs@FreeBSD.org Subject: Re: ports/47303: Update biology/p5-bioperl to latest release Message-ID: <200301221500.h0MF0Hvl060716@freefall.freebsd.org>
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The following reply was made to PR ports/47303; it has been noted by GNATS. From: Fernan Aguero <fernan@iib.unsam.edu.ar> To: "Simon 'corecode' Schubert" <corecode@corecode.ath.cx> Cc: FreeBSD-gnats-submit@FreeBSD.org, freebsd-ports-bugs@FreeBSD.org Subject: Re: ports/47303: Update biology/p5-bioperl to latest release Date: Wed, 22 Jan 2003 11:57:26 -0300 +----[ 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 To Unsubscribe: send mail to majordomo@FreeBSD.org with "unsubscribe freebsd-ports-bugs" in the body of the message
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