New version released to developers. Reproducible: Always Steps to Reproduce:
Created attachment 49477 [details] Initial Ebuild Installs clean on my x86.
please make attachments as plain/text.
sorry. I set it as auto assuming that it would be recognized correctly.
There are a lot of updates to bioperl-run as well. That should be updated too. Would be nice to have a bioperl-cvs. ;)
1.5.1 or bioperl and bioperl-run are now available. http://news.open-bio.org/archives/2005_10.html#000084
1.5 or better is needed for generic-genome-browser-1.64 and this works fine on my amd64 box also
(In reply to comment #6) Just tried building bioperl-1.5.1 with this ebuild and noticed that a few of the dependencies have moved from dev-perl to perl-core. I've adjusted the ebuild and attached it. Builds fine on x86
Created attachment 89596 [details] updated ebuild for bioperl-1.5.1
The tarball of a current cvs snapshot can be downloaded from http://code.open-bio.org/cgi/viewcvs.cgi/bioperl-live/bioperl-live.tar.gz?tarball=1 Thsi is the "Download tarball" link from http://code.open-bio.org/cgi/viewcvs.cgi/bioperl-live/
With the updated ebuild I am getting: # ebuild bioperl-1.5.1.ebuild digest /usr/portage/sci-biology/bioperl/bioperl-1.5.1.ebuild: line 7: CATEGORY: readonly variable >>> Downloading 'http://distfiles.gentoo.org/distfiles/bioperl-1.5.1.tar.bz2' --23:59:24-- http://distfiles.gentoo.org/distfiles/bioperl-1.5.1.tar.bz2 => `/usr/portage/distfiles/bioperl-1.5.1.tar.bz2' It seems tha line can be removed. And 'perl-module' renamed to 'perl-app'.
In CVS. Thanks for your work.
Still, I thing having in addition to the release also the bioperl-live ebuild would be really helpfull. I only do not know how to make portage to re-fetch the tarball on 'emerge -u' always. Regarding the deps, see http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix#DEPENDENCIES_AND_Bundle::BioPerl
Olivier, are those messages about readonly variable benign or not? --- !empty dir /usr/lib/perl5/5.8.8/i686-linux --- !empty dir /usr/lib/perl5/5.8.8 --- !empty dir /usr/lib/perl5 --- !empty dir /usr/lib --- !empty dir /usr/bin --- !empty dir /usr /var/db/pkg/sci-biology/bioperl-1.5.1/bioperl-1.5.1.ebuild: line 7: CATEGORY: readonly variable /var/db/pkg/sci-biology/bioperl-1.5.1/bioperl-1.5.1.ebuild: line 7: CATEGORY: readonly variable >>> Regenerating /etc/ld.so.cache... >>> Original instance of package unmerged safely. /usr/portage/sci-biology/bioperl/bioperl-1.5.1.ebuild: line 7: CATEGORY: readonly variable * Man pages are not installed for most modules now. * Please use perldoc instead. >>> Regenerating /etc/ld.so.cache... >>> sci-biology/bioperl-1.5.1 merged. /usr/portage/sci-biology/bioperl/bioperl-1.5.1.ebuild: line 7: CATEGORY: readonly variable >>> No packages selected for removal by clean. >>> Auto-cleaning packages... >>> No outdated packages were found on your system. * GNU info directory index is up-to-date. #
