Bugzilla Bug 79459

New version released to developers.

Reproducible: Always
Steps to Reproduce:

Created an attachment (id=49477) [edit]
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 an attachment (id=89596) [edit]
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.

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