79459 2005-01-25 06:48 0000 Bioperl New Version 1.5.1 2006-09-19 14:41:59 0000 1 1 1 Unclassified Gentoo Linux Ebuilds unspecified All Linux RESOLVED FIXED EBUILD P2 enhancement --- 1 drakos7@gmail.com sci@gentoo.org mmokrejs@ribosome.natur.cuni.cz nshephard@gmail.com drakos7@gmail.com 2005-01-25 06:48:41 0000 New version released to developers. Reproducible: Always Steps to Reproduce: drakos7@gmail.com 2005-01-25 06:49:58 0000 Created an attachment (id=49477) Initial Ebuild Installs clean on my x86. ka0ttic@gentoo.org 2005-01-25 08:10:36 0000 please make attachments as plain/text. drakos7@gmail.com 2005-01-25 08:27:55 0000 sorry. I set it as auto assuming that it would be recognized correctly. drakos7@gmail.com 2005-05-12 08:55:17 0000 There are a lot of updates to bioperl-run as well. That should be updated too. Would be nice to have a bioperl-cvs. ;) drakos7@gmail.com 2005-12-02 09:47:48 0000 1.5.1 or bioperl and bioperl-run are now available. http://news.open-bio.org/archives/2005_10.html#000084 drakos7@gmail.com 2006-04-28 13:38:01 0000 1.5 or better is needed for generic-genome-browser-1.64 and this works fine on my amd64 box also nshephard@gmail.com 2006-06-19 21:28:10 0000 (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 nshephard@gmail.com 2006-06-19 21:29:49 0000 Created an attachment (id=89596) updated ebuild for bioperl-1.5.1 mmokrejs@ribosome.natur.cuni.cz 2006-08-30 09:14:06 0000 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/ mmokrejs@ribosome.natur.cuni.cz 2006-08-30 15:02:45 0000 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'. ribosome@gentoo.org 2006-09-12 18:24:28 0000 In CVS. Thanks for your work. mmokrejs@ribosome.natur.cuni.cz 2006-09-18 12:17:35 0000 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 mmokrejs@ribosome.natur.cuni.cz 2006-09-19 14:41:59 0000 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. # 49477 2005-01-25 06:49 0000 Initial Ebuild bioperl-1.5.0.ebuild text/plain IyBDb3B5cmlnaHQgMTk5OS0yMDA1IEdlbnRvbyBGb3VuZGF0aW9uCiMgRGlzdHJpYnV0ZWQgdW5k ZXIgdGhlIHRlcm1zIG9mIHRoZSBHTlUgR2VuZXJhbCBQdWJsaWMgTGljZW5zZSB2MgojICRIZWFk ZXI6IC92YXIvY3Zzcm9vdC9nZW50b28teDg2L3NjaS1iaW9sb2d5L2Jpb3BlcmwvYmlvcGVybC0x LjUuMC5lYnVpbGQsdiAxLjQgMjAwNS8wMS8yNSAwOTo0MDo0OCAgRXhwICQKCmluaGVyaXQgcGVy bC1tb2R1bGUgZXV0aWxzCgpDQVRFR09SWT0ic2NpLWJpb2xvZ3kiCgpERVNDUklQVElPTj0iY29s bGVjdGlvbiBvZiB0b29scyBmb3IgYmlvaW5mb3JtYXRpY3MsIGdlbm9taWNzIGFuZCBsaWZlIHNj aWVuY2UgcmVzZWFyY2giCkhPTUVQQUdFPSJodHRwOi8vd3d3LmJpb3Blcmwub3JnLyIKU1JDX1VS ST0iaHR0cDovL3d3dy5iaW9wZXJsLm9yZy9ESVNULyR7UH0udGFyLmJ6MiIKCkxJQ0VOU0U9IkFy dGlzdGljIEdQTC0yIgpTTE9UPSIwIgpLRVlXT1JEUz0ifng4NiIKSVVTRT0ibXlzcWwgZ2QiCgpE RVBFTkQ9IgoJZGV2LXBlcmwvRmlsZS1UZW1wCglkZXYtcGVybC9IVE1MLVBhcnNlcgoJZGV2LXBl cmwvSU8tU3RyaW5nCglkZXYtcGVybC9JTy1zdHJpbmd5CglkZXYtcGVybC9TT0FQLUxpdGUKCWRl di1wZXJsL1N0b3JhYmxlCglkZXYtcGVybC9YTUwtRE9NCglkZXYtcGVybC9YTUwtUGFyc2VyCglk ZXYtcGVybC9YTUwtV3JpdGVyCglkZXYtcGVybC9YTUwtVHdpZwoJZGV2LXBlcmwvbGlieG1sLXBl cmwKCWRldi1wZXJsL2xpYnd3dy1wZXJsCglkZXYtcGVybC9HcmFwaAoJZGV2LXBlcmwvVGV4dC1T aGVsbHdvcmRzCglnZD8gKAoJCQk+PWRldi1wZXJsL0dELTEuMzItcjEKCQkJZGV2LXBlcmwvU1ZH CgkJCWRldi1wZXJsL0dELVNWRwoJCSkKCW15c3FsPyAoID49ZGV2LXBlcmwvREJELW15c3FsLTIu MTAwNC1yMyApIgoKc3JjX2NvbXBpbGUoKSB7Cgl5ZXMgIiIgfCBwZXJsIE1ha2VmaWxlLlBMICR7 bXljb25mfSBcCgkgICAgICAgICBQUkVGSVg9JHtEfS91c3IgSU5TVEFMTERJUlM9dmVuZG9yCn0K CnNyY190ZXN0KCkgewoJcGVybC1tb2R1bGVfc3JjX3Rlc3QgfHwgZGllICJUZXN0IGZhaWxlZCIK fQoKc3JjX2luc3RhbGwoKSB7CglteWRvYz0iQVVUSE9SUyBCVUdTIEZBUSIKCXBlcmwtbW9kdWxl X3NyY19pbnN0YWxsCn0K 89596 2006-06-19 21:29 0000 updated ebuild for bioperl-1.5.1 bioperl-1.5.1.ebuild text/plain IyBDb3B5cmlnaHQgMTk5OS0yMDA1IEdlbnRvbyBGb3VuZGF0aW9uCiMgRGlzdHJpYnV0ZWQgdW5k ZXIgdGhlIHRlcm1zIG9mIHRoZSBHTlUgR2VuZXJhbCBQdWJsaWMgTGljZW5zZSB2MgojICRIZWFk ZXI6IC92YXIvY3Zzcm9vdC9nZW50b28teDg2L3NjaS1iaW9sb2d5L2Jpb3BlcmwvYmlvcGVybC0x LjUuMC5lYnVpbGQsdiAxLjQgMjAwNS8wMS8yNSAwOTo0MDo0OCAgRXhwICQKCmluaGVyaXQgcGVy bC1tb2R1bGUgZXV0aWxzCgpDQVRFR09SWT0ic2NpLWJpb2xvZ3kiCgpERVNDUklQVElPTj0iY29s bGVjdGlvbiBvZiB0b29scyBmb3IgYmlvaW5mb3JtYXRpY3MsIGdlbm9taWNzIGFuZCBsaWZlIHNj aWVuY2UgcmVzZWFyY2giCkhPTUVQQUdFPSJodHRwOi8vd3d3LmJpb3Blcmwub3JnLyIKU1JDX1VS ST0iaHR0cDovL3d3dy5iaW9wZXJsLm9yZy9ESVNULyR7UH0udGFyLmJ6MiIKCkxJQ0VOU0U9IkFy dGlzdGljIEdQTC0yIgpTTE9UPSIwIgpLRVlXT1JEUz0ifng4NiIKSVVTRT0ibXlzcWwgZ2QiCgpE RVBFTkQ9IgoJcGVybC1jb3JlL0ZpbGUtVGVtcAoJZGV2LXBlcmwvSFRNTC1QYXJzZXIKCWRldi1w ZXJsL0lPLVN0cmluZwoJZGV2LXBlcmwvSU8tc3RyaW5neQoJZGV2LXBlcmwvU09BUC1MaXRlCglw ZXJsLWNvcmUvU3RvcmFibGUKCWRldi1wZXJsL1hNTC1ET00KCWRldi1wZXJsL1hNTC1QYXJzZXIK CWRldi1wZXJsL1hNTC1Xcml0ZXIKCWRldi1wZXJsL1hNTC1Ud2lnCglkZXYtcGVybC9saWJ4bWwt cGVybAoJZGV2LXBlcmwvbGlid3d3LXBlcmwKCWRldi1wZXJsL0dyYXBoCglkZXYtcGVybC9UZXh0 LVNoZWxsd29yZHMKCWdkPyAoCgkJCT49ZGV2LXBlcmwvR0QtMS4zMi1yMQoJCQlkZXYtcGVybC9T VkcKCQkJZGV2LXBlcmwvR0QtU1ZHCgkJKQoJbXlzcWw/ICggPj1kZXYtcGVybC9EQkQtbXlzcWwt Mi4xMDA0LXIzICkiCgpzcmNfY29tcGlsZSgpIHsKCXllcyAiIiB8IHBlcmwgTWFrZWZpbGUuUEwg JHtteWNvbmZ9IFwKCSAgICAgICAgIFBSRUZJWD0ke0R9L3VzciBJTlNUQUxMRElSUz12ZW5kb3IK fQoKc3JjX3Rlc3QoKSB7CglwZXJsLW1vZHVsZV9zcmNfdGVzdCB8fCBkaWUgIlRlc3QgZmFpbGVk Igp9CgpzcmNfaW5zdGFsbCgpIHsKCW15ZG9jPSJBVVRIT1JTIEJVR1MgRkFRIgoJcGVybC1tb2R1 bGVfc3JjX2luc3RhbGwKfQo=