The dependencies in the ebuilds are quite different. But both packages refer to almost the same web site. GBrowse-2.48 fails to emerge due to file collision: root@impala:/root(12)# emerge -pv GBrowse These are the packages that would be merged, in order: ... [ebuild N ] sci-biology/GBrowse-2.48 USE="mysql postgres sqlite -minimal -vhosts" 0 kB ... !!! Multiple package instances within a single package slot have been pulled !!! into the dependency graph, resulting in a slot conflict: sci-mathematics/pari:0 (sci-mathematics/pari-2.3.5:0/0::gentoo, ebuild scheduled for merge) pulled in by ~sci-mathematics/pari-2.3.5 required by (dev-perl/math-pari-2.10.806.50:0/0::gentoo, ebuild scheduled for merge) ^ ^^^^^ (sci-mathematics/pari-2.5.5-r2:0/0::sage-on-gentoo, installed) pulled in by =sci-mathematics/pari-2.5.5-r2[data,gmp] required by (sci-mathematics/sage-6.2:0/0::sage-on-gentoo, installed) ^ ^^^^^^^^ >=sci-mathematics/pari-2.5.5 required by (sci-mathematics/sage-clib-6.2:0/0::sage-on-gentoo, installed) ^^ ^^^^^ =sci-mathematics/pari-2.5* required by (sci-mathematics/lcalc-1.23-r5:0/0::sage-on-gentoo, installed) gbrowse-2.48 fails to emerge due to missing <=sci-biology/primer3-2. root@impala:/home/rose(87)# emerge -vuDN gbrowse These are the packages that would be merged, in order: Calculating dependencies... done! emerge: there are no ebuilds to satisfy "<=sci-biology/primer3-2". (dependency required by "sci-biology/gbrowse-2.48::science[-minimal]" [ebuild]) There is only: root@impala:/home/rose(88)# eix primer [I] sci-biology/primer3 Available versions: 2.3.1 (~)2.3.4 (~)2.3.5 Installed versions: 2.3.5(12:04:12 PM 02/17/2013) It would be really nice if both packages could be united to one working package. Reproducible: Always
Yes. Same upstream package, completely different ebuilds.
In the past I tried a lot to improve the ebuild. Andrey Kislyuk wasn't happy with some ebuild coding style and brought a different (improved) version to the main tree. But, I had some issues with the official ebuild not working in some cases. You can find the details in (maybe already closed) bug reports on gbrowse. The original improvements andrey made were about using perl classes and webapp classes by the ebuild. While being a bad ebuild writer I got access to the sci overlay where I hack some new ebuilds for new packages time to time. That is also why the ebuild in the overlay has some more patches. I just do update some ebuild in the overlay, so the official tree will be always lagging. Commit logs for the ebuild in overlay say: commit 583d5ee61844e8de863d6133fe83c2fbb00b4bfc Author: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> Date: Tue Feb 28 17:25:27 2012 +0100 sci-biology/gbrowse-2.48: added dependency on <=sci-biology/primer3-2, per http://generic-model-organism-system-database.450254.n5.nabble.com/PrimerDesigner-working-in-2-40-tp4724773p5479669.html I don't know whether it works with newer versions or either gbrowse or primer3.
The bug has been referenced in the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=3ef36b7c1ea596ab58fdf49c866e41f3e949f2b3 commit 3ef36b7c1ea596ab58fdf49c866e41f3e949f2b3 Author: David Seifert <soap@gentoo.org> AuthorDate: 2022-03-19 15:39:03 +0000 Commit: David Seifert <soap@gentoo.org> CommitDate: 2022-03-19 15:39:03 +0000 profiles: last-rite sci-biology/GBrowse Bug: https://bugs.gentoo.org/402849 Bug: https://bugs.gentoo.org/513594 Bug: https://bugs.gentoo.org/690042 Bug: https://bugs.gentoo.org/828702 Signed-off-by: David Seifert <soap@gentoo.org> profiles/package.mask | 6 ++++++ 1 file changed, 6 insertions(+)
The bug has been closed via the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=f71d2fd07f0ec1a96b6772fa4412e6ece900c6e2 commit f71d2fd07f0ec1a96b6772fa4412e6ece900c6e2 Author: Jakov Smolić <jsmolic@gentoo.org> AuthorDate: 2022-04-17 20:26:33 +0000 Commit: Jakov Smolić <jsmolic@gentoo.org> CommitDate: 2022-04-17 20:26:33 +0000 sci-biology/GBrowse: treeclean Closes: https://bugs.gentoo.org/828702 Closes: https://bugs.gentoo.org/690042 Closes: https://bugs.gentoo.org/513594 Closes: https://bugs.gentoo.org/402849 Signed-off-by: Jakov Smolić <jsmolic@gentoo.org> profiles/package.mask | 6 -- sci-biology/GBrowse/GBrowse-2.48-r1.ebuild | 71 --------------------- sci-biology/GBrowse/Manifest | 1 - .../GBrowse/files/GBrowseInstall.pm-2.39.patch | 72 ---------------------- sci-biology/GBrowse/metadata.xml | 11 ---- 5 files changed, 161 deletions(-)
