'emerge GBrowse' fails with: root@impala:/usr/local/portage/media-video(87)# emerge -pvuDN GBrowse These are the packages that would be merged, in order: Calculating dependencies... done! [ebuild U #] sci-biology/bioperl-9999-r1 [1.6.1] USE="db graphviz network run -minimal (-sqlite%*)" 0 kB [0] [ebuild U #] sci-biology/bioperl-db-9999-r1 [1.6.0] 0 kB [0] [ebuild U #] sci-biology/bioperl-network-9999-r1 [1.6.0] USE="-test" 0 kB [0] [ebuild U #] sci-biology/bioperl-run-9999-r1 [1.6.1] USE="-minimal -test" 0 kB [0] [ebuild N ] dev-perl/Bio-SamTools-1.29 0 kB [1] [ebuild N ] sci-biology/GBrowse-2.39 USE="mysql postgres sqlite -minimal -vhosts" 0 kB [0] Total: 6 packages (4 upgrades, 2 new), Size of downloads: 0 kB Portage tree and overlays: [0] /usr/portage [1] /var/lib/layman/science The following keyword changes are necessary to proceed: #required by sci-biology/bioperl-9999-r1[run], required by sci-biology/bioperl-network-9999-r1 >=sci-biology/bioperl-run-9999-r1 ** #required by sci-biology/bioperl-9999-r1[db], required by sci-biology/bioperl-network-9999-r1 >=sci-biology/bioperl-db-9999-r1 ** #required by sci-biology/bioperl-network-9999-r1 >=sci-biology/bioperl-9999-r1 ** #required by sci-biology/bioperl-9999-r1[network], required by sci-biology/bioperl-run-9999-r1 >=sci-biology/bioperl-network-9999-r1 ** I have dev-perl/Bio-SamTools at two places (/usr/portage/dev-perl/Bio-SamTools and /var/lib/layman/science/dev-perl/Bio-SamTools). At both places is only one ebuild (Bio-SamTools-1.29.ebuild): root@impala:/root(59)# ll /usr/portage/dev-perl/Bio-SamTools/Bio* /var/lib/layman/science/dev-perl/Bio-SamTools/Bio* -rw-r--r-- 1 root root 895 Jul 20 02:43 /usr/portage/dev-perl/Bio-SamTools/Bio-SamTools-1.29.ebuild -rw-r--r-- 1 root root 1096 Aug 7 13:38 /var/lib/layman/science/dev-perl/Bio-SamTools/Bio-SamTools-1.29.ebuild /usr/portage/dev-perl/Bio-SamTools/Bio-SamTools-1.29.ebuild depends on sci-biology/bioperl. /var/lib/layman/science/dev-perl/Bio-SamTools/Bio-SamTools-1.29.ebuild depends on >=sci-biology/bioperl-1.6.901. Reproducible: Always
It seems to as if you are installing every new sci package available? Do you like to be come an official herd tester for the sci team? This would give you several upgrades including bugzilla editing rights, so that you can directly assign your bugs.
Hi Justin, I think there are about 1000 scientific packages in the normal portage tree and in some overlays: root@moose:/root(34)# for d in /usr/portage/sci-*/* /usr/local/portage/sci-*/* /var/lib/layman/*/sci-*/* ; do if [ -d $d ] ; then echo ${d##*/} ;fi ; done | sort | uniq | wc -l 971 As a physicist working mainly in the field of bioinformatics I have some interest in mathematics, physics, biology and geoscience. So I have active installed about 90 scientific packages: root@moose:/root(36)# grep sci- /var/lib/portage/world | wc -l 91 Because of the dependencies more than 200 scientific packages are installed: root@moose:/root(39)# qlist -I | grep sci- | wc -l 227 I.e. I have only contact to 20 % of the gentoo scientific packages. These packages are installed on about 10 computers (mostly x86_64 and some i686). I would like to support Gentoo, but my knowledge about the interna of ebuild writing is very limited. So what can I do to support the sci team more? Regards Juergen
I don't see a bug here, other than that Bio-SamTools in sci overlay shadows the one in main tree. I just deleted the one in the overlay.
Juergen, to clarify... the BioPerl ebuilds are in the main tree - there are none in the overlay - so I don't see how the overlay affects this. The messages you pasted are standard keyword mismatch messages.
I did not said that the bioperl ebuilds are in the overlay. I said only that there is a Bio-SamTools-1.29 ebuild in the science overlay and in the main tree. 'emerge -uvDN world' prefers the Bio-SamTools-1.29 ebuild in the science overlay which depends on >=sci-biology/bioperl-1.6.901, which results in the attempt to install the masked bioperl-9999-r1: root@impala:/root(2)# emerge -pvuDN GBrowse These are the packages that would be merged, in order: Calculating dependencies... done! [ebuild U *] sci-biology/bioperl-9999-r1 [1.6.9] USE="db graphviz network run -minimal (-sqlite%*)" 0 kB [0] [ebuild U *] sci-biology/bioperl-db-9999-r1 [1.6.9] USE="(-test%)" 0 kB [0] [ebuild U *] sci-biology/bioperl-network-9999-r1 [1.6.9] USE="-test" 0 kB [0] [ebuild U *] sci-biology/bioperl-run-9999-r1 [1.6.9] USE="-minimal -test" 0 kB [0] [ebuild N ] dev-perl/Bio-SamTools-1.29 0 kB [1] [ebuild N ] sci-biology/GBrowse-2.39 USE="mysql postgres sqlite -minimal -vhosts" 0 kB [0] Total: 6 packages (4 upgrades, 2 new), Size of downloads: 0 kB Portage tree and overlays: [0] /usr/portage [1] /var/lib/layman/science The following keyword changes are necessary to proceed: #required by sci-biology/bioperl-9999-r1[run], required by sci-biology/bioperl-network-9999-r1 >=sci-biology/bioperl-run-9999-r1 ** #required by sci-biology/bioperl-9999-r1[db], required by sci-biology/bioperl-network-9999-r1 >=sci-biology/bioperl-db-9999-r1 ** #required by sci-biology/bioperl-network-9999-r1 >=sci-biology/bioperl-9999-r1 ** #required by sci-biology/bioperl-9999-r1[network], required by sci-biology/bioperl-run-9999-r1 >=sci-biology/bioperl-network-9999-r1 **
With the removal of the dev-perl/Bio-SamTools package from the science overlay the issue disappeared for me.
