I did the following commands: root@condor:/usr/local/portage(48)# grep rebase /var/lib/portage/world root@condor:/usr/local/portage(49)# grep emboss /var/lib/portage/world root@condor:/usr/local/portage(50)# grep transfac /var/lib/portage/worldroot@condor:/usr/local/portage(51)# emerge -puvNDt world These are the packages that would be merged, in reverse order: Calculating dependencies... done! [nomerge ] sci-mathematics/freemat-4.2 USE="volpack vtk" [ebuild U ] sci-libs/vtk-6.1.0-r1::gentoo [6.0.0::local] USE="R X boost cg doc examples ffmpeg gdal%* java mpi mysql odbc postgres python qt4 rendering smp%* tbb%* tcl theora tk -all-modules% (-aqua) -imaging -json% -kaapi% -offscreen {-test} -views -web% -xdmf2%" PYTHON_TARGETS="python2_7" VIDEO_CARDS="-nvidia" 0 KiB [nomerge ] sci-biology/rebase-1501 USE="emboss -minimal" [nomerge ] sci-biology/emboss-6.3.1_p4-r1 USE="X doc mysql pdf png postgres -minimal -static-libs" [ebuild N ] sci-biology/transfac-3.2:3 USE="emboss -minimal" 0 KiB [ebuild N ] sci-biology/rebase-1501 USE="emboss -minimal" 0 KiB [ebuild N ] sci-biology/emboss-6.3.1_p4-r1 USE="X doc mysql pdf png postgres -minimal -static-libs" 0 KiB Total: 4 packages (1 upgrade, 3 new), Size of downloads: 0 KiB WARNING: One or more updates/rebuilds have been skipped due to a dependency conflict: ,,, I.e., neither transfac, rebase nor emboss is installed or in /var/lib/portage/world. So these packages are dependencies of other packages. But as I understand the "t" parameter of emerge, 'emerge -puvNDt world' should show these dependencies. The further problem is that emboss-6.3.1_p4-r1 is a masked package and "emerge emboss-6.3.1_p4-r1" fails. It looks if no further embassy-* programm is installed, but there are some sci-biology packages. I hoped, that 'emerge -puvNDt world' shows me, what program tries to install emboss as dependency, Any hint is appreciated. Reproducible: Always
rebase and emboss are already installed. Apparently nothing depends on these but they are still considered for updates. I don't see a bug here. Try the forums.
(In reply to Jeroen Roovers from comment #1) > rebase and emboss are already installed. Apparently nothing depends on these > but they are still considered for updates. > > I don't see a bug here. Try the forums. If rebase or emboss were installed, I would understand, but there are not, as you can see from my report. 'emerge -puvNDt world' want to make a new install of emboss and rebase. Only the following sci-biology packages are installed: root@condor:/usr/local/portage(69)# qlist -Iv sci-biology sci-biology/aaindex-9.1 sci-biology/bioperl-1.6.9 sci-biology/bioperl-db-1.6.9 sci-biology/bioperl-network-1.6.9 sci-biology/bioperl-run-1.6.9 sci-biology/biopython-1.64 sci-biology/biosql-1.0.1 sci-biology/clustalw-2.1 sci-biology/clustalx-2.1-r1 sci-biology/cluster-1.50-r1 sci-biology/cutg-160 sci-biology/mrbayes-3.1.2-r1 sci-biology/ncbi-tools-2.2.26-r2 sci-biology/phylip-3.69-r1 sci-biology/primer3-2.3.5 sci-biology/prints-39.0 sci-biology/prosite-20.72 sci-biology/readseq-20100513 sci-biology/treeviewx-0.5.1-r2 sci-biology/vienna-rna-2.1.8 root@condor:/usr/local/portage(70)#
'emerge -p --depclean' says: root@condor:/usr/local/portage(81)# emerge -p --depclean * Always study the list of packages to be cleaned for any obvious ... * `emerge --update --newuse --deep @world` prior to depclean. Calculating dependencies... done! * Dependencies could not be completely resolved due to * the following required packages not being installed: * * sci-biology/emboss pulled in by: * sci-biology/cutg-160 * * sci-biology/emboss pulled in by: * sci-biology/aaindex-9.1 * * sci-biology/emboss pulled in by: * sci-biology/prints-39.0 * * sci-libs/vtk pulled in by: * sci-mathematics/freemat-4.2 * * sci-biology/emboss pulled in by: * sci-biology/prosite-20.72 ... So cutg-160, aaindex-9.1, prints-39.0 or prosite-20.72 seems to be responsible for dependency of rebase-1501, emboss-6.3.1_p4-r1 and transfac-3.2. But why this is not shown by 'emerge -puvNDt world'?
