'emerge -pvuDN jmol' fails with: ... root@lynx:/root(7)# emerge -pvuDN jmol These are the packages that would be merged, in order: Calculating dependencies... done! [ebuild N ] sci-chemistry/sage-jmol-bin-14.2.11-r1::sage-on-gentoo 0 KiB [ebuild N ] sci-libs/vecmath-objectclub-1.14::gentoo 74 KiB [ebuild N ] dev-java/saxon-6.5.5-r1:6.5::gentoo USE="doc examples -source" 3,268 KiB [ebuild N ] sci-libs/jmol-acme-1.0::gentoo 468 KiB [ebuild N ] sci-libs/naga-2.1::gentoo 22 KiB [ebuild N ] sci-chemistry/jspecview-1169-r1::sage-on-gentoo USE="applet" 49,040 KiB [ebuild N ] sci-chemistry/jmol-12.3.27::sage-on-gentoo USE="client-only -vhosts" 37,788 KiB [blocks B ] sci-chemistry/jmol ("sci-chemistry/jmol" is blocking sci-chemistry/sage-jmol-bin-14.2.11-r1) Total: 7 packages (7 new), Size of downloads: 90,658 KiB Conflict: 1 block (1 unsatisfied)
Yes you have to choose between `jmol` and `sage-jmol-bin` the latter being a silly name that escaped to production. You have to choose between an old source of jmol or a more recent binary package of jmol (sage-jmol-bin). They should both provide the same functionality.