Current STABLE samtools-0.1.12 does not install header and libraries so it is quite useless if one needs those for downstream applications. I still think samtools package should be installed in SLOTs because too downstream many packages require different samtools version so the mess cannot be solved by a single version installed.
Hi Martin, please have a look at my new samtools-0.1.20:0.1-legacy ebuild. I totally agree with SLOTing, and hence why I changed the build system significantly. All binaries are installed in separate folders, and the shared objects have been renamed, to prevent any accidental linking to them. My proposal is to have a look at revdeps relying on <samtools-1.0 packages and changing them to depend on samtools:0.1-legacy. Currently, the dependency on this outdated samtools version is holding back the whole stack. What do you think?
Hi David, thank you very much for your efforts on this. I do not feel competent to really judge quality of the ebuild but from my naive, more user's perspective: 1. I still think 0.1.19-r2 should hit the STABLE tree, the 0.1.12 is really crap. It will take a while until the SLOTed ebuilds hits the main tree. 2. I do not see samtools available in "eselect list" 3. It would be great if you patched apps depending on specific versions to use these SLOTed samtools. 4. Not sure why is there the '-legacy' but I do not mind that much. 5. Would you mind going through the samtools and depending apps in science overlay? I put there quite a lot of ebuilds and it would be more easy for me to test the new SLOTed ebuilds there along with other apps. In general, anything what is KEYWORDED can be moved into main tree, especially ebuilds with -r# improving existing ebuilds in the main tree. 6. I installed 0.1.20-r1, I see perl dependency was dropped although it install *.pl files. Not sure how /usr/bin/samtools-0.1-legacy/samtools.pl is supposed to execute /usr/bin/samtools-0.1-legacy/samtools if in my /usr/bin/samtools is my 0.1.19-r2 at the moment (unless eselect creates the symlinks). If you want to to path all those perl files, fine with me. I have no idea if there are eventually some hardcoded paths in the binaries. Thank you. Martin
Hi Martin, about the perl dependency, yes, I will put it back in. Having something SLOTed is orthogonal to being eselect'able. Have a look at the latest cufflinks ebuild, it's the first package to use the 0.1-legacy SLOT. The idea is to port all packages depending on the old 0.1.18-20 API to this SLOT, and then stabilise 0.1.20.
Hi David, I just installed Gentoo:Prefix on one host and it seems portage thinks it installed -0.1.19-r2 version. However, as you can see later, 0.1.20-r2 is likely the version installed. Where is the old version number hiding in the ebuild? >>> Installing (1 of 1) sci-biology/bcftools-1.2::science * This package will overwrite one or more files that may belong to other * packages (see list below). You can use a command such as `portageq * owners / <filename>` to identify the installed package that owns a * file. If portageq reports that only one package owns a file then do * NOT file a bug report. A bug report is only useful if it identifies at * least two or more packages that are known to install the same file(s). * If a collision occurs and you can not explain where the file came from * then you should simply ignore the collision since there is not enough * information to determine if a real problem exists. Please do NOT file * a bug report at http://bugs.gentoo.org unless you report exactly which * two packages install the same file(s). See * http://wiki.gentoo.org/wiki/Knowledge_Base:Blockers for tips on how to * solve the problem. And once again, please do NOT file a bug report * unless you have completely understood the above message. * * package sci-biology/bcftools-1.2 NOT merged * * Detected file collision(s): * * /scratch/mmokrejs/gentoo/usr/bin/bcftools * /scratch/mmokrejs/gentoo/usr/bin/vcfutils.pl * * Searching all installed packages for file collisions... * * Press Ctrl-C to Stop * * sci-biology/samtools-0.1.19-r2:0::gentoo_prefix * /usr/bin/bcftools * /usr/bin/vcfutils.pl * * Package 'sci-biology/bcftools-1.2' NOT merged due to file collisions. * If necessary, refer to your elog messages for the whole content of the * above message. $ emerge --unmerge samtools * This action can remove important packages! In order to be safer, use * `emerge -pv --depclean <atom>` to check for reverse dependencies before * removing packages. sci-biology/samtools selected: 0.1.20-r2 1.3-r1 protected: none omitted: none ^C $ emerge --unmerge =sci-biology/samtools-0.1.19-r2 * This action can remove important packages! In order to be safer, use * `emerge -pv --depclean <atom>` to check for reverse dependencies before * removing packages. --- Couldn't find '=sci-biology/samtools-0.1.19-r2' to unmerge. >>> No packages selected for removal by unmerge BTW: I think bcftools and vcfutils.pl should be taken out from 0.1.20-r2 package and installed as bcftools-0.1.20-r2. They are incompatible with newer bcftools, so bcftools-1.2 cannot be used with samtool-0.1.20-r2 files. Therefore, I think the best is to install them as a separate, bcftools-0.1.20 bundle (albeit with a different SRC_URI compared with the one in bcftools-1.2.ebuild). :(
any updates on this?
all reverse deps set proper slots, slot 0 is stable and the legacy slot is not needed by any stable package
(In reply to Martin Mokrejš from comment #4) > > BTW: I think bcftools and vcfutils.pl should be taken out from 0.1.20-r2 > package and installed as bcftools-0.1.20-r2. They are incompatible with > newer bcftools, so bcftools-1.2 cannot be used with samtool-0.1.20-r2 files. > Therefore, I think the best is to install them as a separate, > bcftools-0.1.20 bundle (albeit with a different SRC_URI compared with the > one in bcftools-1.2.ebuild). :( To summarize current situation, the sci-biology/bcftools package provides only 1.2 version, the "hack" which I proposed to rip out the below two files from old samtools package did not happen. Users who need older version of these tools can get them from: $ equery files samtools | grep bcftoo /usr/bin/samtools-0.1-legacy/bcftools $ equery files samtools | grep vcfuti /usr/bin/samtools-0.1-legacy/vcfutils.pl $
