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vloux / ProteoRE

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goprofiles not available in conda #243

Closed lecorguille closed 5 years ago

lecorguille commented 5 years ago 

Loading channels: done
No match found for: goprofiles. Search: *goprofiles*
# Name                       Version           Build  Channel
bioconductor-goprofiles          1.44.0          r351_0  bioconda
bioconductor-goprofiles          1.44.0          r351_1  bioconda
bioconductor-goprofiles          1.46.0           r36_1  bioconda
yvandenb commented 5 years ago

see also #89

vloux commented 5 years ago

Thanks @lecorguille to point this out , we will test with latest goprofiles packages from bioconda. Last time we tried it we had conflict issues with org.*.db packages . See #13

lecorguille commented 5 years ago

So, so far, were you using your own Conda channel to fetch goprofiles?

vloux commented 5 years ago

Yes, only for goprofiles (channel : liennguyen) https://anaconda.org/liennguyen/goprofiles and one tool listing it as a dependency Cf https://github.com/ifb-git/ProteoRE/blob/c5df340110b84ca4195c21ebecdbe8320c27196c/tools/goprofiles/goprofiles.xml

lecorguille commented 5 years ago

It's also not a good idea to target a specific version of R in the deps: https://github.com/ifb-git/ProteoRE/blob/c5df340110b84ca4195c21ebecdbe8320c27196c/tools/goprofiles/goprofiles.xml#L4

Lets Conda deal with that. Because in 1 year, you aren't sure that the tool is still installable.

vloux commented 5 years ago

Thanks for the advice. We've done that because, from previous test we have seen that if we didnt' lock versions of R/packages and org.*.db packages, we encountered bugs. Not at installation (all went fine with conda) but at execution. Nevertheless we will follow your advice, update the requirements and toroughly test the tools.

vloux commented 5 years ago

UnsatisfiableError: The following specifications were found to be in conflict:

  • bioconductor-goprofiles 1.44.0*
  • bioconductor-org.mm.eg.db 3.5.0* Use "conda info " to see the dependencies for each package.

bioconductor-goprofiles 1.44.0 r351_1

file name : bioconductor-goprofiles-1.44.0-r351_1.tar.bz2 name : bioconductor-goprofiles version : 1.44.0 build string: r351_1 build number: 1 channel : https://conda.anaconda.org/bioconda/noarch size : 511 KB arch : None constrains : () license : GPL-2 md5 : ce3c735759fd462fe31a5ef02fc23eb7 noarch : generic package_type: noarch_generic platform : None subdir : noarch timestamp : 1552301126759 url : https://conda.anaconda.org/bioconda/noarch/bioconductor-goprofiles-1.44.0-r351_1.tar.bz2 dependencies: bioconductor-annotationdbi >=1.44.0,<1.45.0 bioconductor-biobase >=2.42.0,<2.43.0 bioconductor-go.db >=3.7.0,<3.8.0 r-base >=3.5.1,<3.5.2.0a0 r-compquadform r-stringr

bioconductor-org.mm.eg.db 3.5.0 r3.4.1_0

file name : bioconductor-org.mm.eg.db-3.5.0-r3.4.1_0.tar.bz2 name : bioconductor-org.mm.eg.db version : 3.5.0 build string: r3.4.1_0 build number: 0 channel : https://conda.anaconda.org/bioconda/osx-64 size : 5 KB arch : None constrains : () license : Artistic-2.0 md5 : e0d85efccab91d4a50910bbfc9761500 platform : None subdir : osx-64 url : https://conda.anaconda.org/bioconda/osx-64/bioconductor-org.mm.eg.db-3.5.0-r3.4.1_0.tar.bz2 dependencies: bioconductor-annotationdbi >=1.39.3 r-base 3.4.1* wget

bioconductor-org.mm.eg.db 3.5.0 r3.4.1_1

file name : bioconductor-org.mm.eg.db-3.5.0-r3.4.1_1.tar.bz2 name : bioconductor-org.mm.eg.db version : 3.5.0 build string: r3.4.1_1 build number: 1 channel : https://conda.anaconda.org/bioconda/osx-64 size : 5 KB arch : None constrains : () license : Artistic-2.0 md5 : 103acabd76dfa084e909bd50f0013db7 platform : None subdir : osx-64 url : https://conda.anaconda.org/bioconda/osx-64/bioconductor-org.mm.eg.db-3.5.0-r3.4.1_1.tar.bz2 dependencies: bioconductor-annotationdbi >=1.39.3 r-base 3.4.1* wget

vloux commented 5 years ago

We have to update org.mm.eg.db to 3.6.0 ? That should resolve the R version conflicts but will update the relese of org*db -> Next update ?

bioconductor-org.mm.eg.db 3.6.0 r351_0

file name : bioconductor-org.mm.eg.db-3.6.0-r351_0.tar.bz2 name : bioconductor-org.mm.eg.db version : 3.6.0 build string: r351_0 build number: 0 channel : https://conda.anaconda.org/bioconda/osx-64 size : 6 KB arch : None constrains : () license : Artistic-2.0 md5 : f5ea77ae0f118d0c5d59344234da7081 platform : None subdir : osx-64 timestamp : 1539962942645 url : https://conda.anaconda.org/bioconda/osx-64/bioconductor-org.mm.eg.db-3.6.0-r351_0.tar.bz2 dependencies: bioconductor-annotationdbi >=1.42.1,<1.44.0 r-base >=3.5.1,<3.5.2.0a0 wget

vloux commented 5 years ago

Update to latest version of org*db (3.8.2) seems Ok

conda search bioconductor-org.mm.eg.db|grep r36 bioconductor-org.mm.eg.db 3.8.2 r36_1 bioconda onda search bioconductor-org.rn.eg.db|grep r36 bioconductor-org.rn.eg.db 3.8.2 r36_1 bioconda conda search bioconductor-org.hs.eg.db|grep r36 bioconductor-org.hs.eg.db 3.8.2 r36_1 bioconda

conda search bioconductor-goprofiles|grep r36 bioconductor-goprofiles 1.46.0 r36_1 bioconda