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mskcc / facets

Algorithm to implement Fraction and Copy number Estimate from Tumor/normal Sequencing.
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dependency pctGCdata has unclear requirements #160

Closed jbedo closed 3 years ago

jbedo commented 3 years ago

Facets requires pctGCdata >= 3.0.0 as declared in DESCRIPTION, however no such release is available, indeed no releases are available in the referenced veseshan/pctGCdata repository. Can you clarify which revision of pctGCdata should be used with facets v0.6.1?

stevekm commented 3 years ago

@jbedo maybe helpful, this is the Dockerfile used with facets-suite which includes a facets installation;

https://github.com/mskcc/facets-suite/blob/master/Dockerfile

in the container listed here; https://hub.docker.com/layers/stevekm/facets-suite/2.0.6/images/sha256-1809a092ab07bace2c3d3bd32017487f976ed8b6dbdd17f26126f2d5d5079978?context=explore

It appears that pctGCdata 0.3.0 is installed.

jbedo commented 3 years ago

Unfortunately that doesn't clarify things. The pctGCdata repo does not have any releases tagged for 0.3.0. Looking at the commits, the DESCRIPTION file was updated to 0.3.0 in https://github.com/mskcc/pctGCdata/commit/961dc95f75722d0cf60baabf5f667fd60d0ae188, but there has been 10 commits since then with the same 0.3.0 version. For reproducibility, I'd like to know which revision the latest release of facets should be used with.

This possibly should be an issue in pctGCdata requesting a release of version 0.3.0, but the issue tracker there is disabled.

veseshan commented 3 years ago

pctGDdata is a data package. Nothing had changed in the data or the single accessor function in the package. So I believe you should have reproducible results no matter what.

doliv071 commented 3 years ago

I would like to second @jbedo 's concerns. The issue I think is that the installation process involved using devtools::install_github() which has the disadvantage of changing with each commit. If there is a change to this repo then all installation procedures which deploy pctGCdata using the recommended devtools::install_github() will have unexpected results.

If I could make a suggestion, the simplest solution would be to simply tag the repo as it exists now as v0.3.0 so that the error provided by facets matches a release of the pctGCdata package.

veseshan commented 3 years ago

I have created a v0.3.0 release of pctGCdata. If devtools::install_github() doesn't work the package can be downloaded and installed using R CMD INSTALL pkgsrc