update tool script to use BiocManager instead of online R script

[LiNk-NY]

Hi Kirill, @krlmlr As you may be aware, Bioconductor now uses BiocManager to install and update Bioconductor packages. In the near future, the online biocLite.R script may no longer be supported.

Note. You may want to use an alternative version of downloading the BiocManager, for example, as part of the CRAN package list. See BiocManager on CRAN here.

The current pull request installs BiocManager when the R_USE_BIOC_CMD is invoked.

Best regards, Marcel

[jimhester]

@LiNk-NY If biocLite.R is no longer going to be supported what is the maintenance / migration plan for older versions of R? BiocManager requires R 3.5+

[LiNk-NY]

Hi all, I chatted with Martin about this and was told that we will keep biocLite.R around for legacy reasons. But we prefer that our users, with compatible versions of R, move over to BiocManager. cc: @mtmorgan

[LiNk-NY]

Hi Kirill and Jim, @krlmlr @jimhester Please see the updated PR. It should be compatible with R versions above and below 3.5.0.

[LiNk-NY]

Any word on merging this? @jimhester @krlmlr

[LiNk-NY]

https://ci.appveyor.com/project/krlmlr/r-appveyor/builds/20659718

[mbstadler]

Are there any news regarding the merging of this pull request? It would be great to be able to use appveyor with R >= 3.5.0. @jimhester @krlmlr

[csoneson]

Hi @krlmlr, @jimhester - any updates on the merging of this PR? Or is there any other way of using r-appveyor with the current Bioconductor version? Thanks!

[mjsteinbaugh]

+1 on updating this -- I'd love to be able to test some of my single-cell RNA-seq code against Bioconductor 3.8 on Windows

[LiNk-NY]

Hi Jim and Kirill, @jimhester @krlmlr I'd be happy to make any changes to the PR here. Let me know. Best regards, Marcel

[krlmlr]

Thanks!