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rocker-org / rocker-versioned

Run current & prior versions of R using docker
https://hub.docker.com/r/rocker/r-ver
GNU General Public License v2.0
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update Dockerfiles to use BiocManager instead of online R script #105

Closed LiNk-NY closed 6 years ago

LiNk-NY commented 6 years ago

Hi Carl, @cboettig Bioconductor is now using the BiocManager CRAN package instead of an online R script (https://bioconductor.org/biocLite.R). I didn't find any R code using biocLite but if you can point me to it, I'd be happy to change that too. Thanks!

cboettig commented 6 years ago

Nice, thanks for this.

I believe it was originally included because devtools suggests BiocInstaller from bioconductor repos (and this image installs devtools with dep=TRUE so it includes suggested packages).

I think some downstream images may be using the biocLite scripts to install, but as this impacts only the >= 3.5.1 images perhaps that's okay to break those and force an update to the new installer(?)

LiNk-NY commented 6 years ago

Thanks for the insight Carl. I just checked devtools and it does suggests both BiocInstaller and BiocManager possibly because BiocManager is only supported on R versions newer than 3.5.0.

We are keeping the biocLite.R script available for legacy reasons. BiocManager will only affect versions going forward (>=3.5.0) so images with older versions of R shouldn't break.

cboettig commented 6 years ago

Okay, sounds good. here goes.