install_deps uses wrong Bioc version

[grst]

When using install_deps(dependencies = TRUE) on a package with Bioconductor dependencies in an older R version (e.g. 3.5.1), the installation fails as remotes seems to try to install packages from the most recent Bioconductor release which is incompatible with R 3.5.1.

>Rscript -e 'remotes::install_deps(dependencies=TRUE)'

BiocGenerics (NA -> fc7c3af4a...) [Bioc]
Downloading Bioconductor repo https://git.bioconductor.org/packages/BiocGenerics
'/usr/bin/git' clone --depth 1 --no-hardlinks --branch RELEASE_3_9 https://git.bioconductor.org/packages/BiocGenerics /home/sturm/tmp/RtmpzuopSG/file7ce5687e27cc
Cloning into '/home/sturm/tmp/RtmpzuopSG/file7ce5687e27cc'...
remote: Enumerating objects: 153, done.
remote: Counting objects: 100% (153/153), done.
remote: Compressing objects: 100% (150/150), done.
remote: Total 153 (delta 56), reused 0 (delta 0)
Receiving objects: 100% (153/153), 74.40 KiB | 440.00 KiB/s, done.
Resolving deltas: 100% (56/56), done.
Running `R CMD build`...
* checking for file ‘/home/sturm/tmp/RtmpzuopSG/file7ce5687e27cc/DESCRIPTION’ ... OK
* preparing ‘BiocGenerics’:
* checking DESCRIPTION meta-information ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘BiocGenerics_0.30.0.tar.gz’
ERROR: this R is version 3.5.1, package 'BiocGenerics' requires R >=  3.6.0
Error in i.p(...) : 
  (converted from warning) installation of package ‘/home/sturm/tmp/RtmpzuopSG/file7ce532169184/BiocGenerics_0.30.0.tar.gz’ had non-zero exit status
Calls: <Anonymous> ... with_rprofile_user -> with_envvar -> force -> force -> i.p
Execution halted

Expected behavior

remotes always uses the most recent Bioconductor release that is compatible with the current version of R (in the case of 3.5.1, Bioc v3.7)

Steps to reproduce

Setup R 3.5.1

conda create -n test_remotes -c conda-forge r-base=3.5.1 r-remotes
conda activate test_remotes

> R --version
R version 3.5.1 (2018-07-02) -- "Feather Spray"```

create empty package:

Rscript -e "usethis::create_package("test.remotes")

Append the following lines to DESCRIPTION

Depends:
  BiocGenerics
Remotes:
  bioc::BiocGenerics

Run the installation in the conda environment:

Rscript -e 'remotes::install_deps(dependencies=TRUE)'

[jimhester]

This is a common misconception of what the purpose of the bioc remotes is. This remote is for installing the current development version of a Bioconductor package. If you want the release version you don't need to use a Remote at all, just put the bioconductor package in your Imports Depends etc as normal.

[grst]

Hmm, I stumbled upon this because remotes is used by travis to resolve all dependencies.
This works fine when testing against the development version of R, but, in that case expectedly, fails when testing other R versions.

If I don't put the Bioconductor packages in Remotes at all, it just doesn't find the packages.

Is that something I should report to travis? Or can you hint me at what's the proper way of doing it?

[jimhester]

You need to add a BiocViews field to your DESCRIPTION file, this indicates your package is a Bioconductor package and the repos will then be set up appropriately, it can be empty, but when you submit your package to Bioconductor you will need to add some views, so you could probably do it now.

[grst]

ok, that seems to work nicely for a package that only contains CRAN and Bioc dependencies (and no Remotes: section at all.

I have a package that depends on both github and Bioc packages. As soon as I add a Remotes section to my DESCRIPTION file, the Bioc packages are not downloaded any more.

[jimhester]

The issue is actually not in your package. It seems to be that xCell does not have BiocViews, despite depending on Bioconductor packages

https://github.com/dviraran/xCell/blob/fe6d5e6b02993315270ecd808b3eb1af3af30261/DESCRIPTION#L27-L28

[grst]

I see now. Thanks a lot for your help!