krlmlr/r-appveyor

Bioconductor integration

LiNk-NY opened this issue · 3 comments

LiNk-NY commented

Hi all,
I'm opening this issue as requested by @krlmlr.
There are a few issues related to integrating Bioconductor already open.
See: #125, #65, ~ #57

Support for BiocManager

Bioconductor has recently switched to using BiocManager CRAN package to install and update Bioconductor packages. This makes it
a bit easier to support via CI services by just adding BiocManager to the list of CRAN packages.

I've created a PR #125 to support this:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

Unfortunately, this method only works with R versions >= 3.5.0. Support for packages
wishing to test against older versions of R is still needed.

Support for BiocCheck

This could be implemented as a field in the the appveyor.yml file for running BiocCheck
on a Bioconductor package such as - travis-tool.sh bioc_check.
I'm willing to look into this and provide some guidance / PR.
Note. This has been implemented in the Travis CI builds.

Using BiocManager::repositories

Support installations from Bioconductor repositories by using BiocManager::repositories.
It will potentially avoid issues such as #57.

mjsteinbaugh commented

I'm up for helping fix r-appveyor and getting Bioconductor 3.8 deployed as the default

LiNk-NY commented

Hi Michael, @mjsteinbaugh
I think the PR should be enough to get it working with Bioconductor 3.8.
It would be good to address the other objectives here such as supporting
the use of BiocCheck as part of the testing process.

-MR

  • 👍1
krlmlr commented

The PR is merged, closing. Please open a new issue if necessary.