Don't allow remotes::install_github() to convert warnings to errors on unavailable PACKAGES file

[mtmorgan]

remotes::install_github() converts warnings about dependencies that cannot be installed (e.g., because of missing binaries) into errors. This is different from the install.packages() behavior in non-github installations by BiocManager.

This can be made consistent by setting an environment variable Sys.setenv(R_REMOTES_NO_ERRORS_FROM_WARNINGS, FALSE) prior to calling remotes::install_github().

Is this a good idea?

Actually, the use case is that the PACKAGES index isn't available for all types of packages, even though the package of interest is not found in the repository where PACKAGES does not exist.

See https://stat.ethz.ch/pipermail/bioc-devel/2019-January/014560.html

@seandavi

[seandavi]

Having the user (me) set the environment variable seems like a reasonable compromise. I haven't thought through all the ramifications of setting it in BiocManager::install.

After CRAN binaries for Mac become available, this will be a moot point, anyway, at least for the case I mentioned in the email.

Just a note that the incantation is, I think:

Sys.setenv("R_REMOTES_NO_ERRORS_FROM_WARNINGS"=TRUE)