Ignore .Renviron

[frenkiboy]

The pipeline reads the .Renviron files in the current directory.

This can mess up R dependencies.

[rekado]

The R manual says

Unless --no-environ was given, R searches for user and site files to process for setting environment variables. The name of the site file is the one pointed to by the environment variable R_ENVIRON; if this is unset, R_HOME/etc/Renviron.site is used (if it exists). The user file is the one pointed to by the environment variable R_ENVIRON_USER if this is set; otherwise, files .Renviron in the current or in the user’s home directory (in that order) are searched for. These files should contain lines of the form ‘name=value’. (See help("Startup") for a precise description.) Variables you might want to set include R_PAPERSIZE (the default paper size), R_PRINTCMD (the default print command) and R_LIBS (specifies the list of R library trees searched for add-on packages).

So... we should probably add --no-environ to the list of options for all invocations of R and Rscript.