Hypothesis: R_LIBS_SITE set to NULL by RStudio Server before /etc/Renviron execution

meztez · May 28, 2020, 2:42am

Debian buster, R latest, RStudio latest.

R_LIBS_SITE env seems to be set but null when executing /etc/Renviron from RStudio server.

Following https://pubs.opengroup.org/onlinepubs/9699919799/utilities/V3_chap02.html#tag_18_06_02,
base/Rprofile keeps the null value. End-user end up with an empty R_LIBS_SITE.

I'll try to narrow down where the variable is set and compare to previous RStudio release, seems to be from RVersionsPosix.hpp. I'll come back here if I find something else.

meztez · June 4, 2020, 2:54pm

github.com/rstudio/rstudio

setLibrary breaks R_LIBS_SITE on Debian

opened 03:11AM - 28 May 20 UTC

closed 06:54PM - 28 May 20 UTC

meztez

bug r interface

### System details RStudio Edition : Server RStudio Version : Latest (1.3.959) OS Version : Debian Buster R Version : 4.0.0 ### Steps to reproduce the problem Run R from shell on Debian buster, printenv, check `R_LIBS_SITE`, should be a list of 3 values Should match what's in `/etc/R/Renviron` under `R_LIBS_SITE` ### Describe the problem in detail Since 1330290, `setLibrary` sets `R_LIBS_SITE` when `R_LIBS_SITE` was not previously set. ```cpp const std::string& library() const { return library_; } void setLibrary(const std::string& library) { library_ = library; core::system::setenv(&environment_, "R_LIBS_SITE", library); } ``` This cause `/etc/R/Renviron` on Debian buster to ignore `R_LIBS_SITE` since parameter expansion used is `${parameter-word}`. (https://pubs.opengroup.org/onlinepubs/9699919799/utilities/V3_chap02.html#tag_18_06_02) `/etc/R/Renviron` sample ```r R_LIBS_SITE=${R_LIBS_SITE-'/usr/local/lib/R/site-library:/usr/lib/R/site-library:/usr/lib/R/library'} ``` ### Describe the behavior you expected R_LIBS_SITE should be unset when /etc/R/Renviron is executed I guess. ### Mitigation Replace R_LIBS_SITE line in `etc/R/Renviron` by ```r R_LIBS_SITE=${R_LIBS_SITE:-'/usr/local/lib/R/site-library:/usr/lib/R/site-library:/usr/lib/R/library'} ```  - [x] I have read the guide to submitting good bug reports at https://github.com/rstudio/rstudio/wiki/Writing-Good-Bug-Reports . - [x] I have installed the latest version of RStudio and confirmed that the issue still persists. - [ ] If I am reporting a RStudio crash, I have included a diagnostics report. https://support.rstudio.com/hc/en-us/articles/200321257-Running-a-Diagnostics-Report - [x] I have done my best to include a minimal, self-contained set of instructions for consistently reproducing the issue.

system · June 11, 2020, 2:55pm

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