Proposed addition to check() [using .libPaths() in .Rprofile]

[csgillespie]

In my .Rprofile I've recently added .libPaths("/path/")

Interestingly, this usually works, but occasionally it doesn't. For example,

• RStudio console and terminal picks up path/
• Running a check package works
• Running a build package doesn't

Likewise, a standard R CMD build XXX doesn't work.

Proposal: have check() detect and warn as necessary. Happy to attempt a PR.

---

The reason I have it in my .Rprofile was due to littler ignoring .Renviron files (https://github.com/eddelbuettel/littler/issues/64)

[HenrikBengtsson]

Wow, interesting. I wonder if this should also be reported as a bug in R. For future records, what version of R are you observing this on?

[csgillespie]

There's a couple of screenshots as well.

R> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.1 LTS

Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C               LC_TIME=en_GB.UTF-8       
 [4] LC_COLLATE=en_GB.UTF-8     LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8   
 [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] roxygen2_6.1.1   prettycode_1.0.2 colorout_1.2-0  

loaded via a namespace (and not attached):
 [1] compiler_3.5.1   R6_2.3.0         magrittr_1.5     tools_3.5.1      withr_2.1.2     
 [6] rstudioapi_0.9.0 Rcpp_1.0.0       crayon_1.3.4     xml2_1.2.0       stringi_1.2.4   
[11] stringr_1.3.1    packrat_0.5.0    commonmark_1.7   fortunes_1.5-4  

[HenrikBengtsson]

And just to be 100% on the same page, will running that devtools::document(...) from the RStudio Console also fail?

[csgillespie]

• devtools::document() works in both the Rstudio console and RStudio terminal.
• Check package (CTRL + Shift + E) on RStudio also works

[HenrikBengtsson]

Likewise, a standard R CMD build XXX doesn't work.

I'd like to confirm this in order to rule out that it's a devtools bug. As a test trying to figure out what's going on, I've added the following to my ~/.Rprofile:

system2("echo", args = "[system] .Rprofile ...")
.libPaths(c(tempfile(), .libPaths())
system2("echo", args = c("[system] .libPaths: ", .libPaths()))
system2("echo", args = "[system] .Rprofile ... done")

to confirm that R CMD build does indeed source .Rprofile:

$ R CMD build listenv
[system] .Rprofile ...
[system] .libPaths: /home/hb/R/x86_64-pc-linux-gnu-library/3.5 /usr/local/lib/R/site-library /usr/lib/R/site-library /usr/lib/R/library
[system] .Rprofile ... done
* checking for file ‘listenv/DESCRIPTION’ ... OK
* preparing ‘listenv’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘listenv_0.7.0-9000.tar.gz’

So, it's not that ~/.Rprofile is skipped by R CMD build itself at the top level. However, it could still be that there are some internal system calls that R CMD build performs that runs with --vanilla or similar.

[csgillespie]

One further step forward.

# The first dir is the one with knitr and loaded in .Rprofile
> .libPaths()
[1] "/data/ncsg3/Rpackages"   "/usr/lib/R/site-library"
[3] "/usr/lib/R/library"     
> tools:::.build_packages("benchmarkme/")
* checking for file ‘benchmarkme/DESCRIPTION’ ... OK
* preparing ‘benchmarkme’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
Error in loadVignetteBuilder(vigns$pkgdir) : 
  vignette builder 'knitr' not found
Calls: <Anonymous> -> loadVignetteBuilder
Execution halted
Error in do_exit(1L) : .build_packages() exit status 1

See https://github.com/wch/r-source/blob/47b75782bb459cd481e6635852ec5c234b4f530e/src/library/tools/R/build.R#L22 for function reference