.Rprofile not picked up by RStudio installed through Nix

[alan-groot]

Hi,

Thanks for the very interesting package!

I was trying out this package to see how easily it would be able to create development environments with RStudio as the IDE, as described in the docs. However, it seems that .Rprofile is not picked up when starting rstudio from the shell, even though it is picked up when I run $(which R) in the Nix shell. See the screenshot below.

Am I doing something wrong, or should I source the file from within RStudio? See the files default.nix and .Rprofile.

[b-rodrigues]

that is quite weird, is the R session within rstudio starting in the right folder? It looks like it from your screenshot though... can you paste the output of .libPaths() here (from RStudio and from an R session)

[alan-groot]

From within the shell:

[nix-shell:/tmp/.pRhJ]$ pwd
/tmp/.pRhJ

[nix-shell:/tmp/.pRhJ]$ $(which R)

R version 4.1.0 (2021-05-18) -- "Camp Pontanezen"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> .libPaths()
[1] "/nix/store/afyixhqzjh6c0fy8619hyjgkj4r6l9w9-r-data.table-1.14.0/library"
[2] "/nix/store/992970dl4h9xzzcjmkqb59k77sy5brda-R-4.1.0/lib/R/library"      
> 

From RStudio:

> .libPaths()
 [1] "/home/agroot/R/x86_64-pc-linux-gnu-library/4.1"                          
 [2] "/nix/store/afyixhqzjh6c0fy8619hyjgkj4r6l9w9-r-data.table-1.14.0/library" 
 [3] "/nix/store/992970dl4h9xzzcjmkqb59k77sy5brda-R-4.1.0/lib/R/library"       
 [4] "/nix/store/gvgxyzha3pf29qh98qhqcm2xlj4bh372-r-boot-1.3-28/library"       
 [5] "/nix/store/6l48x3ymc4y191bf43hsssfv5fjhwjkl-r-class-7.3-19/library"      
 [6] "/nix/store/fxlx7xwz020bpqsf68000f40236l05fx-r-MASS-7.3-54/library"       
 [7] "/nix/store/m0arnbdgmm7xqha1a3dpn7bn69gzhbrj-r-cluster-2.1.2/library"     
 [8] "/nix/store/as32vb3x18daf7qnjbx5ffbpymw0z96p-r-codetools-0.2-18/library"  
 [9] "/nix/store/ngczy6k0h1fr41cjnhmf01r39afrnhdk-r-foreign-0.8-81/library"    
[10] "/nix/store/111fgjn7j3rq2zx50rl3n08j9ci1mivr-r-KernSmooth-2.23-20/library"
[11] "/nix/store/k62v8c2rps9shj56wm2przdxqfvgls99-r-lattice-0.20-44/library"   
[12] "/nix/store/9lsyd2k6bh9965yg00w9jb4cyjynizgq-r-Matrix-1.3-4/library"      
[13] "/nix/store/q172n2w2f3bdzjkidxdrczyllk14lx1x-r-mgcv-1.8-36/library"       
[14] "/nix/store/fhy8vwcqz95vrdn5vp3b39qcvrjbiv46-r-nlme-3.1-152/library"      
[15] "/nix/store/40731svpcvhgzhzngkwfz1shb3spfnsx-r-nnet-7.3-16/library"       
[16] "/nix/store/ab8m6fl0x3kp99za4iq8450a5767ia50-r-rpart-4.1-15/library"      
[17] "/nix/store/a3s8dv5y5am1r7lf3mnq5mqzjhjqxv0n-r-spatial-7.3-14/library"    
[18] "/nix/store/rvfvgqxzb8g20nw08cnfi29bg8cv8rg2-r-survival-3.2-11/library" 

[b-rodrigues]

Yeah that .libPaths() from within RStudio doesn’t look good, it should be like the first one. can you try Sys.getenv("RSTUDIO") from the rstudio session? what does it return?

[alan-groot]

I agree that the RStudio .libPaths() do not look good. Oddly enough, the value of Sys.getenv("RSTUDIO") is 1:

> Sys.getenv("RSTUDIO")
[1] "1"

[alan-groot]

A workaround is simply sourcing the .Rprofile myself, but I was hoping it would be picked up automatically.

[b-rodrigues]

it really should be automatic, I’m rebuilding the env and will try to reproduce.

[alan-groot]

Great, thanks! Let me know if I can help any further!

[b-rodrigues]

ok so I was able to reproduce this: I don't use RStudio so I never noticed this, but still I'm surprised I never did in 2 years we've been developing rix! It seems to be related to this bug: NixOS/nixpkgs#85840

I'll try to see how to fix this

[alan-groot]

Thanks in advance!

[alan-groot]

Just summarizing NixOS/nixpkgs#85840, it seems that the .Rprofile file in the working directory is not picked up because the RStudio wrapper sets Sys.getenv("R_PROFILE_USER").

As mentioned in Section 10.8 Customizing the environment of An Introduction to R, "If the environment variable R_PROFILE_USER is set, the file it points to is used instead of the .Rprofile files." (See also https://cran.r-project.org/web/packages/startup/vignettes/startup-intro.html.)

Indeed, in RStudio I get

> Sys.getenv("R_PROFILE_USER")
[1] "/nix/store/svsgpgghlyc73ywk7cqw2aql01h1vb9z-RStudio-2022.07.1+554-wrapper/fix_libs.R"

while

> Sys.getenv("R_PROFILE_USER")
[1] ""

in the shell.

The file .../fix_libs.R contains the following:

# Autogenerated by wrapper-rstudio.nix from R_LIBS_SITE
.libPaths(c(.libPaths(), "/nix/store/gvgxyzha3pf29qh98qhqcm2xlj4bh372-r-boot-1.3-28/library", "/nix/store/6l48x3ymc4y191bf43hsssfv5fjhwjkl-r-class-7.3-19/library", "/nix/store/fxlx7xwz020bpqsf68000f40236l05fx-r-MASS-7.3-54/library", "/nix/store/m0arnbdgmm7xqha1a3dpn7bn69gzhbrj-r-cluster-2.1.2/library", "/nix/store/as32vb3x18daf7qnjbx5ffbpymw0z96p-r-codetools-0.2-18/library", "/nix/store/ngczy6k0h1fr41cjnhmf01r39afrnhdk-r-foreign-0.8-81/library", "/nix/store/111fgjn7j3rq2zx50rl3n08j9ci1mivr-r-KernSmooth-2.23-20/library", "/nix/store/k62v8c2rps9shj56wm2przdxqfvgls99-r-lattice-0.20-44/library", "/nix/store/9lsyd2k6bh9965yg00w9jb4cyjynizgq-r-Matrix-1.3-4/library", "/nix/store/q172n2w2f3bdzjkidxdrczyllk14lx1x-r-mgcv-1.8-36/library", "/nix/store/fhy8vwcqz95vrdn5vp3b39qcvrjbiv46-r-nlme-3.1-152/library", "/nix/store/40731svpcvhgzhzngkwfz1shb3spfnsx-r-nnet-7.3-16/library", "/nix/store/ab8m6fl0x3kp99za4iq8450a5767ia50-r-rpart-4.1-15/library", "/nix/store/a3s8dv5y5am1r7lf3mnq5mqzjhjqxv0n-r-spatial-7.3-14/library", "/nix/store/rvfvgqxzb8g20nw08cnfi29bg8cv8rg2-r-survival-3.2-11/library", "/nix/store/afyixhqzjh6c0fy8619hyjgkj4r6l9w9-r-data.table-1.14.0/library"))

I hope this helps!

I am not sure if the .Rprofile that is created by rix can be appended to the fix_libs.R file through Nix or any other method.

[b-rodrigues]

I opened a PR to wrap R_PROFILE instead NixOS/nixpkgs#382071
that works but there seems to be something else: the local .Rprofile gets loaded, however, the .libPaths() still shows the system-level library of packages. So I get the install.packages(), remove.packages() and update.packages() in my environment tab (so I know .Rprofile was read), but .libPaths() is still wrong. Sourcing .Rprofile again then sets the correct .libPaths(). It seems that maybe one cannot set .libPaths() when executing .Rprofile?

[b-rodrigues]

So there might be solution: if that PR gets merged, then it seems that creating an .Renviron in the project folder with this:

R_LIBS_USER=""

and then changing the lines in the .Rprofile to this:

        current_paths <- .libPaths()
        .libPaths(current_paths)

seems to work to at least get rid of the user/ level library... but there's still wrong paths from other packages being loaded.

[philipp-baumann]

So there might be solution: if that PR gets merged, then it seems that creating an .Renviron in the project folder with this:

R_LIBS_USER=""

and then changing the lines in the .Rprofile to this:

        current_paths <- .libPaths()
        .libPaths(current_paths)

seems to work to at least get rid of the user/ level library... but there's still wrong paths from other packages being loaded.

Interesting approach! the RStudio hickup override mechanism is not new to me, but it's good to have a quick-fix for one part at least. I think RStudio has specific override mechanisms for the defaults, that happen even after loading .Rprofile in project dir. It has to be somewhere in the docs.