Can't install packages in a fresh project

[mikkmart]

After creating a fresh project, I can't install any packages with renv. Here's the steps I've taken:

usethis::create_project("projects/renv-test")

# In the new project
renv::init()
renv::install("praise")
#> Retrieving 'https://cran.rstudio.org/bin/windows/contrib/4.1/praise_1.0.0.zip' ...
#> 	OK [downloaded 19.4 Kb in 0.4 secs]
#> Installing praise [1.0.0] ...
#> 	FAILED
#> Error installing package 'praise':
#> ==================================
#> 
#> * installing to library 'C:/Users/mikkmart/OneDrive - Orion Corporation/Tiedostot/R/win-library/4.1'
#> package 'praise' successfully unpacked and MD5 sums checked
#> Error: install of package 'praise' failed ["~/R/projects/renv-test/renv/staging/1/praise" does not exist]
dir.exists("~/R/projects/renv-test/renv/staging")
#> [1] TRUE

Maybe ~ is not expanded "correctly"? This has caused me headaches before:

path.expand("~")
#> [1] "C:/Users/mikkmart/OneDrive - Orion Corporation/Tiedostot"

The "installing to library" location also looks strange -- that's not somewhere I'd want my packages to go. (I normally set R_LIBS_USER="C:/Users/mikkmart/R/win-library/4.1")

[kevinushey]

Do you know why the renv private library isn't being used in your project? What is the output of .libPaths()?

[Danny-dK]

Could this be because you are using a network drive (OneDrive). I've had this staging issue on various occasions when working on Windows in a network drive. In the Project Rprofile folder I added:

	# Use following only when package installation fails. The symlink one tells renv to not look in 
	# the global renv library install cache located somewhere on the c drive (which may happen when working
	# from a network drive). The transactional indicates whether to install libraries first into a temp 
	# library (staging) before copying it into the actual project library. this again may cause issues if 
	# TRUE when working on network drives.
	
        # options(renv.config.cache.symlinks = FALSE)
	 options(renv.config.install.transactional = FALSE)

 source("renv/activate.R")

The transactional option worked. If it still would not work, the symlink option could possibly solve it as well (remove the # in front of that option if the transactional option did not solve it).

[mikkmart]

@kevinushey no, I have no idea. .libPaths() in the active project seems to indicate the private library should be there:

.libPaths()
#> [1] "C:/Users/mikkmart/OneDrive - Orion Corporation/Tiedostot/R/projects/renv-test/renv/library/R-4.1/x86_64-w64-mingw32"
#> [2] "C:/Users/mikkmart/R/R-4.1.2/library" 

... Although that said, I thought it would have been created under AppData -- at least that's what happened on my personal Windows PC.

@Danny-dK Thanks for sharing! I tried adding that option, but unfortunately to no effect. I don't think our OneDrive is a network drive, it should be just a local folder that gets synced to the cloud -- so this is probably related to something else.

[mikkmart]

Here's the full renv::diagnostics() output, in case there's something useful to be found there:

Diagnostics

> renv::diagnostics()
Diagnostics Report [renv 0.15.2]
================================

# Session Info =======================
R version 4.1.2 (2021-11-01)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19042)

Matrix products: default

locale:
[1] LC_COLLATE=English_United Kingdom.1252 
[2] LC_CTYPE=English_United Kingdom.1252   
[3] LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C                           
[5] LC_TIME=English_United Kingdom.1252    

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

loaded via a namespace (and not attached):
[1] compiler_4.1.2 tools_4.1.2    renv_0.15.2   

# Project ============================
Project path: "~/R/projects/renv-test"

# Status =============================
* The project is already synchronized with the lockfile.

# Packages ===========================
           Library Source Lockfile Source Path Dependency
KernSmooth 2.23-20   CRAN     <NA>   <NA>  [2]       <NA>
MASS        7.3-54   CRAN     <NA>   <NA>  [2]       <NA>
Matrix       1.3-4   CRAN     <NA>   <NA>  [2]       <NA>
boot        1.3-28   CRAN     <NA>   <NA>  [2]       <NA>
class       7.3-19   CRAN     <NA>   <NA>  [2]       <NA>
cluster      2.1.2   CRAN     <NA>   <NA>  [2]       <NA>
codetools   0.2-18   CRAN     <NA>   <NA>  [2]       <NA>
foreign     0.8-81   CRAN     <NA>   <NA>  [2]       <NA>
lattice    0.20-45   CRAN     <NA>   <NA>  [2]       <NA>
mgcv        1.8-38   CRAN     <NA>   <NA>  [2]       <NA>
nlme       3.1-153   CRAN     <NA>   <NA>  [2]       <NA>
nnet        7.3-16   CRAN     <NA>   <NA>  [2]       <NA>
renv        0.15.2   CRAN   0.15.2   CRAN  [1]     direct
rpart       4.1-15   CRAN     <NA>   <NA>  [2]       <NA>
spatial     7.3-14   CRAN     <NA>   <NA>  [2]       <NA>
survival    3.2-13   CRAN     <NA>   <NA>  [2]       <NA>
utils         <NA>   <NA>     <NA>   <NA>  [2]   indirect

[1]: C:/Users/mikkmart/OneDrive - Orion Corporation/Tiedostot/R/projects/renv-test/renv/library/R-4.1/x86_64-w64-mingw32
[2]: C:/Users/mikkmart/R/R-4.1.2/library                                                                                

# ABI ================================
* ABI conflict checks are not yet implemented on Windows.

# User Profile =======================
                                                              Source  Package Require Version   Dev
1 C:/Users/mikkmart/OneDrive - Orion Corporation/Tiedostot/.Rprofile fortunes                 FALSE

# Settings ===========================
List of 10
 $ bioconductor.version     : chr(0) 
 $ external.libraries       : chr(0) 
 $ ignored.packages         : chr(0) 
 $ package.dependency.fields: chr [1:3] "Imports" "Depends" "LinkingTo"
 $ r.version                : chr(0) 
 $ snapshot.type            : chr "implicit"
 $ use.cache                : logi TRUE
 $ vcs.ignore.cellar        : logi TRUE
 $ vcs.ignore.library       : logi TRUE
 $ vcs.ignore.local         : logi TRUE

# Options ============================
List of 8
 $ defaultPackages                     : chr [1:6] "datasets" "utils" "grDevices" "graphics" ...
 $ download.file.method                : chr "wininet"
 $ download.file.extra                 : NULL
 $ install.packages.compile.from.source: chr "interactive"
 $ pkgType                             : chr "both"
 $ repos                               : Named chr [1:2] "http://orpdev.orion.fi/r-packages/latest" "https://cran.rstudio.org"
  ..- attr(*, "names")= chr [1:2] "orion" "CRAN"
 $ renv.consent                        : logi TRUE
 $ renv.verbose                        : logi TRUE

# Environment Variables ==============
HOME                        = C:/Users/mikkmart/OneDrive - Orion Corporation/Tiedostot
LANG                        = <NA>
MAKE                        = <NA>
R_LIBS                      = <NA>
R_LIBS_SITE                 = <NA>
R_LIBS_USER                 = C:/Users/mikkmart/OneDrive - Orion Corporation/Tiedostot/R/projects/renv-test/renv/library/R-4.1/x86_64-w64-mingw32;C:/Users/mikkmart/R/R-4.1.2/library
RENV_DEFAULT_R_ENVIRON      = <NA>
RENV_DEFAULT_R_ENVIRON_USER = C:\Users\mikkmart\OneDrive - Orion Corporation\Tiedostot\.Renviron
RENV_DEFAULT_R_LIBS         = <NA>
RENV_DEFAULT_R_LIBS_SITE    = <NA>
RENV_DEFAULT_R_LIBS_USER    = C:\Users\mikkmart/R/win-library/4.1
RENV_DEFAULT_R_PROFILE      = //sfisp-sasdatap/biostat/R/setup/config/Rprofile.site
RENV_DEFAULT_R_PROFILE_USER = <NA>
RENV_PROJECT                = C:/Users/mikkmart/OneDrive - Orion Corporation/Tiedostot/R/projects/renv-test

# PATH ===============================
- C:\Users\mikkmart\R\Rtools-4.0\usr\bin
- C:\Users\mikkmart\R\Rtools-4.0\mingw64\bin
- C:\Users\mikkmart\R\Rtools-4.0\usr\bin
- C:\Users\mikkmart\R\Rtools-4.0\usr\bin
- C:\Users\mikkmart\R\Rtools-4.0\mingw64\bin
- C:\Users\mikkmart\R\Rtools-4.0\usr\bin
- C:\Users\mikkmart\R\R-4.1.2\bin\x64
- C:\Users\mikkmart\R\R-4.1.2\bin\x64
- C:\Program Files (x86)\Microsoft SDKs\Azure\CLI2\wbin
- C:\Oracle\Ora11g2\bin
- C:\Program Files (x86)\Common Files\Oracle\Java\javapath
- C:\WINDOWS\system32
- C:\WINDOWS
- C:\WINDOWS\System32\Wbem
- C:\WINDOWS\System32\WindowsPowerShell\v1.0\
- C:\WINDOWS\System32\OpenSSH\
- C:\Program Files\Docker\Docker\resources\bin
- C:\ProgramData\DockerDesktop\version-bin
- C:\Users\mikkmart\AppData\Local\Programs\Python\Python39\Scripts\
- C:\Users\mikkmart\AppData\Local\Programs\Python\Python39\
- C:\Users\mikkmart\AppData\Local\Programs\Python\Launcher\
- C:\Users\mikkmart\AppData\Local\Microsoft\WindowsApps
- C:\Users\mikkmart\AppData\Local\Programs\Git\cmd
- C:\Users\mikkmart\AppData\Local\Programs\Microsoft VS Code\bin
- C:\Users\mikkmart\AppData\Local\gitkraken\bin
- C:\Users\mikkmart\R\R-4.1.2\bin
- C:\Users\mikkmart\R\Rtools-4.0\usr\bin
- C:\Users\mikkmart\bin
- C:\Users\mikkmart\opt\node-v14.15.4-win-x64
- C:\Users\mikkmart\opt\highlight-4.1-x64
- C:\Users\mikkmart\opt\sqlite-tools-win32-x86-3360000
- C:\Users\mikkmart\Miniconda3\condabin
- C:\Users\mikkmart\OneDrive - Orion Corporation\scripts
- C:\Users\mikkmart\AppData\Roaming\TinyTeX\bin\win32

# Cache ==============================
There are a total of 0 package(s) installed in the renv cache.
Cache path: "C:/Users/mikkmart/AppData/Local/R/cache/R/renv/cache/v5/R-4.1/x86_64-w64-mingw32"

[mikkmart]

Okay so I've narrowed this down a bit: the problem seems to be caused by these lines in my Rprofile.site:

user_libs <- function() {
  libs <- strsplit(Sys.getenv("R_LIBS_USER"), ";")[[1]]
  suppressWarnings(normalizePath(libs))
}

.libPaths(c(user_libs(), .libPaths()))

(Which I'm honestly not quite sure why it's there anyways -- I thought that's essentially what setting R_LIBS_USER does anyway. However, I'm hesitant to go changing that, since it affects other users, too.)

[Danny-dK]

I'm certainly not as versed and an expert as Kevin (not even remotely coming close), so apologies if this is diluting the conversation.

@mikkmart That is not a default contents of Rprofile.site? Never had that in my Rprofile.site. My limited info on that is that the Rprofile.site are site wide settings overruling any other settings set in Rprofile or Renviron settings. I made the mistake of adding specific library paths in the Rprofile.site as well which did not play nice with renv. I removed it and placed those settings in the .Rprofile in Sys.getenv('HOME'). Then renv::install did pickup the project library. Could you try renv::install("praise", library = "C:/Users/mikkmart/OneDrive - Orion Corporation/Tiedostot/R/projects/renv-test/renv/library/R-4.1/x86_64-w64-mingw32") to see if specifically setting the library is able to install into that location.

Your diagnostics show C:\Users\mikkmart\R\R-4.1.2\bin\x64. Is that where your R is installed to and where you found the rprofile.site file at R\R-4.1.2\etc\? If so, than adjusting the rprofile.site would only affect your user, as other users have their own C user folder. Did you install R yourself or has this been packaged by your organization and made available to its employees (a process done in my organization as well, which gave some headaches in using R). Just curious what the result is of Sys.getenv("HOME") for you.

I'm not sure if adding a .Renviron file to your project root directory with RENV_PATHS_LIBRARY=${HOME}/projects/renv-test/renv would help in overruling the Rprofile.site settings.

[mikkmart]

Thanks @Danny-dK, I appreciate you taking the time to troubleshoot this with me!

You're right, that code is certainly not in a default Rprofile.site. It's my own doing from setting this up a few years back. We don't have a packaged R set-up, but I've instructed colleagues to run a set-up script after installation. The script appends to their .Renviron the location of this profile file using the R_PROFILE variable. The Rprofile.site file itself is hosted on a network drive, which is why changing it would affect other users, too.

The purpose of the Rprofile.site at the moment is two-fold:

• It appends our internal package repository URL to getOption("repos").
• It sets the default library location to point to "${USERPROFILE}/R/win-library/%v" rather than the corresponding under $HOME. This is to avoid installing packages in a OneDrive synced location.

The need for the second point indeed caused by HOME (managed by IT with most other (non-R) users in mind):

Sys.getenv("HOME")
#> [1] "C:/Users/mikkmart/OneDrive - Orion Corporation/Tiedostot"

However, since I seem to have already baked in the default library configuration into the .Renviron template with R_LIBS_USER, I'm not sure that Rprofile.site needs to worry about that anymore. As I mentioned, removing the setting of .libPaths() seems to resolve the issue with renv, and it looks like R_LIBS_USER alone handles the library location for non-renv use.

That said, shouldn't activating renv still also override any .libPaths() set in Rprofile.site? Strangely enough it seems to work on the project level (in the interactive R session .libPaths() points to the private library), but not with renv::install().

[mikkmart]

And to answer some of your specific questions I managed to side-step earlier: Setting the library option in renv::install() doesn't help -- I still get the same error. Strangely enough, adding a .Renviron in the project directory also doesn't help -- I would have thought it would override my user .Renviron and thus solve the problem indirectly.

[Danny-dK]

Yeah I did not get that either, apparently the rprofile.site is overruling on everything. Would you be able to write a .Rprofile instead of a Rprofile.site that contains the same contents? The .Rprofile is normally also located at the $HOME variable which R always checks for its presence at startup. Thus any user running R will run the .Rprofile file present in their $HOME location (whatever that drive actually is) and set the library paths required. I had the same thing where I placed my contents of Rprofile.site in a .Rprofile in my $HOME and R/Rstudio picked up the correct settings. When running renv, this resulted in the correct library present in the renv project for me.

Did you try the renv::install with library specification using the aforementioned option setting in the .Rprofile found in your project root directory? If that does not work. Could you try renv::purge("praise") and try again with library specification and the aforementioned options?

If all above fails.... then I'm out of options.

[mikkmart]

I can't really co-opt the user's personal .Rprofile for these settings, because then that would take away their ability to manage settings that should be specific to them only (e.g. getOption("usethis.full_name")).

And yeah, I'm not having any luck with setting the options you mentioned. I've also been repeatedly purge()ing the installation after it's been successful by disabling the Rprofile.site.

I think this just boils down to setting .libPaths() in Rprofile.site. I added a line to print .libPaths() just before setting it there, and here's what I'm getting:

Restarting R session...

.libPaths() is:
C:/Users/mikkmart/R/win-library/4.1
C:/Users/mikkmart/R/R-4.1.2/library
Prepending user libs:
C:\Users\mikkmart\R\win-library\4.1
* Project '~/R/projects/renv-test' loaded. [renv 0.15.2]
> .libPaths()
[1] "C:/Users/mikkmart/OneDrive - Orion Corporation/Tiedostot/R/projects/renv-test/renv/R-4.1/x86_64-w64-mingw32"
[2] "C:/Users/mikkmart/R/R-4.1.2/library"                                                                        
> renv::install("praise")
Retrieving 'https://cran.rstudio.org/bin/windows/contrib/4.1/praise_1.0.0.zip' ...
	OK [file is up to date]
Installing praise [1.0.0] ...
	FAILED
Error installing package 'praise':
==================================

.libPaths() is:
C:/Users/mikkmart/OneDrive - Orion Corporation/Tiedostot/R/projects/renv-test/renv/staging/1
C:/Users/mikkmart/OneDrive - Orion Corporation/Tiedostot/R/projects/renv-test/renv/R-4.1/x86_64-w64-mingw32
C:/Users/mikkmart/R/R-4.1.2/library
C:/Users/mikkmart/OneDrive - Orion Corporation/Tiedostot/R/win-library/4.1
Prepending user libs:
C:\Users\mikkmart\OneDrive - Orion Corporation\Tiedostot\R\win-library\4.1
* installing to library 'C:/Users/mikkmart/OneDrive - Orion Corporation/Tiedostot/R/win-library/4.1'
package 'praise' successfully unpacked and MD5 sums checked
Error: install of package 'praise' failed ["~/R/projects/renv-test/renv/staging/1/praise" does not exist]                                                            

If I comment out the .libPaths() setting in Rprofile.site, I instead just get:

Restarting R session...

.libPaths() is:
C:/Users/mikkmart/R/win-library/4.1
C:/Users/mikkmart/R/R-4.1.2/library
* Project '~/R/projects/renv-test' loaded. [renv 0.15.2]
> .libPaths()
[1] "C:/Users/mikkmart/OneDrive - Orion Corporation/Tiedostot/R/projects/renv-test/renv/R-4.1/x86_64-w64-mingw32"
[2] "C:/Users/mikkmart/R/R-4.1.2/library"                                                                        
> renv::install("praise")
Retrieving 'https://cran.rstudio.org/bin/windows/contrib/4.1/praise_1.0.0.zip' ...
	OK [file is up to date]
Installing praise [1.0.0] ...
	OK [installed binary]
Moving praise [1.0.0] into the cache ...
	OK [moved to cache in 11 milliseconds]

[mikkmart]

@kevinushey is this something to be addressed in renv, or is it just necessary to avoid .libPaths() in Rprofile.site?

[Danny-dK]

You don't have to replace the .Rprofile though, you can add lines to .Rprofile. Renv does this as well if you have a project that included a .Rprofile and you later on initialize renv in the already existing project, renv will then only add source(renv/activate.R), it will not delete or overwrite any existing text in that file. That would mean that any other user settings someone has, still remains intact. (maybe I'm misunderstanding, I'll let the more experts take over :) )

[kevinushey]

This probably should be addressed in renv. We should find a way to ensure the library path requested by renv still takes precedence over anything that's happening in Rprofile.site when a package is installed.

I was able to reproduce with this script:

override <- file.path(tempdir(), "library")
dir.create(override)

# use a custom Rprofile.site
site <- file.path(tempdir(), "Rprofile.site")

fmt <- '
.libPaths(c(%s, .libPaths()))
writeLines("Library paths:")
writeLines(.libPaths())
'

text <- sprintf(fmt, shQuote(normalizePath(override, winslash = "/")))
writeLines(text, con = site)
Sys.setenv(R_PROFILE = site)

# try installing a package
renv::install("praise")

Strangely, it seems to only effect renv on Windows, not on other platforms?

[kevinushey]

Should be fixed up now by 86edb40. Thank you for the bug report!

[mikkmart]

Thank you for the fix! I can confirm that it's worked for me, too.

And thank you @Danny-dK for the helpful discussion!