tidyverse loading difference between JupyterLab and RStudio

Bug description

The R package tidyverse loads successfully in JupyterLab but fails in RStudio.

We use as an example this repository that contains the description of a R environment with the tidyverse package installed with conda.

Expected behaviour

The R instruction

library(tidyverse)

should work without any error.

Actual behaviour

In JupyterLab, we can load tidyverse both in a R notebook:

and in a terminal:

In RStudio, this fails:

For debugging purpose, here is the output of the sessionInfo() instruction:

R version 4.1.3 (2022-03-10)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Ubuntu 18.04.6 LTS

Matrix products: default
BLAS/LAPACK: /srv/conda/envs/notebook/lib/libopenblasp-r0.3.20.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

loaded via a namespace (and not attached):
 [1] fansi_1.0.3     utf8_1.2.2      digest_0.6.29   crayon_1.5.1   
 [5] IRdisplay_1.1   repr_1.1.4      lifecycle_1.0.1 jsonlite_1.8.0 
 [9] evaluate_0.15   pillar_1.7.0    rlang_1.0.2     cli_3.2.0      
[13] uuid_1.1-0      vctrs_0.4.1     ellipsis_0.3.2  IRkernel_1.2   
[17] tools_4.1.3     glue_1.6.2      fastmap_1.1.0   compiler_4.1.3 
[21] base64enc_0.1-3 pbdZMQ_0.3-7    htmltools_0.5.2

How to reproduce

Create an environment with repo2docker and this repository.

Try to run the R command:

library(tidyverse)

You are sure tidyverse is loaded correctly when you can run this second command also without error:

as_tibble(mtcars)

Your personal set up

• OS: Linux Ubuntu 20.04
• Docker version: 20.10.14, build a224086
• repo2docker version: 2022.02.0+19.g1d218af

A possible lead (or not)

I suspect an issue with the availability of C++ libraries.

In a terminal, in RStudio, I have:

$ strings /usr/lib/x86_64-linux-gnu/libstdc++.so.6 | grep GLIBCXX_3.4.26
$ strings /srv/conda/envs/notebook/lib/libstdc++.so.6 | grep GLIBCXX.3.4.26
GLIBCXX_3.4.26
GLIBCXX_3.4.26

So, I guess R within RStudio should have access to /srv/conda/envs/notebook/lib/libstdc++.so.6 rather to /usr/lib/x86_64-linux-gnu/libstdc++.so.6 only.

What puzzles me is that in RStudio we have:

> Sys.getenv("LD_LIBRARY_PATH")
[1] "/srv/conda/envs/notebook/lib/R/lib"

but in JupyterLab we have:

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

So this lead could be wrong…

[manics]

Some relevant information in https://discourse.jupyter.org/t/openssl-mismatch-between-rstudio-and-conda-environments/14123/

[fkohrt]

I am having a related issue when running Shiny apps:

Starting a Shiny app from within RStudio…

install.packages(c("leaflet", "shinydashboard", "dplyr", "curl"))
options(warn = 1)
shiny::runApp("r/bus-dashboard")

…leads to the following error:

Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/srv/conda/envs/notebook/lib/R/library/Rcpp/libs/Rcpp.so':
  /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.26' not found (required by /srv/conda/envs/notebook/lib/R/library/Rcpp/libs/Rcpp.so)

I tried installing libstdc++6 and gcc-8 via apt.txt, but that didn’t help. The Shiny interface at /shiny/r/bus-dashboard/ does work, however, as does running the code above from JupyterLab.

Here’s a repository for you to check: gitlab.com/fkohrt/binder-test

environment.yml

channels:
  - conda-forge
dependencies:
  - python
  - nbgitpuller
  - r-base

Most important, this is only an issue when using environment.yml to install R:

channels:
  - conda-forge
dependencies:
  - python
  - nbgitpuller
  - r-base

If I use requirements.txt instead, none of the issues are present – I can do library(tidyverse) and shiny::runApp("r/bus-dashboard") without any problems, but now the Shiny interface at /shiny/r/bus-dashboard/ does not work (An error has occurred!). This can be verified with the following repository: gitlab.com/fkohrt/RMarkdown-sandbox