Unabble to load some packages in Rstudio interface while it works on Jupyter Lab
CVandiedonck opened this issue · comments
Bug:
1. When loading an environment with this template (and all other environments I tested with an R kernel), it is impossible in the RStudio interface to load tidyverse package with the R console...
2. ...whereas there is not such issue using Jupyter Lab interface:
3. Similarly, when using the RStudio interface and a Rmardown file (cf. next paragraph), the error still occurs when running the chunk to load tidyverse
Need mardown package to test this point cf https://github.com/CVandiedonck/template-r/tree/patch-2
4. But suprinsingly, the error does not longer occur when knitting a .Rmd document.
5. The generated .html file is fine and the sessionInfo() command output shows tidyverse was well loaded (but readxl is not).
Description of the error and extension to other packages
The error indicates an issue when trying to load the readxl package which is part of the tidyverse package. The same error occurs when trying to load this package on its own, as well as several other packages that are installed with this "tempalte-r" in the environment, some being very useful like devtools:
- bslib
- devtools
- isoland
- later
- pkgload
- promises
- rcpp
- rematch
- sass
- testhat
- vroom
- data.table
Question @plasmabio/quantstack
Is this an issue in Plasma, something missing in the configuration files of the template or an issue with the Ubuntu server?
For the server, I tried on different instances (adenine or uracile at Université Paris Cité) or the VM machine you granted us acess too. The screenshots were generated with this VM.
This issue might be related to this discussion and this one "libstdc++.so.6: version `GLIBCXX_3.4.26' not found on Linux"
This bug is also obtained with repo2docker. I created the corresponding issue jupyterhub/repo2docker#1153
For troubleshooting, these commands are useful:
library(tidyverse)
sessionInfo()
Sys.getenv("LD_LIBRARY_PATH")
I just checked with the latest repo2docker and the troubleshooting steps mentioned above, and it looks like it is working fine now?
So hopefully this issue will be fixed by plasmabio/plasma#217, which updates to the latest repo2docker image.
Yes it is all fixed with the update of repo2docker. We checked this during the summer and forgot to close the issue. It has been working well since.