Hello Renku team !
I logged in to my R/Bioconductor projects to find that I lost access to R packages installed from install.R.
For example:
library(dplyr)
Error in library(dplyr) : there is no package called ‘dplyr’
I don’t understand what’s causing the issue, and I’m not sure as to when that happened, but most likely within the last two weeks.
What surprises me is that those packages are inaccessible in all Renku projects using them. I am worried that something went wrong at the Docker layer level…
I should mention that I am working on the EPFL-SV deployment of Renku.
Anyway, if there is a way to trigger a complete rebuild of the project from scratch I will try it.
Thanks !
Cyril Pulver
Hi @bopekno - apologies that this question went unanswered - have you found a solution? If I had to guess I would say that the session probably didn’t start with the correct image.
Hello @rrrrrok, in the end I changed strategy and install bioconductor from the install.R script. But I could not solve the issue with the official renku bionconductor image.
Hi @bopekno, I just tried this with a new project using the bioc template and it seems to work fine. The install.R I am using is just:
install.packages("dplyr")
Then in RStudio:
Bioconductor version 3.12 (BiocManager 1.30.10), ?BiocManager::install for help
> library(dplyr)
Attaching package: ‘dplyr’
The following objects are masked from ‘package:stats’:
filter, lag
The following objects are masked from ‘package:base’:
intersect, setdiff, setequal, union
Can you check that the CI job passed without problems and the image was pushed? You find it if you go to GitLab for your project, then on the left go to CI/CD → jobs
If that all looks fine and the image still looks like it doesn’t have the right dependencies installed, the wrong image might be used for some reason when you launch your environment.