Create
cancel
Showing results for 
Search instead for 
Did you mean: 
Sign up Log in

Pipeline for R code leads to endless download loop and crash

FD
I'm New Here
I'm New Here
Those new to the Atlassian Community have posted less than three times. Give them a warm welcome!
September 26, 2023

Hi,

 

I would like to set up a basic pipeline to check my R package after I made a push or pull request.

The reprex I generated leads to a download loop of the pacman and remotes packages, until the process crashes due to memory limitation and the packages not being available.

The interesting thing is, that the packages always get downloaded with any R command I try.
I already tried rocker/tidyverse and rocker/verse with different versions. Nothing helped.

This is my reprex:

image: rocker/r-base:latest

pipelines:
default:
- step:
name: 'Test'
script:
- Rscript -e 'print("Hello")'

As long as I don't use any R commands my pipelines are working.

My final goal is to have a working pipeline that checks the package

image: rocker/verse:4.3.1

definitions:
caches:
site-library: /usr/local/lib/R/site-library

pipelines:
default:
- step:
name: 'Document and check'
caches:
- site-library
script:
- Rscript -e 'options(repos = c(CRAN = "https://cran.rstudio.com/"))'
- Rscript -e 'install.packages(c("remotes"))'
- Rscript -e 'devtools::install(upgrade = "Never")'
- Rscript -e 'devtools::document()'
- Rscript -e 'devtools::check()'

Thank you.

1 answer

1 vote
Theodora Boudale
Atlassian Team
Atlassian Team members are employees working across the company in a wide variety of roles.
September 27, 2023

Hi FD and welcome to the community!

I am not familiar with R, I just wanted to suggest that you can debug this locally with Docker as per the guide we have here:

This way you can see if the errors seem to be specific to the build running in Pipelines or not.

In case the build needs more memory, you can configure a step to use more memory:

Kind regards,
Theodora

Suggest an answer

Log in or Sign up to answer
DEPLOYMENT TYPE
CLOUD
TAGS
AUG Leaders

Atlassian Community Events