Out of memory during package installation

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1

The following commands

install.packages("BiocManager", repos = "https://cran.r-project.org")
BiocManager::install("BSgenome")

lead eventually to

** byte-compile and prepare package for lazy loading
Killed
ERROR: lazy loading failed for package

I guess the problem is that memory is exhausted. Is there any workaround?

In context, I'm offering an ad hoc course, one of the participants opted to use rstudio.cloud, we're getting to the end of the course (week 5!), and exploring Bioconductor.

The instructions above (install CRAN package BiocManager, use BiocManager to install appropriately versioned BIoconductor packages) is the standard Bioconductor package installation procedure. BSgenome is a fairly important package, and it's failure to install means its 375 reverse dependencies also don't install.

A partial workaround is to use the INSTALL_opts = "--no-byte-compile" of install.packages() / BiocManager::install(), but a second package then fails to install in a way that I have not been able to work around

> BiocManager::install("VariantAnnotation")
...
** preparing package for lazy loading
Killed
ERROR: lazy loading failed for package ‘VariantAnnotation’

Or perhaps this is really just telling me that I've reached the limit of rstudio.cloud use at the free tier?

2

Hello

The best path forward is for the student to file a support ticket with the details you have provided here (and the project id)

thanks
sam

3

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