Unable to install rtracklayer on positcloud

[davhum]

Hi all,

I have noticed older threads with similar issues for this bioconductor package - but back when posit was Rstudio cloud. As no solution was previously identified I am raising this again.

Below is the command and error log when trying to run this command. I don't believe this is a memory issue (using free account to get a feel for posit cloud) as memory bar does not move during install.

BiocManager::install("rtracklayer",update= FALSE)

• installing source package ‘SummarizedExperiment’ ...
  ** using staged installation
  ** R
  ** inst
  ** byte-compile and prepare package for lazy loading
  Killed
  ERROR: lazy loading failed for package ‘SummarizedExperiment’
• removing ‘/cloud/lib/x86_64-pc-linux-gnu-library/4.3/SummarizedExperiment’
  ERROR: dependency ‘SummarizedExperiment’ is not available for package ‘GenomicAlignments’
• removing ‘/cloud/lib/x86_64-pc-linux-gnu-library/4.3/GenomicAlignments’
  ERROR: dependency ‘GenomicAlignments’ is not available for package ‘rtracklayer’
• removing ‘/cloud/lib/x86_64-pc-linux-gnu-library/4.3/rtracklayer’

Regards,
D

[Gabor]

@davhum

** byte-compile and prepare package for lazy loading
Killed

That looks like the out-of-memory killer to me, so you probably need more memory in the machine.

[alex_chisholm]

I think you are right, Gabor. On a professional plan with 8GB RAM and 2CPUs, I did not have issues installing or loading the package.

install.packages("BiocManager")
BiocManager::install("rtracklayer",update= FALSE)
library(rtracklayer)

[Gabor]

You probably only need more memory for the installation, so you could also create a binary R package on the larger machine, store it only online in a CRAN-like repo, and install from there. Some extra work, but helps keep the machine small.

[davhum]

@Gabor

only need more memory for the installation

Great! Thanks for letting me know.