Unable to install rtracklayer on positcloud

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
    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’


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

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.

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

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.

Great! Thanks for letting me know.

This topic was automatically closed 21 days after the last reply. New replies are no longer allowed.

If you have a query related to it or one of the replies, start a new topic and refer back with a link.