Out of memory package installation

I am trying the following code on a Free Rstudio cloud account

BiocManager::install(version = '3.12')
BiocManager::install("tidybulk", version="devel")

And I get

Bioconductor version 3.12 (BiocManager 1.30.10), R 4.0.2 (2020-06-22)
Installing package(s) 'tidybulk'
trying URL 'https://bioconductor.org/packages/3.12/bioc/src/contrib/tidybulk_1.1.6.tar.gz'
Content type 'application/x-gzip' length 4283900 bytes (4.1 MB)
downloaded 4.1 MB

* installing *source* package ‘tidybulk’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading

The downloaded source packages are in
Installation path not writeable, unable to update packages: MASS, mgcv, nlme,
Warning message:
In install.packages(...) :
  installation of package ‘tidybulk’ had non-zero exit status

Is this expected?

See this post

There are some R packages that require system libraries. If you’re using a package that uses a system library that is not available in RStudio Cloud, you won’t be able to use that package as currently it’s not possible for users to install these. We recommend posting this on RStudio Community as a request to install the system library and the RStudio Cloud team should be able to help.

Thanks for your kind reply. I'm not sure however what system libraries you are referring to. Could you please elabirate?

Packages that require compilation from source rely on various resources in the operating system in what are called shared libraries. When compiling, if the library doesn't exist, many packages will attempt to install it. However, doing so requires user permissions at the system administrator level and will fail for lack of authentication.

1 Like

Hi @ste,

This appears to be the same issue that I've referenced in bioconductor packages fail R4.0. Could you try installing the package after expanding your memory resources?


I ended up requesting temporary more memory 8Gb for the installation and reverted back.

Thanks for the suggestions!

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