Need Help?

Search our documentation and community forum

Terra is a cloud-native platform for biomedical researchers to access data, run analysis tools, and collaborate.
Terra powers important scientific projects like FireCloud, AnVIL, DataSTAGE. Learn more.

R notebook error: installation path not writeable

Comments

4 comments

  • Avatar
    Sushma Chaluvadi

    Hi Beth,

    The team is investigating and we will get bak to you with an update!

    0
    Comment actions Permalink
  • Avatar
    Beri Shifaw

    Hi Beth,

    What do you mean by "Bioconductor preconfigured notebooks"?

    0
    Comment actions Permalink
  • Avatar
    Elizabeth Sheets

    The second option under the runtime configuration environment:

    0
    Comment actions Permalink
  • Avatar
    Beri Shifaw

    Hi Beth, 

    I spoke with the dev team and they mentioned most of these are already installed and current

    pkgs = c("Rsamtools", "data.table", "qqman", "RColorBrewer", "tidyr", "dplyr")
    pkgs %in% rownames(installed.packages())

    A better strategy would be to install only packages that are not yet installed

    pkgs = pkgs[!pkgs %in% rownames(installed.packages())]

    which may only be qqman.

    For Bioconductor, where Rsamtools comes from, the recommend installation approach for CRAN or Bioconductor packages is

    BiocManager::install(pkgs)

    or to install new packages and update any out-of-date packages with

    BiocManager::install(pkgs, ask=FALSE)
    0
    Comment actions Permalink

Please sign in to leave a comment.

Powered by Zendesk