[R-sig-Debian] R Package: 'ggbreak' in Dockerfile

[Gerber, Lauren J]

Hi All,

Thank you all for your help.

I now added the line: library(BiocManager) to my script, as well as deleted the information below about the repo, which was causing an issue in my dockerfile:

RUN R -e "install.packages('BiocManager', repos='http://cran.us.r-project.org')"
RUN R -e "BiocManager::install('ggbreak')"

I really appreciate that this forum exists.

Br,
Lauren
--
Lauren J. Gerber
Bioinformatician
Precision Systems Medicine (Kallioniemi) Research Group
iCAN � Digital Precision Cancer Medicine Flagship
Institute for Molecular Medicine Finland (FIMM)
Nordic EMBL Partnership for Molecular Medicine
Biomedicum Helsinki 2U, D301a1
P.O. Box 20 (Tukholmankatu 8)
FI-00014 University of Helsinki, Finland
lauren.gerber using helsinki.fi

From: Dirk Eddelbuettel <edd using debian.org>
Date: Tuesday, 15. October 2024 at 17.12
To: Gerber, Lauren J <lauren.gerber using helsinki.fi>
Cc: r-sig-debian using r-project.org <r-sig-debian using r-project.org>
Subject: Re: R Package: 'ggbreak' in Dockerfile

Lauren,

On 15 October 2024 at 13:51, Gerber, Lauren J wrote:
| I just tried fixing my script and added library(BiocManager) before library
| (ggbreak), then rebuilt the image, and am still getting the same error.

You need _two_ distinct commands. First

    install.packages("BiocManager")

and second once that is done use it to install 'ggbreak' from BioConductor

    BiocManager::install("ggreak")

The two wrappers I showed in my earlier email do this for you, from the
command-line, which I find pleasant for both shell and docker use.
Preferences of course vary but the key here is that a) ggbreak is a
BioConductor package and b) you must use BiocManager::install() to install
those.

Dirk

--
dirk.eddelbuettel.com | @eddelbuettel | edd using debian.org

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