Question

Help in installing certain pacakges

3

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lirongrossmann ▴ 40

@lirongrossmann-23954

Last seen 3.2 years ago

Hi all,

I have been trying to install several packages recently, both from R studio and from R and received the following error, for example for one of the packages, using:

BiocManager::install("monocle3")

"package ‘monocle3’ is not available (for R version 4.0.2)". I know that the packages I am looking for are in Bioconductor but cannot install them for some reason.

Any thoughts or recs?

Thanks!

software error install • 4.4k views

ADD COMMENT • link updated 3.7 years ago by Martin Morgan 25k • written 3.7 years ago by lirongrossmann ▴ 40

score 1 · Answer 1 · 2020-08-07

1

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Kevin Blighe ★ 3.9k

@kevin

Last seen 11 days ago

Republic of Ireland

Hello again,

The installation instructions for Monocle are here: https://cole-trapnell-lab.github.io/monocle3/docs/installation/

For all intents and purposes, you should be able to install via:

install.packages("devtools")
devtools::install_github('cole-trapnell-lab/leidenbase')
devtools::install_github('cole-trapnell-lab/monocle3')

I have just tested on R 4.0.2 and it installs okay.

You may need the additional Bioconductor dependencies:

BiocManager::install(c('BiocGenerics', 'DelayedArray', 'DelayedMatrixStats',
                       'limma', 'S4Vectors', 'SingleCellExperiment',
                       'SummarizedExperiment', 'batchelor', 'Matrix.utils'))

As a package, it is neither on the CRAN nor Bioconductor repositories.

Kevin

ADD COMMENT • link 3.7 years ago Kevin Blighe ★ 3.9k

3

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Or better yet

> library(BiocManager)
## have to do this because the remotes package has stupid defaults
## and will error on something as trivial as a binary package being built on a slightly different R version
> Sys.setenv(R_REMOTES_NO_ERRORS_FROM_WARNINGS = "true")
> BiocManager::install("cole-trapnell-lab/monocle3")

Which if you are on a Windows box requires Rtools to be installed first. And which will get and install whatever dependencies you may need.

As a general rule, it is best to just install pretty much any package using BiocManager::install because it automates the install.

ADD REPLY • link 3.7 years ago James W. MacDonald 65k