https://github.com/vjcitn/biocoffpiste
Code that aids experts who wish to use incompatible versions of R and Bioconductor
https://github.com/vjcitn/biocoffpiste
Last synced: 4 months ago
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Code that aids experts who wish to use incompatible versions of R and Bioconductor
- Host: GitHub
- URL: https://github.com/vjcitn/biocoffpiste
- Owner: vjcitn
- Created: 2023-05-13T11:51:18.000Z (about 2 years ago)
- Default Branch: main
- Last Pushed: 2023-05-14T01:26:23.000Z (about 2 years ago)
- Last Synced: 2025-01-09T13:46:14.347Z (5 months ago)
- Language: R
- Size: 2.93 KB
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 2
-
Metadata Files:
- Readme: README.md
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README
# BiocOffPiste
Code that aids experts who wish to use incompatible versions of R and Bioconductor
Function `installOffPiste(x, version=v)` will arrange to set up the repositories for
`install.packages` to use to install packages named in vector `x`, based on version `v` of Bioconductor.
The primary use case is the installation of Bioconductor packages in R-devel
in the interval I from April to October of each year, when the official version
of R in use for Bioconductor is R-patched.
We call this activity "off piste" because protections of consistency and
coherence provided by BiocManager and the Bioconductor repository system
are lost. `BiocManager::valid()` won't even run in interval I
# Installation
```
devtools::install_github("vjcitn/BiocOffPiste")
```
# Gotchas
If a Bioconductor package hasn't "propagated" in the Bioconductor build system,
you might need to set `version` in your call to `installOffPiste` to find any
viable source version of the unpropagated package.
For example, om May 13, 2023, I needed to do
```
installOffPiste("GenomeInfoDbData", version="3.17")
```
in order to install the 3.18 version of DESeq2 in R 4.4.