affxparser: Affymetrix File Parsing SDK

Installation

R package affxparser is available on Bioconductor and can be installed in R as:

install.packages("BiocManager")
BiocManager::install("affxparser")

Pre-release version

To install the pre-release version that is available in Git branch develop on GitHub, use:

remotes::install_github("HenrikBengtsson/affxparser", ref="develop")

This will install the package from source. Because of this and because this package also compiles native code, Windows users need to have Rtools installed and macOS users need to have Xcode installed.

Development workflow

The Bioconductor development version of the affxparser package is available at https://bioconductor.org/packages/devel/bioc/html/affxparser.html. Bioconductor builds and checks this development version based on the source code in the devel branch of the package Git repository available at https://code.bioconductor.org/browse/affxparser/devel/.

The master branch of this GitHub repository is is manually kept in sync with the devel branch on the Bioconductor Git repository. If there's an update made directly to the Bioconductor devel branch, we merge it into the master branch on GitHub. Vice versa, if there are updates to the GitHub master branch, we merge those into the devel branch on Bioconductor.

The most common, and recommend workflow is to develop toward GitHub instead of directly toward the Bioconductor servers. By working toward GitHub first, we get instant checking of the code across different operating systems and R versions on GitHub Actions. This way, we can validate the code immediately, instead of having to way 24-36 hours for it to be validated on the Bioconductor check servers.

Contributing

To contribute to this package, please see CONTRIBUTING.md.