[Bioc-devel] Bioconductor extra/ repository

[Obenchain, Valerie]

Hi,

On August 7, 2017 we are planning to deprecate the devel Bioconductor extra/ repository. We currently maintain 4 Bioconductor repositories: software, annotation, data experiment and extra.

> library(BiocInstaller)
> biocinstallRepos()
                                               BioCsoft
           "https://bioconductor.org/packages/3.6/bioc"<https://bioconductor.org/packages/3.6/bioc>
                                                BioCann
"https://bioconductor.org/packages/3.6/data/annotation"<https://bioconductor.org/packages/3.6/data/annotation>
                                                BioCexp
"https://bioconductor.org/packages/3.6/data/experiment"<https://bioconductor.org/packages/3.6/data/experiment>
                                              BioCextra
          "https://bioconductor.org/packages/3.6/extra"<https://bioconductor.org/packages/3.6/extra>
                                                   CRAN
                             "https://cran.rstudio.com"<https://cran.rstudio.com>

The extra/ is a legacy repo created years ago to provide access to packages 'under development' but not yet in CRAN or Bioconductor. As things evolved, our package guidelines became more firm on the requirement that dependencies be offered in CRAN or Bioconductor so we'd like to do away with extra/.

We've contacted package authors that depend (import, suggests, enhances ...) on a package in extra/ and asked that they either find a reasonable replacement or submit the dependency to CRAN/Bioconductor. If these packages aren't fixed by August 7 (when extra/ is removed) they will fail to build. Some of you may depend on these packages so I wanted to pass this on as a heads up.

a4 (and family)  ## no response

RCytoscape ## author chose to deprecate in favor of RCy3

microRNA ## Martin fixed this one

arrayQualityMetrics  ## no response

AnalysisPageServer  ## no response


Valerie






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