[Bioc-devel] Bioconductor extra/ repository

[Kasper Daniel Hansen]

Might be useful to list their dependencies in /extra, in case you want more
eyes to look at this?

On Fri, Jul 21, 2017 at 8:44 AM, Obenchain, Valerie <
Valerie.Obenchain at roswellpark.org> wrote:

> 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"<htt
> ps://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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