[Bioc-devel] Bioconductor extra/ repository

[Obenchain, Valerie]

These are the dependencies in extra/:

- a4 (and family) uses nlcv

- RCytoscape uses XMLRPC

- microRNA uses Rlibstree

- arrayQualityMetrics uses SVGAnnotation

- AnalysisPageServer uses SVGAnnotation

Valerie



On 07/21/2017 05:58 AM, Michael Lawrence wrote:

You can just look at the package splash page and see the deps without links.

On Fri, Jul 21, 2017 at 5:56 AM, Kasper Daniel Hansen
<kasperdanielhansen at gmail.com><mailto:kasperdanielhansen at gmail.com> wrote:


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<mailto: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><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><
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><
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><https://
bioconductor.org/packages/3.6/extra><https://bioconductor.org/packages/3.6/extra>
                                                   CRAN
                             "https://cran.rstudio.com"<https://cran.rstudio.com><htt
ps://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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