[Bioc-devel] Bioconductor extra/ repository

[Michael Lawrence]

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> 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> 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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