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 <[email protected]><mailto:[email protected]> 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 < [email protected]<mailto:[email protected]>> 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 This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. [[alternative HTML version deleted]] _______________________________________________ [email protected]<mailto:[email protected]> mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] _______________________________________________ [email protected]<mailto:[email protected]> mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. [[alternative HTML version deleted]] _______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
