So, I'm attempting to update my CRAN package and it depends on several other packages. What I notice is that many packages fail with errors on OSX checks due to Bioconductor packages not being visible when CRAN checks are run. I guess I'm posting first to Bioconductor because I know that the community probably knows the ins and outs of package development when working with Bioconductor packages better than the r package developer list. I haven't yet checked there, but I'm wondering if the community has any insight in how to solve these issues.
For example: https://www.r-project.org/nosvn/R.check/r-release-osx-x86_64/PlasmaMutationDetector-00check.html Displays the following error. checking package dependencies ... ERROR Packages required but not available: 'GenomicRanges', 'VariantAnnotation', 'S4Vectors', 'Rsamtools', 'rtracklayer', 'SummarizedExperiment'
A similar thing happens for other packages: https://cran.r-project.org/web/checks/checkresultsgkmSVM.html http://cran.cnr.berkeley.edu/web/checks/checkresultsXGR.html http://mirror.math.princeton.edu/pub/CRAN-archive/web/checks/2018-03-05checkresults_QNB.html
I don't know if I am personally responsible to keep these working on OSX, but from trying to update my package, I notice these errors crop up on OSX. Is there something I can do personally to fix this?
CRAN 'knows' about Bioconductor repositories, because R does, via
setRepositories()
,tools:::.BioC_version_associated_with_R_version()
andfile.path(R.home("etc"), "repositories")
(the values returned by these functions are not always consistent with what Bioconductor would like, which is why BiocManager exists). The above mostly looks like a problem with CRAN's configuration, and only CRAN can help with that.Might be an idea for the future. My code is fairly well documented and has good vignettes at this point. It took a LOT of work to get CRAN to take it, though. I imagine the process for getting accepted on Bioconductor is very difficult, like CRAN. Thanks for the insights into the mechanics. That's precisely what I needed.