RMySQL availiability with Bioconductor 3.0
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@panagiotis-moulos-6764
Last seen 7.1 years ago
Greece

Dear all,

I made some functionality updates to my package metaseqR which use and depend on the package RMySQL. The lateset check results indicate check errors in Windows and Mac OS X Mavericks. I know that RMySQL is a CRAN package for which currently, there are no devel binaries for the respective operating systems. My question is whether there is some planned Bioconductor support for the respective package or I should wait for the binaries to be released and thus in the meanwhile, the package check on Bioconductor will fail. Do you advise that I should work on a work-around solution in case the RMySQL binaries are not ready for the next Bioconductor release?

Thanks!

Install RMySQL Windows • 1.3k views
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Any reason in particular that forces you to use RMySQL? I have been using RSQLite  for my package, rTRM, and other Bioconductor packages use it (e.g. AnnotationDbi) without any platform support problems.

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Hi, yes, actually the package under circumstances connects to the UCSC Genome Browser database, over the web. I am not sure if this can be achieved with RSQLite.

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I see. Then maybe you are stuck with RMySQL. But move this conversation to bioc-devel as suggested by Herve- there others may offer some alternatives.

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@martin-morgan-1513
Last seen 17 days ago
United States

The CRAN page describing why RMySQL is not available indicates that this is because the package needs to link to the specific version of MySQL the user has installed, so it doesn't make sense to distribute the binary. I don't think this situation will change, so I suppose that binary versions of your package will not be available.

The user will need to install the package from source biocLite('metaseqR', type='source'), and this implies that they will be required to have the appropriate build tools and MySQL files available for their platform.

From the build system perspective you need to add a file .BBSoptions to the root of your SVN repository to indicate that the build system should not try to build your package with the single line

UnsupportedPlatforms: win, mac

There is a documented version of this file in the Biostrings pacakge.

From a user perspective, you'd like to make it as clear as possible why the package is not available on the platform of choice. You might indicate this in the Description: field of the DESCRIPTION  file, or a README file in the top level of the package directory. The former will be easily visible on the package landing page; the latter will be linked to the package landing page and could contain more extensive information.

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Martin, thank you very much for your extensive reply. It's now clear that if I want the package to be flawlessly available to as many users as possible, I have to find a way to bypass the need for RMySQL, with some less elegant solution.

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BTW, RMySQL *should* be available for Mavericks, it's not, though, simply because the maintainer of the Mavericks build machine at CRAN has not installed MySQL despite repeated requests.

So assuming that it is available some day, then Windows is the only platform that would not be supported (unless users build RMySQL themselves).

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@herve-pages-1542
Last seen 38 minutes ago
Seattle, WA, United States

Hi,

Please use the bioc-devel mailing lists for questions about package development. Thanks!

H.