Question

RMySQL availiability with Bioconductor 3.0

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Panagiotis Moulos ▴ 30

@panagiotis-moulos-6764

Last seen 9.3 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 • 2.0k views

ADD COMMENT • link updated 10.2 years ago by Martin Morgan 25k • written 10.2 years ago by Panagiotis Moulos ▴ 30

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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.

ADD REPLY • link 10.2 years ago Diego Diez ▴ 760

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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.

ADD REPLY • link 10.2 years ago Panagiotis Moulos ▴ 30

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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.

ADD REPLY • link 10.2 years ago Diego Diez ▴ 760

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Hervé Pagès 16k

@herve-pages-1542

Last seen 3 days ago

Seattle, WA, United States

Hi,

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

http://bioconductor.org/help/support/

H.

ADD COMMENT • link 10.2 years ago Hervé Pagès 16k

score 4 · Accepted Answer · 2014-09-23

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.