Re: [Rd] CRAN package with dependencies on Bioconductor

From: Duncan Murdoch <murdoch.duncan_at_gmail.com>
Date: Thu, 16 Jun 2011 04:56:37 -0400

On 11-06-14 7:21 PM, Kornelius Rohmeyer wrote:
> 2011/6/11 Duncan Murdoch<murdoch.duncan_at_gmail.com>:
> [...]
>> I don't understand. It sounds as though you're saying these two
>> contradictory things:
>>
>> - your package works with any version of graph
>> - CRAN builds a version of graph that is incompatible with your package.
>
> No, the first statement is correct but not the second:
>
> - Installed from source my package works with any version of graph and also:
> - A binary of my package built with graph 1.28 will work with graph 1.28.
> - A binary of my package built with graph 1.30 will work with graph 1.30.
>
> - But a binary of my package built with graph 1.30 will not work with
> graph 1.28.

Thanks, now I understand the issue. It sounds as though it has been solved, but while it is in your mind, it might be worth adding some defensive code in case something similar happens in the future. Can you check on version numbers at load time to give a helpful error message about the problem if it arises again?

Duncan Murdoch

> (If it is surprising for anyone, that this can happen, we can go
> into detail here.
> I doubt that this is the place to fix things, but maybe I am wrong?)
>
> I personally found it unfortunate, that due to different policies of
> CRAN and Bioconductor for R 2.12 there are (up to my knowledge) no
> more any binary packages of gMCP and graph available for R 2.12 that
> are compatible. (In this case the problem can be solved manually by
> installing the graph package binary from Bioconductor for R 2.13 that
> works also for R 2.12.)
>
>> I am not involved with setting CRAN policy, but their current policy (build
>> the most recent version of a package that declares itself compatible with
>> the relevant version of R) seems reasonable.
>
> Personally I find it more reasonable to apply the Bioconductor policy
> to Bioconductor packages that are installed on CRAN for building
> packages that depend on those. But you and Uwe seem to disagree. Since
> this is (IMHO) a matter of taste and where one assigns priorities and
> these seem to differ, there is not much to discuss…
>
> Thanks for the clear advise and also thanks to all CRAN maintainers
> for the great services nevertheless!
>
> Best regards, Kornelius.



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