[Rd] CRAN package with dependencies on Bioconductor

Uwe Ligges ligges at statistik.tu-dortmund.de
Wed Jun 15 09:19:00 CEST 2011

On 15.06.2011 01:21, 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.
>    (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?)

Sure, this can happen, particularly with compiled code or S4 stuff in 
the packages.

> 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.)

Your package has been recompiled against graph 1.28.

Triggering an install.packages(yourpackage) will install a version that 
works, even for R-2.12.x

>> 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.

No no no! graph was a CRAN package up to few weeks ago. AAnd as a CRAN 
package the CRAN policy applied. Now that it was removed, it is fine and 
handled as a BioC package anayway. It was just the case that graph 1.30 
was a CRAN package once and hence your package was built against that 
one. Now that you told us we rebuilt your package after graph 1.30 was 
removed from CRAN and it should be fine. But it looks like you have not 
even tested!


> 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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