[Rd] CRAN package with dependencies on Bioconductor

Kornelius Rohmeyer kornelius.rohmeyer at small-projects.de
Wed Jun 15 11:04:27 CEST 2011

Am 15. Juni 2011 09:19 schrieb Uwe Ligges <ligges at statistik.tu-dortmund.de>:
> 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!

The package was already built 18 days after graph was removed from CRAN…
I'll try to ignore the "But it looks like you have not even tested!"
since I tested it 4 days ago, when it did not work. And since I had no
notice up to today that it was rebuilt with a new (i.e. old) version
of the graph package, I did not expect that it had changed already
(also my computer is not a Windows machine, which makes testing more

Nevertheless a big, big thank you and I'm sorry that such a small
problem caused such a lengthy conservation.

Thanks and best regards, Kornelius.

> Uwe
>> 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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