From kornelius.rohmeyer at small-projects.de  Wed Jun 15 11:04:27 2011
From: kornelius.rohmeyer at small-projects.de (Kornelius Rohmeyer)
Date: Wed, 15 Jun 2011 11:04:27 +0200
Subject: [Rd] CRAN package with dependencies on Bioconductor
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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
complicated).

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.
>>
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>



[Rd] CRAN package with dependencies on Bioconductor
Kornelius Rohmeyer