R devel - Jun 2011 - CRAN package with dependencies on Bioconductor

Dear all,

for a CRAN-package that depends on another Bioconductor-package I find two
things annoying and would like to know whether there are some workarounds:

1) Is there some inevitable problem that install.packages does not install
uninstalled packages (on which the specified package depends) also from
Bioconductor (in the correct version)?

2) In my understanding (please correct me if I'm wrong!) CRAN uses
bioconductor packages in another version than biocLite would install. For
example:

Our package gMCP depends on the package graph that has recently switched to
the bioconductor repositories. But even the following commands will fail
(i.e. install incompatible versions) for R 2.12 under Windows (and most
likely MacOS):

source("http://www.bioconductor.org/biocLite.R")
biocLite("graph")
install.packages("gMCP")

This results in errors like the following:
> BonferroniHolmGraph(2)
Error in validObject(.Object) :
  invalid class "graphMCP" object: superclass "graphBase"
not defined in the
environment of the object's class

The superclass graphBase is introduced in graph 1.30. In my understanding
the problem is that our package gMCP is build on CRAN for R 2.12 with the
package graph in version 1.30. Unfortunately biocLite installs
graph_1.28.0.zip for R 2.12.

Are there ways to make dependencies on Bioconductor less complicated?

Thanks and best regards, Kornelius

	[[alternative HTML version deleted]]

I'm sorry for sending a wrongly formated mail before. This is the missing
text:

Dear all,

for a CRAN-package that depends on another Bioconductor-package I find
two things annoying and would like to know whether there are some
workarounds:

1) Is there some inevitable problem that install.packages does not
install uninstalled packages (on which the specified package depends)
also from Bioconductor (in the correct version)?

2) In my understanding (please correct me if I'm wrong!) CRAN uses
bioconductor packages in another version than biocLite would install.
For example:

Our package gMCP depends on the package graph that has recently
switched to the bioconductor repositories. But even the following
commands will fail (i.e. install incompatible versions) for R 2.12
under Windows (and most likely MacOS):

source("http://www.bioconductor.org/biocLite.R")
biocLite("graph")
install.packages("gMCP")

This results in errors like the following:
> BonferroniHolmGraph(2)
Error in validObject(.Object) :
  invalid class "graphMCP" object: superclass "graphBase"
not defined
in the environment of the object's class

The superclass graphBase is introduced in graph 1.30. In my
understanding the problem is that our package gMCP is build on CRAN
for R 2.12 with the package graph in version 1.30. Unfortunately
biocLite installs graph_1.28.0.zip for R 2.12.

Are there ways to make dependencies on Bioconductor less complicated?

Thanks and best regards, Kornelius

2011/6/11 Prof Brian Ripley <ripley at
stats.ox.ac.uk>:
> On Sat, 11 Jun 2011, Kornelius Rohmeyer wrote:
>> 2011/6/11 Prof Brian Ripley <ripley at stats.ox.ac.uk>:
>>> Note that until May 8 graph was a CRAN packge and the current
version was
>>> 1.30.0.  So of course CRAN binary packages built between April 26
and May
>>> 8
>>> were built against the current CRAN version of graph, for any
version of
>>> R.
>>
>> Thanks for the notice! But if I am not wrong, a version of my package
>> that was published on May 26 and build therefore after the time period
>> specified by you still suffers from these version incompatibilities.
>> (Nevertheless it is of course possible that the problem is only caused
>> by the migration to Bioconductor and in this case less problematic and
>> only unfortunate in this one case). Perhaps the version downgrade of
>> the graph package caused problems?
>
>> So you say that the versions of Bioconductor packages on CRAN for
>> binary builds are already normally the same as you would get by
>> installing them as binaries from Bioconductor?
>
> No, I did not say that.
That means that for a binary package that depends on Bioconductor
packages you sometimes need a bit of luck to select the correct
versions of binary Bioconductor packages? Or is there a way to tell
which (and an easy way to install them)?

Thanks and best regards, Kornelius.

Actually I do not understand what is so hard to understand with CRAN policy.

This is:
Any source package on CRAN is build in binary form with 
R-release/patched and R-oldrelease. This does not happen if you tell 
your package it requires a particular R version - such as the 
declaration R (>= 2.13.0) in the Depends field will cause the package 
not to be build as a binary. Anotehr exception would be if the package 
does not longer pass the checks and gives an ERROR, in that case we also 
keep the old version in the binary repository.

On CRAN we assume that R-2.12.x users may want to get a bugfix release 
of a package without the requirement to upgrade R, hence we distribute 
new or updates packages for the oldrelease version (which is current 
R-2.12.x). And if BioC has a different policy, that is fine with us.


Uwe Ligges



On 11.06.2011 10:20, Kornelius Rohmeyer wrote:
> 2011/6/11 Prof Brian Ripley<ripley at stats.ox.ac.uk>:
>> On Sat, 11 Jun 2011, Kornelius Rohmeyer wrote:
>>> 2011/6/11 Prof Brian Ripley<ripley at stats.ox.ac.uk>:
>>>> Note that until May 8 graph was a CRAN packge and the current
version was
>>>> 1.30.0.  So of course CRAN binary packages built between April
26 and May
>>>> 8
>>>> were built against the current CRAN version of graph, for any
version of
>>>> R.
>>>
>>> Thanks for the notice! But if I am not wrong, a version of my
package
>>> that was published on May 26 and build therefore after the time
period
>>> specified by you still suffers from these version
incompatibilities.
>>> (Nevertheless it is of course possible that the problem is only
caused
>>> by the migration to Bioconductor and in this case less problematic
and
>>> only unfortunate in this one case). Perhaps the version downgrade
of
>>> the graph package caused problems?
>>
>>> So you say that the versions of Bioconductor packages on CRAN for
>>> binary builds are already normally the same as you would get by
>>> installing them as binaries from Bioconductor?
>>
>> No, I did not say that.
>
> That means that for a binary package that depends on Bioconductor
> packages you sometimes need a bit of luck to select the correct
> versions of binary Bioconductor packages? Or is there a way to tell
> which (and an easy way to install them)?
>
> Thanks and best regards, Kornelius.
>
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