[Bioc-devel] problem when building oligo on wilson2

[Benilton Carvalho]

Dear Robert and Patrick,

Thank you very much for your time.

Patrick, I just exposed the function, thanks for the heads up.

Robert, thanks for the hint. I'll get r49067 and try to reproduce the  
problem.

b

On Aug 7, 2009, at 2:17 PM, Patrick Aboyoun wrote:

> Benilton,
> I pushed an early report of the builds today that don't include  
> Windows
> because those machines haven't completed the build process yet. For
> today's report oligo isn't building on wilson2 (Linux), pitt (Mac OS X
> Tiger), pelham (Mac OSX Leopard).
>
> http://www.bioconductor.org/checkResults/2.5/bioc-LATEST/oligo/wilson2-buildsrc.html
> http://www.bioconductor.org/checkResults/2.5/bioc-LATEST/oligo/pitt-buildsrc.html
> http://www.bioconductor.org/checkResults/2.5/bioc-LATEST/oligo/pelham-buildsrc.html
>
> because of the error
>
> Error: processing vignette 'oligo.Rnw' failed with diagnostics:
> chunk 3 (label=crlmm)
> Error in crlmm(fullFilenames, outputDir, verbose = FALSE) :
>  could not find function "requireAnnotation"
> Execution halted
>
>
> This missing symbol could be masking the more subtler problem you
> mentioned, but at least the current error should be easy to correct.
>
>
>
> Patrick
>
>
>
>
> Robert Gentleman wrote:
>> Hi Benilton,
>>  It could be any one of a number of things, not necessarily the build
>> of R (although that could be a factor).  Someone here will likely  
>> need
>> to try to run this and see if it is reproducible from the command  
>> line
>> and if so, to try and find the problem.  Alternatively you could  
>> check
>> out that version of R and see if the problem is reproducible on a
>> computer near you.
>>
>>  best wishes
>>    Robert
>>
>>
>> Benilton Carvalho wrote:
>>> (resending the message as my initial attempts were refused)
>>>
>>> Hi,
>>>
>>> I'm looking for some insight on the source of the problem reported  
>>> by
>>> 'wilson2' when building oligo:
>>>
>>> http://www.bioconductor.org/checkResults/2.5/bioc-LATEST/oligo/wilson2-buildsrc.html
>>>
>>>
>>> This machine has R-devel r49067... The other machines have r49060  
>>> and
>>> r49021.
>>>
>>> So, because the pkg builds just fine on other machines but  
>>> wilson2, I
>>> thought that the source of the problem would be on changes between
>>> r49060 and r49067.
>>>
>>> Looking at the log of R-devel for all these revisions, I don't see
>>> any change that would cause the error "'dimnames' applied to
>>> non-array" to come up.
>>>
>>> I just installed the latest R-devel and I can't reproduce the
>>> problem. So, is it just a matter of waiting until R-devel is updated
>>> on the machines used to build the packages?
>>>
>>> Thanks a lot,
>>>
>>> b
>>>
>>> _______________________________________________
>>> Bioc-devel at stat.math.ethz.ch mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>
>