[Bioc-devel] problem when building oligo on wilson2

[Benilton Carvalho]

I got the revision 49067, but wasn't able to reproduce the problem on  
the machine I have access to... so I'll just wait for the next build  
and see what comes up.

Thank you very much,

b

On Aug 7, 2009, at 2:27 PM, Benilton Carvalho wrote:

> 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
>>>>
>>>
>>
>
> _______________________________________________
> Bioc-devel at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel