[Bioc-devel] problem when building oligo on wilson2

[Patrick Aboyoun]

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
>>
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>