[Bioc-devel] Build failing for MutationalPatterns

[Martin Morgan]

On 11/29/2017 11:14 AM, Janssen-10, R.R.E. wrote:
> Hi Martin,
> 
> Thanks for your reply!
> 
> Martin Morgan writes:
> 
>> On 11/29/2017 09:58 AM, Janssen-10, R.R.E. wrote:
>>> Dear Bioconductor,
>>>
>>> The build for MutationalPatterns has been failing for a week.  The exact same code built fine, because the last commit ups the version number to 1.4.1, which is the version that is available on Bioconductor.
>>>
>>> I also cannot reproduce the error with the code from upstream on my computer. What can we do about this to fix the build on your infrastructure?
>>
>> I reproduced this on my linux laptop, installing the package and then
>> running
>>
>>    MutationalPatterns/vignettes master$ Rdev CMD Sweave --pdf
>> Introduction_to_MutationalPatterns.Rnw
>>
>> The key to reproducibility is using the same software as the build
>> system -- currently, R-devel and Bioc-devel with current packages
>>
>>    $ Rdev -e "BiocInstaller::biocVersion()" # 3.7
>>    $ Rdev -e "BiocInstaller::isDevel()"   # TRUE
>>    $ Rdev -e "BiocInstaller::biocValid()" # TRUE
>>
>> and to be sure that you're running in a clean checkout of your package,
>> e.g., by cloning into tmp
>>
>>    $ cd /tmp
>>    $ git clone https://git.bioconductor.org/packages/MutationalPatterns
> 
> 
> Apparently, I need to use a version of R that hasn't been released yet:
> 
> $ R
> R version 3.4.2 (2017-09-28) -- "Short Summer"
> ...
>> library(BiocInstaller)
> Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help
>> useDevel()
> Error: 'devel' version requires a more recent R
> 
> It seems that R version 3.4.3 is going to be released tomorrow, so I'll wait for that.
> 
> Thanks for verifying that this error can be reproduced.

For the current Bioconductor cycle, we are using the 'devel' version of 
R, see

   http://bioconductor.org/developers/how-to/useDevel/

The 'devel' version of R is always available, e.g., after clicking 
through to your operating system of choice at 
https://cran.r-project.org/bin/ and looking for something along the 
lines of r-devel snapshot.

Martin



> 
> Kind regards,
> Roel Janssen
> 
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