[Bioc-devel] Build failing for MutationalPatterns

[Janssen-10, R.R.E.]

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.

Kind regards,
Roel Janssen

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