[Bioc-devel] Build failing for MutationalPatterns

Janssen-10, R.R.E. R.R.E.Janssen-10 at umcutrecht.nl
Thu Nov 30 16:01:54 CET 2017

Dear Martin,

Martin writes:

> 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.


I have Ubuntu "xenial", for which I installed "r-base-dev" following the instructions here:

sudo apt-get install r-base-dev

This provides R 3.4.2, from which I cannot use the devel stuff.

I then upgraded GNU Guix's R to 3.4.3, but from there I also cannot use the devel stuff from Bioconductor.
I attached the dependency graph for that R environment, including the dependencies for MutationalPatterns.

So, I tested this in a container with the attached dependency graph, and I still receive the same error:
Error: 'devel' version requires a more recent R

On R 3.4.3 I cannot reproduce the issue, so I suspect it's how our package integrates with Bioconductor 3.7.
Is there a complete guide to get the development version up and running?

Also, should packages in Bioconductor release 3.6 be built with the development version of R?

Thank you for your time.

Kind regards,
Roel Janssen


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