[Bioc-devel] Build failing for MutationalPatterns

[Sean Davis]

On Thu, Nov 30, 2017 at 10:01 AM, Janssen-10, R.R.E. <
R.R.E.Janssen-10 at umcutrecht.nl> wrote:

> 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.
>
> Thanks.
>
> I have Ubuntu "xenial", for which I installed "r-base-dev" following the
> instructions here:
> https://cran.r-project.org/bin/linux/ubuntu/
>
> 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?
>

Not a recommendation, but here is a quick way to go:

docker run -p 8787:8787 bioconductor/devel_core2

After doing so, navigating to:

http://127.0.0.1:8787/

will open up Rstudio running on R-devel with core bioc-devel packages
installed.

Full details are here: http://bioconductor.org/help/docker/

Sean



> 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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