[R-pkg-devel] rhub, docker and Bioconductor

[brian knaus]

I was tracking down problems with my package yesterday that were specific
to r-devel and I had trouble reproducing the errors. I believe the issue is
that the rhub and the docker/rocker r-devel were not using the most recent
version of r-devel. My solution was to add r-devel to my travis ci.

https://towardsdatascience.com/travis-ci-for-r-advanced-guide-719cb2d9e0e5

This allowed me to reproduce the errors.

Brian

On Tue, Jan 7, 2020 at 6:35 AM Christian Martin Hennig <
christian.hennig using unibo.it> wrote:

> That's good to know. I'm still at a loss what to do though. How are you
> checking your packages on systems that are not available to you, other
> than using rhub?
>
> Chances are if something from Bioconductor is required by one of the
> packages that I require, I can't get rid of it, right?
>
> Thanks,
>
> Christian
>
> On 1/7/20 3:06 PM, Gábor Csárdi wrote:
> > It is an R-hub bug: https://github.com/r-hub/rhub/issues/318
> >
> > Gabor
> >
> > On Tue, Jan 7, 2020 at 2:05 PM Christian Martin Hennig
> > <christian.hennig using unibo.it> wrote:
> >> I should maybe add that I'm not even sure why I need Bioconductor, the
> >> package has:
> >>
> >> Imports: MASS, cluster, mclust, flexmix, prabclus, class, diptest,
> >> robustbase, kernlab, grDevices, graphics, methods, stats, utils,
> parallel
> >> Suggests: tclust, pdfCluster, EMMIXskew, mvtnorm
> >>
> >> Christian
> >>
> >> On 1/7/20 2:54 PM, Christian Martin Hennig wrote:
> >>> Hi there,
> >>>
> >>> I'm trying to track down some errors and issues of my fpc package. As
> I can't reproduce any of these on my machine, I'm using rhub and docker.
> >>>
> >>> I'm getting Bioconductor related issues with both
> >>>
> >>>     local_check_linux("fpc_2.2-3.tar.gz", image =
> "rhub/debian-clang-devel")
> >>>
> >>> and
> >>>
> >>> rhub::check("fpc_2.2-3.tar.gz", platform = "debian-clang-devel")
> >>>
> >>> namely locally:
> >>>
> >>> source('https://bioconductor.org/biocLite.R')
> >>> Error: With R version 3.5 or greater, install Bioconductor packages
> using BiocManager; see https://bioconductor.org/install
> >>> Execution halted
> >>> Error in run(bash, c(file.path(wd, "rhub-linux.sh"), args), echo =
> TRUE,  :
> >>>     System command error
> >>>
> >>> ...and on rhub:
> >>>
> >>> 91<
> https://builder.r-hub.io/status/fpc_2.2-3.tar.gz-2492f95fc1c94fcbbff4d6f47cb423f8#L91>#>
> Error: package or namespace load failed for 'BiocManager':
> >>>
> >>> 92<
> https://builder.r-hub.io/status/fpc_2.2-3.tar.gz-2492f95fc1c94fcbbff4d6f47cb423f8#L92>#>
> .onAttach failed in attachNamespace() for 'BiocManager', details:
> >>>
> >>> 93<
> https://builder.r-hub.io/status/fpc_2.2-3.tar.gz-2492f95fc1c94fcbbff4d6f47cb423f8#L93>#>
> call: if (version[, 1:2] != version) return(sprintf("version '%s' must have
> two components, e.g., '3.7'",
> >>>
> >>> 94<
> https://builder.r-hub.io/status/fpc_2.2-3.tar.gz-2492f95fc1c94fcbbff4d6f47cb423f8#L94>#>
> error: argument is of length zero
> >>>
> >>> 95<
> https://builder.r-hub.io/status/fpc_2.2-3.tar.gz-2492f95fc1c94fcbbff4d6f47cb423f8#L95>#>
> Error: loading failed
> >>>
> >>> 96<
> https://builder.r-hub.io/status/fpc_2.2-3.tar.gz-2492f95fc1c94fcbbff4d6f47cb423f8#L96>#>
> Execution halted
> >>>
> >>> 97<
> https://builder.r-hub.io/status/fpc_2.2-3.tar.gz-2492f95fc1c94fcbbff4d6f47cb423f8#L97>#>
> ERROR: loading failed
> >>>
> >>> (To be totally honest, I'm not even sure whether the latter rhub issue
> doesn't refer to the local docker thing as well, because this was linked
> from an R-hub builder PREPERROR email, it also mentions docker, and all the
> time indications don't make it unambiguously clear to what build they
> refer.)
> >>>
> >>> Not sure what to do about this. Are there any other options apart from
> rhub/docker to get wiser about my errors and issues (error on debian-clang
> in a routine that shows nothing suspicious on my machine, additional
> issues  ATLAS<https://www.stats.ox.ac.uk/pub/bdr/Rblas/ATLAS/fpc.out> MKL<
> https://www.stats.ox.ac.uk/pub/bdr/Rblas/MKL/fpc.out> noLD<
> https://www.stats.ox.ac.uk/pub/bdr/noLD/fpc.out> OpenBLAS)?<
> https://www.stats.ox.ac.uk/pub/bdr/Rblas/OpenBLAS/fpc.out>
> >>>
> >>> Yesterday I was able to check a prabclus noLD error on rhub, but no
> luck yet with fpc.
> >>>
> >>> Thanks a lot,
> >>>
> >>> Christian
> >>>
> >>> --
> >>> Christian Hennig
> >>> Dipartimento di Scienze Statistiche "Paolo Fortunati",
> >>> Universita di Bologna, phone +39 05120 98163
> >>> christian.hennig using unibo.it<mailto:christian.hennig using unibo.it>
> >>>
> >>>        [[alternative HTML version deleted]]
> >>>
> >>> ______________________________________________
> >>> R-package-devel using r-project.org mailing list
> >>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
> >> --
> >> Christian Hennig
> >> Dipartimento di Scienze Statistiche "Paolo Fortunati",
> >> Universita di Bologna, phone +39 05120 98163
> >> christian.hennig using unibo.it
> >>
> >> ______________________________________________
> >> R-package-devel using r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>
> --
> Christian Hennig
> Dipartimento di Scienze Statistiche "Paolo Fortunati",
> Universita di Bologna, phone +39 05120 98163
> christian.hennig using unibo.it
>
> ______________________________________________
> R-package-devel using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>

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