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

[Gábor Csárdi]

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
>
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