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

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 at 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 at unibo.it<mailto:christian.hennig at unibo.it>

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--
Christian Hennig
Dipartimento di Scienze Statistiche "Paolo Fortunati",
Universita di Bologna, phone +39 05120 98163
christian.hennig at unibo.it