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

[Christian Martin Hennig]

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