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

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, G?bor Cs?rdi 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 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>

       [[alternative HTML version deleted]]

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

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