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.hen...@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.hen...@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.hen...@unibo.it<mailto:christian.hen...@unibo.it> > >>> > >>> [[alternative HTML version deleted]] > >>> > >>> ______________________________________________ > >>> R-package-devel@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.hen...@unibo.it > >> > >> ______________________________________________ > >> R-package-devel@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.hen...@unibo.it > > ______________________________________________ > R-package-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-package-devel > [[alternative HTML version deleted]] ______________________________________________ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
