Hi Ludwig, I think this actually a result of changes in rtracklayer that aren't playing well with Gviz::IdeogramTrack(). It looks like the error message is a bit misleading, it's not really a connection issue, just that something unexpected happens because some of the rtracklayer::ucscTableQuery() arguments are no longer in the same order.
I've submitted a pull request to Gviz at https://github.com/ivanek/Gviz/pull/40 which allows Gviz to pass build/check. Hopefully that'll straighten things out for you if it gets accepted. Cheers, Mike On Fri, 1 Jan 2021 at 23:38, Geistlinger, Ludwig < ludwig_geistlin...@hms.harvard.edu> wrote: > I am not 100% sure what the problem is but it seems as if there is a > problem with receiving resources from UCSC, a problem that also other > packages encounter, eg > > Gviz (http://bioconductor.org/checkResults/devel/bioc-LATEST/Gviz/) > ensembldb ( > http://bioconductor.org/checkResults/devel/bioc-LATEST/ensembldb< > http://bioconductor.org/checkResults/devel/bioc-LATEST/ensembldb/malbec2-buildsrc.html > >) > > or more generally an internet connection problem on the devel builders as > CNVRanger builds fine for me locally using > a recent version of R-devel. Also, the exact same code builds fine in the > release branch: > > http://bioconductor.org/checkResults/release/bioc-LATEST/CNVRanger/ > > sessionInfo for my local setup: > > > sessionInfo() > R Under development (unstable) (2020-12-23 r79675) > Platform: x86_64-apple-darwin18.6.0 (64-bit) > Running under: macOS Mojave 10.14.5 > > Matrix products: default > BLAS: /Users/ludwig/Downloads/R-devel/lib/libRblas.dylib > LAPACK: /Users/ludwig/Downloads/R-devel/lib/libRlapack.dylib > > locale: > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] parallel stats4 stats graphics grDevices utils datasets > [8] methods base > > other attached packages: > [1] CNVRanger_1.7.2 RaggedExperiment_1.15.1 GenomicRanges_1.43.1 > [4] GenomeInfoDb_1.27.3 IRanges_2.25.6 S4Vectors_0.29.6 > [7] BiocGenerics_0.37.0 > > loaded via a namespace (and not attached): > [1] lattice_0.20-41 matrixStats_0.57.0 > [3] bitops_1.0-6 grid_4.1.0 > [5] zlibbioc_1.37.0 XVector_0.31.1 > [7] Matrix_1.2-18 tools_4.1.0 > [9] Biobase_2.51.0 RCurl_1.98-1.2 > [11] DelayedArray_0.17.6 MatrixGenerics_1.3.0 > [13] compiler_4.1.0 SummarizedExperiment_1.21.1 > [15] GenomeInfoDbData_1.2.4 > > > > ________________________________ > From: Kern, Lori <lori.sheph...@roswellpark.org> > Sent: Wednesday, December 23, 2020 7:23 AM > To: Geistlinger, Ludwig <ludwig_geistlin...@hms.harvard.edu> > Subject: Bioconductor package CNVRanger > > Hello Package Maintainer, > > The Bioconductor Team would like to notify you that your package is > currently > failing on the devel 3.13 version of Bioconductor, and has been for an > extended > period of time. Please fix your package to R CMD build and R CMD check > cleanly > immediately to avoid deprecation of your package. While devel is a place to > experiment with new features, we expect packages to build and check > cleanly in a > reasonable time period and not stay broken for any extended period of > time. If > you are having trouble or have any further questions please do not > hesitate to > reach out to the developers mailing list at bioc-devel@r-project.org. The > package has been failing consistently since 12/07/20 > > bioconductor.org/checkResults/devel/bioc-LATEST/CNVRanger > > > Lori Shepherd > > Bioconductor Core Team > > Roswell Park Comprehensive Cancer Center > > Department of Biostatistics & Bioinformatics > > Elm & Carlton Streets > > Buffalo, New York 14263 > > This email message may contain legally privileged and/or confidential > information. If you are not the intended recipient(s), or the employee or > agent responsible for the delivery of this message to the intended > recipient(s), you are hereby notified that any disclosure, copying, > distribution, or use of this email message is prohibited. If you have > received this message in error, please notify the sender immediately by > e-mail and delete this email message from your computer. Thank you. > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel