Great, many thanks for looking into this, Mike! Best, Ludwig ________________________________ From: Mike Smith <grimbo...@gmail.com> Sent: Friday, January 8, 2021 3:48 AM To: Geistlinger, Ludwig <ludwig_geistlin...@hms.harvard.edu> Cc: bioc-devel@r-project.org <bioc-devel@r-project.org> Subject: Re: [Bioc-devel] Bioconductor package CNVRanger
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<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_ivanek_Gviz_pull_40&d=DwMFaQ&c=WO-RGvefibhHBZq3fL85hQ&r=yPjzQ73-fmNXaJPV1gz9oHaqor6pHH3nhMisHpNHdtLiyt1ggXxpbN7zgyhVaqsX&m=xjNCIPgIQYebG-XX4IWcuBKasx9A31GNW_9696oXfrw&s=ZAkFjwmoynKiXPlDPnujma_HBMvu8XGnWjmmiLDfv5M&e=> 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<mailto: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/<https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_devel_bioc-2DLATEST_Gviz_&d=DwMFaQ&c=WO-RGvefibhHBZq3fL85hQ&r=yPjzQ73-fmNXaJPV1gz9oHaqor6pHH3nhMisHpNHdtLiyt1ggXxpbN7zgyhVaqsX&m=xjNCIPgIQYebG-XX4IWcuBKasx9A31GNW_9696oXfrw&s=AsxayxSbEsjOWU33mgR06il-dYIkZDKKqAPqcei-JKo&e=>) ensembldb (http://bioconductor.org/checkResults/devel/bioc-LATEST/ensembldb<https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_devel_bioc-2DLATEST_ensembldb&d=DwMFaQ&c=WO-RGvefibhHBZq3fL85hQ&r=yPjzQ73-fmNXaJPV1gz9oHaqor6pHH3nhMisHpNHdtLiyt1ggXxpbN7zgyhVaqsX&m=xjNCIPgIQYebG-XX4IWcuBKasx9A31GNW_9696oXfrw&s=7Up0KcZFZW84NjJocHHRAGj9eT0ttJqfZZtDEdJqmBM&e=><http://bioconductor.org/checkResults/devel/bioc-LATEST/ensembldb/malbec2-buildsrc.html<https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_devel_bioc-2DLATEST_ensembldb_malbec2-2Dbuildsrc.html&d=DwMFaQ&c=WO-RGvefibhHBZq3fL85hQ&r=yPjzQ73-fmNXaJPV1gz9oHaqor6pHH3nhMisHpNHdtLiyt1ggXxpbN7zgyhVaqsX&m=xjNCIPgIQYebG-XX4IWcuBKasx9A31GNW_9696oXfrw&s=l_43RRL9l9uXO4XOkXwCJZn09GaLfaI2QWGBkT2gqp0&e=>>) 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/<https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_release_bioc-2DLATEST_CNVRanger_&d=DwMFaQ&c=WO-RGvefibhHBZq3fL85hQ&r=yPjzQ73-fmNXaJPV1gz9oHaqor6pHH3nhMisHpNHdtLiyt1ggXxpbN7zgyhVaqsX&m=xjNCIPgIQYebG-XX4IWcuBKasx9A31GNW_9696oXfrw&s=mNtFTxaVcMHSgqm1vuI8qjK5AzQq6aE3AQ0gd3Fc4QM&e=> 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<mailto: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<mailto:bioc-devel@r-project.org>. The package has been failing consistently since 12/07/20 bioconductor.org/checkResults/devel/bioc-LATEST/CNVRanger<https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_devel_bioc-2DLATEST_CNVRanger&d=DwMFaQ&c=WO-RGvefibhHBZq3fL85hQ&r=yPjzQ73-fmNXaJPV1gz9oHaqor6pHH3nhMisHpNHdtLiyt1ggXxpbN7zgyhVaqsX&m=xjNCIPgIQYebG-XX4IWcuBKasx9A31GNW_9696oXfrw&s=FnEUIBbUmR3SggutZ4HradkkWrrUOLoIrajUkKjIeSk&e=> 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<mailto:Bioc-devel@r-project.org> mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel<https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwMFaQ&c=WO-RGvefibhHBZq3fL85hQ&r=yPjzQ73-fmNXaJPV1gz9oHaqor6pHH3nhMisHpNHdtLiyt1ggXxpbN7zgyhVaqsX&m=xjNCIPgIQYebG-XX4IWcuBKasx9A31GNW_9696oXfrw&s=sJNaCoC0GlShrlpffncHY8KbBcY8mVN71VVIiFT8ptw&e=> [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
