[Bioc-devel] Bioconductor package CNVRanger

[Mike Smith]

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_Geistlinger using 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.Shepherd using RoswellPark.org>
> Sent: Wednesday, December 23, 2020 7:23 AM
> To: Geistlinger, Ludwig <Ludwig_Geistlinger using 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 using 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
>
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