[Bioc-devel] Bioconductor package CNVRanger

[Geistlinger, Ludwig]

Great, many thanks for looking into this, Mike!

Best,
Ludwig
________________________________
From: Mike Smith <grimbough using gmail.com>
Sent: Friday, January 8, 2021 3:48 AM
To: Geistlinger, Ludwig <Ludwig_Geistlinger using hms.harvard.edu>
Cc: bioc-devel using r-project.org <bioc-devel using 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_Geistlinger using hms.harvard.edu<mailto: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/<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.Shepherd using RoswellPark.org>
Sent: Wednesday, December 23, 2020 7:23 AM
To: Geistlinger, Ludwig <Ludwig_Geistlinger using hms.harvard.edu<mailto: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<mailto:bioc-devel using 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

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