Error with accessing DNA methylation data

[j-lawson]

Hello,

This package is really useful. However, when I try to access the DNA methylation data with this commands:

library("curatedTCGAData") dlbc <- curatedTCGAData("DLBC", assays = "Methylation", FALSE)

I get the following error:

snapshotDate(): 2018-10-30 snapshotDate(): 2018-10-30 Error in loadResources(ExperimentHub, "curatedTCGAData", res)[[1L]] : subscript out of bounds

Do you know why this error is occurring?

My session info:

R version 3.5.1 (2018-07-02) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 16.04.4 LTS

Matrix products: default BLAS: /usr/lib/libblas/libblas.so.3.6.0 LAPACK: /usr/lib/lapack/liblapack.so.3.6.0

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8
[6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets methods base

other attached packages: [1] curatedTCGAData_1.4.0 MultiAssayExperiment_1.8.1 SummarizedExperiment_1.12.0 DelayedArray_0.8.0 BiocParallel_1.16.5
[6] matrixStats_0.54.0 Biobase_2.42.0 GenomicRanges_1.34.0 GenomeInfoDb_1.18.1 IRanges_2.16.0
[11] S4Vectors_0.20.1 BiocGenerics_0.28.0

loaded via a namespace (and not attached): [1] Rcpp_1.0.0 later_0.7.5 compiler_3.5.1 BiocManager_1.30.4 XVector_0.22.0
[6] AnnotationHub_2.14.2 bitops_1.0-6 tools_3.5.1 zlibbioc_1.28.0 digest_0.6.18
[11] bit_1.1-14 RSQLite_2.1.1 memoise_1.1.0 lattice_0.20-38 pkgconfig_2.0.2
[16] Matrix_1.2-15 shiny_1.2.0 DBI_1.0.0 curl_3.3 yaml_2.2.0
[21] GenomeInfoDbData_1.2.0 httr_1.4.0 bit64_0.9-7 grid_3.5.1 R6_2.3.0
[26] AnnotationDbi_1.44.0 ExperimentHub_1.8.0 magrittr_1.5 blob_1.1.1 promises_1.0.1
[31] htmltools_0.3.6 xtable_1.8-3 mime_0.6 interactiveDisplayBase_1.20.0 httpuv_1.4.5.1
[36] RCurl_1.95-4.11

Thanks, John Lawson

[LiNk-NY]

Hi John, @j-lawson Thanks for the report. We are aware of this and a fix has been committed to the RELEASE_3_8 branch.

Please check back again tomorrow to see if the issue persists (after Bioconductor release builds). Also, don't forget to clear your ExperimentHub cache by doing:

library(ExperimentHub)
eh <- ExperimentHub()
removeCache(eh)

Best regards, Marcel

[j-lawson]

Hi Marcel, @LiNk-NY

Thanks! It looks like your new version has not yet propogated to the Bioc release (I see version 1.4.1 on the build report but the release version is still 1.4.0, which still has the error). I'll check back in once the new version goes to release.

Thanks, John

[LiNk-NY]

Hi John, @j-lawson My apologies for the late response. You will have to wait a bit since we are still working out a bug in ExperimentHub that caused the removal of methylation files from the database in the RELEASE_3_8 branch of the package. I would recommend using the devel version of the package in Bioc-devel.

Best regards, Marcel

[j-lawson]

No problem. Thanks for the update!

Best, John

[LiNk-NY]

Hi John, @j-lawson This issue should've been resolved on the ExperimentHub side. Thank you for your patience! Best, Marcel