plotRegionGeneAssociationGraphs error

[dougbarrows]

Hello! I've been using your package for a long time now, but recently started getting an error with the 'plotRegionGeneAssociationGraphs()' function. I've had this problem with my own data, but I can recreate it with the examples from the help pages. The code and my sessionInfo is below and the error I get is:

Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, : line 1 did not have 2 elements Error in parseRegionGeneAssociationFile(f_all) : Downloading seems interrupted. Please re-run your command.

Thank you in advance for any help you can provide!

set.seed(123)
bed = circlize::generateRandomBed(nr = 1000, nc = 0)
job = submitGreatJob(bed, version = "3.0.0")
job

plotRegionGeneAssociationGraphs(job)

sessionInfo:

R version 4.0.2 Patched (2020-06-30 r78761) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS High Sierra 10.13.6

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/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] stats4 parallel stats graphics grDevices utils datasets methods base

other attached packages: [1] rGREAT_1.20.0 org.Mm.eg.db_3.11.4 AnnotationDbi_1.50.3 profileplyr_1.4.3 SummarizedExperiment_1.18.2 [6] DelayedArray_0.14.1 matrixStats_0.56.0 Biobase_2.48.0 GenomicRanges_1.40.0 GenomeInfoDb_1.24.2
[11] IRanges_2.22.2 S4Vectors_0.26.1 BiocGenerics_0.34.0

loaded via a namespace (and not attached): [1] ChIPseeker_1.24.0 backports_1.1.8 circlize_0.4.10
[4] fastmatch_1.1-0 BiocFileCache_1.12.1 soGGi_1.20.0
[7] plyr_1.8.6 igraph_1.2.5 splines_4.0.2
[10] BiocParallel_1.22.0 ggplot2_3.3.2 urltools_1.7.3
[13] digest_0.6.25 GOSemSim_2.14.1 tiff_0.1-5
[16] viridis_0.5.1 GO.db_3.11.4 gdata_2.18.0
[19] fansi_0.4.1 EnrichedHeatmap_1.18.2 magrittr_1.5
[22] memoise_1.1.0 cluster_2.1.0 ComplexHeatmap_2.4.3
[25] Biostrings_2.56.0 graphlayouts_0.7.0 R.utils_2.9.2
[28] askpass_1.1 enrichplot_1.8.1 prettyunits_1.1.1
[31] jpeg_0.1-8.1 colorspace_1.4-1 blob_1.2.1
[34] rappdirs_0.3.1 ggrepel_0.8.2 dplyr_1.0.2
[37] crayon_1.3.4 RCurl_1.98-1.2 jsonlite_1.7.0
[40] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 scatterpie_0.1.4 chipseq_1.38.0
[43] glue_1.4.1 polyclip_1.10-0 gtable_0.3.0
[46] zlibbioc_1.34.0 XVector_0.28.0 TxDb.Hsapiens.UCSC.hg38.knownGene_3.10.0 [49] GetoptLong_1.0.2 shape_1.4.4 scales_1.1.1
[52] DOSE_3.14.0 pheatmap_1.0.12 DBI_1.1.0
[55] TxDb.Mmusculus.UCSC.mm9.knownGene_3.2.2 Rcpp_1.0.5 plotrix_3.7-8
[58] viridisLite_0.3.0 progress_1.2.2 clue_0.3-57
[61] gridGraphics_0.5-0 bit_4.0.4 europepmc_0.4
[64] preprocessCore_1.50.0 httr_1.4.2 fgsea_1.14.0
[67] gplots_3.0.4 RColorBrewer_1.1-2 ellipsis_0.3.1
[70] R.methodsS3_1.8.0 pkgconfig_2.0.3 XML_3.99-0.5
[73] farver_2.0.3 dbplyr_1.4.4 locfit_1.5-9.4
[76] ggplotify_0.0.5 tidyselect_1.1.0 rlang_0.4.7
[79] reshape2_1.4.4 munsell_0.5.0 tools_4.0.2
[82] cli_2.0.2 generics_0.0.2 RSQLite_2.2.0
[85] ggridges_0.5.2 stringr_1.4.0 yaml_2.2.1
[88] org.Hs.eg.db_3.11.4 bit64_4.0.2 tidygraph_1.2.0
[91] caTools_1.18.0 purrr_0.3.4 ggraph_2.0.3
[94] R.oo_1.23.0 DO.db_2.9 xml2_1.3.2
[97] biomaRt_2.44.1 compiler_4.0.2 rstudioapi_0.11
[100] curl_4.3 png_0.1-7 testthat_2.3.2
[103] tibble_3.0.3 tweenr_1.0.1 stringi_1.4.6
[106] GenomicFeatures_1.40.1 desc_1.2.0 lattice_0.20-41
[109] Matrix_1.2-18 vctrs_0.3.2 pillar_1.4.6
[112] lifecycle_0.2.0 BiocManager_1.30.10 triebeard_0.3.0
[115] GlobalOptions_0.1.2 TxDb.Mmusculus.UCSC.mm10.knownGene_3.10.0 data.table_1.13.0
[118] cowplot_1.0.0 bitops_1.0-6 rtracklayer_1.48.0
[121] qvalue_2.20.0 latticeExtra_0.6-29 hwriter_1.3.2
[124] R6_2.4.1 ShortRead_1.46.0 KernSmooth_2.23-17
[127] gridExtra_2.3 boot_1.3-25 MASS_7.3-52
[130] gtools_3.8.2 assertthat_0.2.1 pkgload_1.1.0
[133] openssl_1.4.2 rprojroot_1.3-2 rjson_0.2.20
[136] withr_2.2.0 GenomicAlignments_1.24.0 Rsamtools_2.4.0
[139] GenomeInfoDbData_1.2.3 hms_0.5.3 grid_4.0.2
[142] tidyr_1.1.1 rvcheck_0.1.8 Cairo_1.5-12.2
[145] ggforce_0.3.2

[jokergoo]

It works fine with the code you provided. Can you send me the data you had error with? You can send me by email.

[dougbarrows]

Thanks for checking on your end. After restarting everything it works now. Must have been an issue with some dependency versions.