loadstudy and cBioDataPack return error in vroom_
Entering edit mode
karam • 0
Last seen 8 months ago
United States

I recently installed BiocManager and cBioPortalData. while attempting to download metadata for a specific study i ran into an error loading the data despite the terminal saying it was in cache

Code should be placed in three backticks as shown below


laml <- cBioDataPack("laml_tcga",use_cache = TRUE)

data <- downloadStudy("laml_tcga")
file_dir <- untarStudy(data, tempdir())

# include your problematic code here with any corresponding output 
# please also include the results of running the following in an R session 

'getStudies' reports that 'laml_tcga' is not currently building.
  Use 'downloadStudy()' to obtain the study data.
  Proceed anyway? [y/n]: 
Study file in cache: laml_tcga
Error in vroom_(file, delim = delim %||% col_types$delim, col_names = col_names,  : 
  bad value

> data <- downloadStudy("laml_tcga")
Study file in cache: laml_tcga
> file_dir <- untarStudy(data, tempdir())
> loadStudy(file_dir)
Error in vroom_(file, delim = delim %||% col_types$delim, col_names = col_names,  : 
  bad value

sessionInfo( )

R version 4.3.1 (2023-06-16) Platform: aarch64-apple-darwin20 (64-bit) Running under: macOS Monterey 12.0.1

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: US/Pacific tzcode source: internal

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

other attached packages: [1] cBioPortalData_2.12.0 MultiAssayExperiment_1.26.0 SummarizedExperiment_1.30.2 Biobase_2.60.0
[5] GenomicRanges_1.52.0 GenomeInfoDb_1.36.4 IRanges_2.34.1 S4Vectors_0.38.2
[9] BiocGenerics_0.46.0 MatrixGenerics_1.12.3 matrixStats_1.0.0 AnVIL_1.12.4
[13] dplyr_1.1.3 BiocManager_1.30.22

loaded via a namespace (and not attached): [1] rstudioapi_0.15.0 jsonlite_1.8.7 magrittr_2.0.3 GenomicFeatures_1.52.2
[5] estimability_1.4.1 nloptr_2.0.3 rmarkdown_2.25 BiocIO_1.10.0
[9] zlibbioc_1.46.0 vctrs_0.6.3 sjPlot_2.8.15 Rsamtools_2.16.0
[13] memoise_2.0.1 minqa_1.2.6 RCurl_1.98-1.12 progress_1.2.2
[17] htmltools_0.5.6.1 S4Arrays_1.0.6 lambda.r_1.2.4 curl_5.1.0
[21] broom_1.0.5 sjmisc_2.8.9 htmlwidgets_1.6.2 futile.options_1.0.1
[25] emmeans_1.8.8 lubridate_1.9.3 cachem_1.0.8 gt_0.10.0
[29] GenomicAlignments_1.36.0 mime_0.12 lifecycle_1.0.3 pkgconfig_2.0.3
[33] sjlabelled_1.2.0 Matrix_1.6-1.1 R6_2.5.1 fastmap_1.1.1
[37] GenomeInfoDbData_1.2.10 shiny_1.7.5 digest_0.6.33 colorspace_2.1-0
[41] RaggedExperiment_1.24.2 AnnotationDbi_1.62.2 RSQLite_2.3.1 gtsummary_1.7.2
[45] filelock_1.0.2 RTCGAToolbox_2.30.0 fansi_1.0.4 RJSONIO_1.3-1.8
[49] timechange_0.2.0 httr_1.4.7 abind_1.4-5 compiler_4.3.1
[53] withr_2.5.1 bit64_4.0.5 backports_1.4.1 BiocParallel_1.34.2
[57] DBI_1.1.3 performance_0.10.5 biomaRt_2.56.1 MASS_7.3-60
[61] rappdirs_0.3.3 sjstats_0.18.2 DelayedArray_0.26.7 rjson_0.2.21
[65] tools_4.3.1 httpuv_1.6.11 glue_1.6.2 restfulr_0.0.15
[69] nlme_3.1-163 promises_1.2.1 grid_4.3.1 generics_0.1.3
[73] gtable_0.3.4 tzdb_0.4.0 tidyr_1.3.0 hms_1.1.3
[77] data.table_1.14.8 xml2_1.3.5 utf8_1.2.3 XVector_0.40.0
[81] pillar_1.9.0 stringr_1.5.0 vroom_1.6.4 RCircos_1.2.2
[85] later_1.3.1 splines_4.3.1 BiocFileCache_2.8.0 lattice_0.21-9
[89] rtracklayer_1.60.1 survival_3.5-7 bit_4.0.5 tidyselect_1.2.0
[93] Biostrings_2.68.1 miniUI_0.1.1.1 knitr_1.44 futile.logger_1.4.3
[97] xfun_0.40 DT_0.30 stringi_1.7.12 yaml_2.3.7
[101] boot_1.3-28.1 codetools_0.2-19 evaluate_0.22 tibble_3.2.1
[105] cli_3.6.1 xtable_1.8-4 munsell_0.5.0 modelr_0.1.11
[109] Rcpp_1.0.11 GenomicDataCommons_1.24.3 ggeffects_1.3.1 dbplyr_2.3.4
[113] png_0.1-8 XML_3.99-0.14 rapiclient_0.1.3 parallel_4.3.1
[117] TCGAutils_1.20.4 tidycmprsk_0.2.0 ellipsis_0.3.2 readr_2.1.4
[121] ggplot2_3.4.3 blob_1.2.4 prettyunits_1.2.0 bayestestR_0.13.1
[125] bitops_1.0-7 lme4_1.1-34 broom.helpers_1.14.0 mvtnorm_1.2-3
[129] scales_1.2.1 insight_0.19.5 purrr_1.0.2 crayon_1.5.2
[133] rlang_1.1.1 rvest_1.0.3 KEGGREST_1.40.1 formatR_1.14

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