loadstudy and cBioDataPack return error in vroom_
0
0
Entering edit mode
karam • 0
@d7e5f1b4
Last seen 14 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

library(BiocManager)
library(cBioPortalData)

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


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


# 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]: 
y
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

cBioPortalData • 434 views
ADD COMMENT

Login before adding your answer.

Traffic: 421 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6