GDCprepare caused R crash

[biosyssun]

Hi , when I downloaded MAF data, I encountered an issue that downloading process is ok for several cancer types but crashed for TCGA-PAAD. Please help.

################################################################
# running code
################################################################
library(SummarizedExperiment)
library(TCGAbiolinks)
library(TCGAbiolinksGUI.data)

#=============================
#Settings
#=============================
#working dir
#setwd('D:/DATA/TCGA')
#project information
projectInfo <- getGDCprojects()
#TCGA project ids
projectIds <- projectInfo$project_id[grep('TCGA',projectInfo$project_id)] 

for(projectId in projectIds){
     cat(projectId,'\n')
     if(!file.exists(paste(projectId,'.harmonized.MaskedSomaticMutation','.rda',sep=''))){
         query.mut <- GDCquery(project = projectId, 
                               legacy = FALSE,
                               data.category = "Simple Nucleotide Variation",
                               data.type = "Masked Somatic Mutation")
         GDCdownload(query.mut, files.per.chunk = 6)
         GDCprepare(query = query.mut, save = TRUE,
                    save.filename = paste(projectId,'.harmonized.MaskedSomaticMutation','.rda',sep=''))
     }
 }

################################################################

output

################################################################

################################################################

Error

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26 Apr 2022 01:47:01 [rsession-rstudio] ERROR session hadabend; LOGGED FROM: rstudio::core::Error {anonymous}::rInit(const rstudio::r::session::RInitInfo&) src/cpp/session/SessionMain.cpp:675

################################################################

sessionInfo

################################################################

sessionInfo() R version 4.1.1 (2021-08-10) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 20.04.2 LTS

Matrix products: default BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.8.so

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=C 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] TCGAbiolinksGUI.data_1.15.1 TCGAbiolinks_2.23.13 SummarizedExperiment_1.22.0 Biobase_2.52.0 GenomicRanges_1.44.0
[6] GenomeInfoDb_1.28.4 IRanges_2.26.0 S4Vectors_0.30.2 BiocGenerics_0.38.0 MatrixGenerics_1.4.3
[11] matrixStats_0.60.1

loaded via a namespace (and not attached): [1] httr_1.4.2 tidyr_1.1.3 bit64_4.0.5 jsonlite_1.7.2 assertthat_0.2.1 BiocFileCache_2.0.0
[7] blob_1.2.2 GenomeInfoDbData_1.2.6 progress_1.2.2 pillar_1.6.2 RSQLite_2.2.9 lattice_0.20-44
[13] glue_1.4.2 downloader_0.4 digest_0.6.27 XVector_0.32.0 rvest_1.0.2 colorspace_2.0-2
[19] Matrix_1.3-4 plyr_1.8.6 XML_3.99-0.8 pkgconfig_2.0.3 biomaRt_2.48.3 zlibbioc_1.38.0
[25] purrr_0.3.4 scales_1.1.1 tzdb_0.3.0 tibble_3.1.4 KEGGREST_1.32.0 generics_0.1.0
[31] ggplot2_3.3.5 ellipsis_0.3.2 cachem_1.0.6 magrittr_2.0.1 crayon_1.4.1 memoise_2.0.0
[37] fansi_0.5.0 xml2_1.3.2 tools_4.1.1 data.table_1.14.0 prettyunits_1.1.1 hms_1.1.1
[43] lifecycle_1.0.0 stringr_1.4.0 munsell_0.5.0 DelayedArray_0.18.0 AnnotationDbi_1.54.1 Biostrings_2.60.2
[49] compiler_4.1.1 rlang_0.4.11 grid_4.1.1 RCurl_1.98-1.5 rstudioapi_0.13 rappdirs_0.3.3
[55] bitops_1.0-7 gtable_0.3.0 DBI_1.1.2 curl_4.3.2 R6_2.5.1 knitr_1.36
[61] dplyr_1.0.7 fastmap_1.1.0 bit_4.0.4 utf8_1.2.2 filelock_1.0.2 readr_2.1.2
[67] stringi_1.7.4 Rcpp_1.0.7 vctrs_0.3.8 png_0.1-7 dbplyr_2.1.1 tidyselect_1.1.1
[73] xfun_0.26

[tiagochst]

Projects not successful prepared:

• TCGA-PAAD
• TCGA-SKCM

[tiagochst]

Breaking probably due files with no daa

[biosyssun]

@tiagochst Thanks for your fixing. It works in my machine.

[biosyssun]

@tiagochst Error happens in the GDCprepare function when downloading DNA Methylation of TCGA-COAD. I used the latest version of TCGAbiolinks (Fixing #507).

projectId <- 'TCGA-COAD' query.meth <- GDCquery(project = projectId, legacy = FALSE, data.category = "DNA Methylation", data.type = "Methylation Beta Value", access = 'open') GDCdownload(query.meth, files.per.chunk = 6) GDCprepare(query = query.meth, save = TRUE,summarizedExperiment = F, save.filename = paste(projectId,'.harmonized.MethylationBetaValues','.rda',sep=''))

[tiagochst]

@biosyssun You need to specify the platform. Also, could you updated it.

query.meth <- GDCquery(
  project = projectId,
  legacy = FALSE,
  data.category = "DNA Methylation",
  data.type = "Methylation Beta Value",
  platform =  "Illumina Human Methylation 27"
  access = 'open'
)

[biosyssun]

It works. Thank you.

[bioinfofuns]

Walk through the case study of TCGAbiolinks, but got error like that: thanks for your help.

[tiagochst]

Do you have the latest version installed?

BiocManager::install("BioinformaticsFMRP/TCGAbiolinksGUI.data")BiocManager::install("BioinformaticsFMRP/TCGAbiolinks")

On Sat, Apr 30, 2022, 10:33 PM bioinfofuns @.***> wrote:

[image: 图片] https://user-images.githubusercontent.com/92902723/166129616-c65ff593-a09b-401b-ad92-832a0dcac386.png Walk through the case study of TCGAbiolinks, but got error like that: [image: 图片] https://user-images.githubusercontent.com/92902723/166129692-c611c665-7c37-41d9-be3b-1190b505d709.png thanks for your help.

— Reply to this email directly, view it on GitHub https://github.com/BioinformaticsFMRP/TCGAbiolinks/issues/507#issuecomment-1114108320, or unsubscribe https://github.com/notifications/unsubscribe-auth/AABDQ6PAKYLW232B62LB53TVHXUQ5ANCNFSM5UKJUCVQ . You are receiving this because you were mentioned.Message ID: @.***>

[bioinfofuns]

yes！the latest version does the work, thanks.