GDCprepare() can never complete request ("Error: cannot allocate vector")
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aush ▴ 40
@aush-9128
Last seen 28 days ago
United States

I'm trying to pull TCGA data as following:

require(TCGAbiolinks)
projects <- TCGAbiolinks:::getGDCprojects()$project_id
projects <- projects[grepl('^TCGA',projects,perl=T)]
query <- GDCquery(project = projects,
                  data.category = "Transcriptome Profiling", 
                  data.type = "Gene Expression Quantification", 
                  workflow.type = "HTSeq - Counts")
GDCdownload(query)
counts <- GDCprepare(query,save = TRUE, save.filename = "all_tumor_htseq_raw_counts.rda")

The last command shows something like "100% Completed after 19 m " and then either gets "frozen" (i.e. nothing happens but R session is shown as busy), or it gives "Error: cannot allocate vector of size 473 Kb". My system paging file (pagefile.sys) grows to 17 Gb (usual size 8 Gb). Session info below. Would be grateful for any hints!

R version 4.0.2 (2020-06-22)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    
system code page: 1251

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

other attached packages:
[1] TCGAbiolinks_2.16.3 vautils_0.1.1.102   magrittr_1.5        data.table_1.13.0  

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.5                  lattice_0.20-41             tidyr_1.1.2                 prettyunits_1.1.1          
 [5] assertthat_0.2.1            digest_0.6.25               BiocFileCache_1.12.1        plyr_1.8.6                 
 [9] R6_2.4.1                    GenomeInfoDb_1.24.2         stats4_4.0.2                RSQLite_2.2.0              
[13] httr_1.4.2                  ggplot2_3.3.2               pillar_1.4.6                zlibbioc_1.34.0            
[17] rlang_0.4.7                 progress_1.2.2              curl_4.3                    rstudioapi_0.11            
[21] blob_1.2.1                  S4Vectors_0.26.1            R.utils_2.10.1              R.oo_1.24.0                
[25] Matrix_1.2-18               downloader_0.4              readr_1.3.1                 stringr_1.4.0              
[29] RCurl_1.98-1.2              bit_4.0.4                   biomaRt_2.44.1              munsell_0.5.0              
[33] DelayedArray_0.14.1         xfun_0.16                   compiler_4.0.2              pkgconfig_2.0.3            
[37] askpass_1.1                 BiocGenerics_0.34.0         openssl_1.4.2               tidyselect_1.1.0           
[41] SummarizedExperiment_1.18.2 tibble_3.0.3                GenomeInfoDbData_1.2.3      IRanges_2.22.2             
[45] matrixStats_0.56.0          XML_3.99-0.5                crayon_1.3.4                dplyr_1.0.2                
[49] dbplyr_1.4.4                bitops_1.0-6                R.methodsS3_1.8.1           rappdirs_0.3.1             
[53] grid_4.0.2                  jsonlite_1.7.0              gtable_0.3.0                lifecycle_0.2.0            
[57] DBI_1.1.0                   scales_1.1.1                stringi_1.4.6               XVector_0.28.0             
[61] xml2_1.3.2                  ellipsis_0.3.1              generics_0.0.2              vctrs_0.3.4                
[65] tools_4.0.2                 bit64_4.0.5                 Biobase_2.48.0              glue_1.4.2                 
[69] purrr_0.3.4                 hms_0.5.3                   parallel_4.0.2              AnnotationDbi_1.50.3       
[73] colorspace_1.4-1            GenomicRanges_1.40.0        rvest_0.3.6                 memoise_1.1.0              
[77] knitr_1.29
TCGAbiolinks TCGA • 186 views
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Entering edit mode
@tiago-chedraoui-silva-8877
Last seen 9 months ago
Brazil - University of São Paulo/ Los A…

Please, how much RAM memory do you have in the machine? Very likely it requires more than the machine has. Did you try preparing the datasets separately?

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Entering edit mode

I have 16 Gb of RAM. I was suspecting having not enough, but it's strange that the error message says "vector of size 473 Kb" only.

Will try splitting the query.

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