Hello all,

Tried downloading raw STAR counts using TCGAbiolinks today using this code snippet

tcga_rna_query <- GDCquery(
  project = "TCGA-LAML",
  data.category = "Transcriptome Profiling",
  data.type = "Gene Expression Quantification",
  workflow.type = "STAR - Counts",
  experimental.strategy = "RNA-Seq"
)
GDCdownload(tcga_rna_query)
tcga_rna_counts <- GDCprepare(tcga_rna_query, summarizedExperiment = FALSE)

Error in `vectbl_as_col_location()`:
! Can't subset columns past the end.
ℹ Locations 2, 3, and 4 don't exist.
ℹ There is only 1 column.
Run `rlang::last_error()` to see where the error occurred.
There were 50 or more warnings (use warnings() to see the first 50)

sessionInfo()
R version 4.1.3 (2022-03-10)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: macOS Big Sur/Monterey 10.16

Matrix products: default
BLAS/LAPACK: /Users/suika-san/opt/miniconda3/lib/libopenblasp-r0.3.20.dylib

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

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

other attached packages:
 [1] forcats_0.5.2       purrr_0.3.4         readr_2.1.2        
 [4] tidyr_1.2.0         tibble_3.1.7        ggplot2_3.3.6      
 [7] tidyverse_1.3.2     edgeR_3.36.0        limma_3.50.1       
[10] stringr_1.4.1       dplyr_1.0.9         TCGAbiolinks_2.25.3

loaded via a namespace (and not attached):
 [1] fs_1.5.2                    bitops_1.0-7               
 [3] matrixStats_0.62.0          lubridate_1.8.0            
 [5] bit64_4.0.5                 filelock_1.0.2             
 [7] progress_1.2.2              httr_1.4.4                 
 [9] GenomeInfoDb_1.30.1         tools_4.1.3                
[11] backports_1.4.1             utf8_1.2.2                 
[13] R6_2.5.1                    DBI_1.1.3                  
[15] BiocGenerics_0.40.0         colorspace_2.0-3           
[17] withr_2.5.0                 tidyselect_1.1.2           
[19] prettyunits_1.1.1           bit_4.0.4                  
[21] curl_4.3.2                  compiler_4.1.3             
[23] cli_3.3.0                   rvest_1.0.3                
[25] Biobase_2.54.0              xml2_1.3.3                 
[27] DelayedArray_0.20.0         scales_1.2.1               
[29] rappdirs_0.3.3              digest_0.6.29              
[31] R.utils_2.12.1              XVector_0.34.0             
[33] pkgconfig_2.0.3             MatrixGenerics_1.6.0       
[35] dbplyr_2.2.1                fastmap_1.1.0              
[37] readxl_1.4.0                rlang_1.0.2                
[39] RSQLite_2.2.8               generics_0.1.3             
[41] jsonlite_1.8.0              vroom_1.5.7                
[43] googlesheets4_1.0.1         R.oo_1.25.0                
[45] RCurl_1.98-1.6              magrittr_2.0.3             
[47] GenomeInfoDbData_1.2.7      Matrix_1.4-1               
[49] Rcpp_1.0.8.3                munsell_0.5.0              
[51] S4Vectors_0.32.3            fansi_1.0.3                
[53] lifecycle_1.0.1             R.methodsS3_1.8.2          
[55] stringi_1.7.6               SummarizedExperiment_1.24.0
[57] zlibbioc_1.40.0             plyr_1.8.7                 
[59] BiocFileCache_2.2.1         grid_4.1.3                 
[61] blob_1.2.3                  parallel_4.1.3             
[63] crayon_1.5.2                lattice_0.20-45            
[65] haven_2.5.0                 Biostrings_2.62.0          
[67] hms_1.1.2                   KEGGREST_1.34.0            
[69] locfit_1.5-9.5              knitr_1.40                 
[71] pillar_1.8.1                GenomicRanges_1.46.1       
[73] TCGAbiolinksGUI.data_1.15.1 biomaRt_2.50.3             
[75] stats4_4.1.3                reprex_2.0.2               
[77] XML_3.99-0.9                glue_1.6.2                 
[79] downloader_0.4              remotes_2.4.2              
[81] modelr_0.1.9                data.table_1.14.2          
[83] BiocManager_1.30.19         png_0.1-7                  
[85] vctrs_0.4.1                 tzdb_0.3.0                 
[87] cellranger_1.1.0            gtable_0.3.1               
[89] assertthat_0.2.1            cachem_1.0.6               
[91] xfun_0.31                   broom_1.0.1                
[93] googledrive_2.0.0           gargle_1.2.1               
[95] AnnotationDbi_1.56.2        memoise_2.0.1              
[97] IRanges_2.28.0              ellipsis_0.3.2

This code has worked for me in the past. Any suggestions for troubleshooting?

Thanks!