GDCprepare error with TARGET-ALL-P2

Hi,

I am failing to apply the GDCprepare function to this query

query2 <- TCGAquery_SampleTypes(barcode = samplesDown_Target,
                                         typesample = "TBM" 

queryDown_Target <- GDCquery(project = "TARGET-ALL-P2", 
                             data.category = "Transcriptome Profiling",
                             data.type = "Gene Expression Quantification", 
                             workflow.type = "HTSeq - Counts", 
                             barcode =  query2)

When using GDCprepare, I get:

> data2 <- GDCprepare(queryDown_Target)
|==============================================================================================|100%                      Completed after 13 s 
Starting to add information to samples
Adding description to TARGET samples
 => Add clinical information to samples
Error in if (any(ret$project_id == "CPTAC-3")) { : 
  missing value where TRUE/FALSE needed

Alternatively, this query causes no issues:

query <- TCGAquery_SampleTypes(barcode = samplesDown_Target,
                                         typesample = "TRBM"

The only difference being that the 'typesample' variable is changed.

Any ideas? Thanks!

session info

``` R version 4.1.0 (2021-05-18) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 22000) Matrix products: default locale: [1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252 [3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C [5] LC_TIME=English_United Kingdom.1252 attached base packages: [1] stats4 stats graphics grDevices utils datasets methods base other attached packages: [1] shiny_1.7.1 styler_1.7.0 reprex_2.0.1 [4] TCGAbiolinks_2.22.4 dplyr_1.0.8 EDASeq_2.28.0 [7] ShortRead_1.52.0 GenomicAlignments_1.30.0 SummarizedExperiment_1.24.0 [10] MatrixGenerics_1.6.0 matrixStats_0.61.0 Rsamtools_2.10.0 [13] GenomicRanges_1.46.1 Biostrings_2.62.0 GenomeInfoDb_1.30.1 [16] XVector_0.34.0 IRanges_2.28.0 S4Vectors_0.32.3 [19] BiocParallel_1.28.3 Biobase_2.54.0 BiocGenerics_0.40.0 loaded via a namespace (and not attached): [1] AnnotationHub_3.2.2 aroma.light_3.24.0 BiocFileCache_2.2.1 [4] plyr_1.8.6 usethis_2.1.5 ggplot2_3.3.5 [7] digest_0.6.29 htmltools_0.5.2 fansi_1.0.2 [10] celldex_1.4.0 magrittr_2.0.2 memoise_2.0.1 [13] remotes_2.4.2 tzdb_0.2.0 readr_2.1.2 [16] R.utils_2.11.0 vroom_1.5.7 prettyunits_1.1.1 [19] jpeg_0.1-9 colorspace_2.0-3 blob_1.2.2 [22] rvest_1.0.2 rappdirs_0.3.3 xfun_0.30 [25] callr_3.7.0 crayon_1.5.0 RCurl_1.98-1.6 [28] jsonlite_1.8.0 glue_1.6.2 gtable_0.3.0 [31] zlibbioc_1.40.0 DelayedArray_0.20.0 pkgbuild_1.3.1 [34] R.cache_0.15.0 clipr_0.8.0 scales_1.1.1 [37] DBI_1.1.2 miniUI_0.1.1.1 Rcpp_1.0.8 [40] xtable_1.8-4 progress_1.2.2 bit_4.0.4 [43] DT_0.21 htmlwidgets_1.5.4 httr_1.4.2 [46] RColorBrewer_1.1-2 ellipsis_0.3.2 pkgconfig_2.0.3 [49] XML_3.99-0.9 R.methodsS3_1.8.1 sass_0.4.0 [52] dbplyr_2.1.1 utf8_1.2.2 tidyselect_1.1.2 [55] rlang_1.0.2 later_1.3.0 AnnotationDbi_1.56.2 [58] munsell_0.5.0 BiocVersion_3.14.0 tools_4.1.0 [61] cachem_1.0.6 downloader_0.4 cli_3.2.0 [64] generics_0.1.2 RSQLite_2.2.10 ExperimentHub_2.2.1 [67] devtools_2.4.3 evaluate_0.15 stringr_1.4.0 [70] fastmap_1.1.0 yaml_2.3.5 processx_3.5.2 [73] knitr_1.37 bit64_4.0.5 fs_1.5.2 [76] purrr_0.3.4 KEGGREST_1.34.0 sparseMatrixStats_1.6.0 [79] mime_0.12 R.oo_1.24.0 xml2_1.3.3 [82] biomaRt_2.50.3 brio_1.1.3 compiler_4.1.0 [85] rstudioapi_0.13 filelock_1.0.2 curl_4.3.2 [88] png_0.1-7 interactiveDisplayBase_1.32.0 testthat_3.1.2 [91] tibble_3.1.6 bslib_0.3.1 stringi_1.7.6 [94] highr_0.9 ps_1.6.0 desc_1.4.1 [97] TCGAbiolinksGUI.data_1.14.0 GenomicFeatures_1.46.5 lattice_0.20-44 [100] Matrix_1.4-0 vctrs_0.3.8 pillar_1.7.0 [103] lifecycle_1.0.1 BiocManager_1.30.16 jquerylib_0.1.4 [106] data.table_1.14.2 bitops_1.0-7 httpuv_1.6.5 [109] rtracklayer_1.54.0 R6_2.5.1 BiocIO_1.4.0 [112] latticeExtra_0.6-29 hwriter_1.3.2 promises_1.2.0.1 [115] sessioninfo_1.2.2 pkgload_1.2.4 assertthat_0.2.1 [118] rprojroot_2.0.2 rjson_0.2.21 withr_2.5.0 [121] GenomeInfoDbData_1.2.7 parallel_4.1.0 hms_1.1.1 [124] grid_4.1.0 tidyr_1.2.0 rmarkdown_2.13 [127] DelayedMatrixStats_1.16.0 restfulr_0.0.13 ```

BioinformaticsFMRP / TCGAbiolinks

GDCprepare error with TARGET-ALL-P2 #490