# cBioPortalData: Data Build Errors

Marcel Ramos & Levi Waldron

#### May 18, 2026

# Contents

# Loading

    library(cBioPortalData)
    library(AnVIL)
    library(jsonlite)

# Overview

This document serves as a reporting tool for errors that occur when running our utility functions on the cBioPortal datasets.

## Data from the cBioPortal API (`cBioPortalData()`)

Typically, the number of errors encountered via the API are low. There are only a handful of packages that error when we apply the utility functions to provide a MultiAssayExperiment data representation.

First, we load the error `Rda` dataset.

    api_errs <- system.file(
        "extdata", "api", "err_api_info.json",
        package = "cBioPortalData", mustWork = TRUE
    )
    err_api_info <- fromJSON(api_errs)

We can now inspect the contents of the data:

    class(err_api_info)

    ## [1] "list"

    length(err_api_info)

    ## [1] 6

    lengths(err_api_info)

    ##                           Barcodes must start with 'TCGA'
    ##                                                         2
    ##                     group length is 0 but data length > 0
    ##                                                         1
    ##   Frequency of NA values higher than the cutoff tolerance
    ##                                                         2
    ##                          Inconsistent build numbers found
    ##                                                        33
    ##         `n` must be a single number, not an integer `NA`.
    ##                                                         1
    ## Argument 1 must be a data frame or a named atomic vector.
    ##                                                         1

There were about 6 unique errors during the last build run.

    names(err_api_info)

    ## [1] "Barcodes must start with 'TCGA'"
    ## [2] "group length is 0 but data length > 0"
    ## [3] "Frequency of NA values higher than the cutoff tolerance"
    ## [4] "Inconsistent build numbers found"
    ## [5] "`n` must be a single number, not an integer `NA`."
    ## [6] "Argument 1 must be a data frame or a named atomic vector."

The most common error was `Inconsistent build numbers found`. This is due to annotations from different build numbers that were not able to be resolved.

To see what datasets (`cancer_study_id` s) have that error we can use:

    err_api_info[['Inconsistent build numbers found']]

    ##  [1] "msk_ch_2020"                       "msk_access_2021"
    ##  [3] "mixed_msk_tcga_2021"               "mixed_impact_subset_2022"
    ##  [5] "pan_origimed_2020"                 "prad_msk_stopsack_2021"
    ##  [7] "pancan_pcawg_2020"                 "prad_pik3r1_msk_2021"
    ##  [9] "skcm_tcga"                         "stad_tcga"
    ## [11] "stad_tcga_pub"                     "skcm_tcga_pan_can_atlas_2018"
    ## [13] "stad_tcga_pan_can_atlas_2018"      "stes_tcga_pub"
    ## [15] "summit_2018"                       "cfdna_msk_2019"
    ## [17] "blca_bcan_hcrn_2022"               "nsclc_ctdx_msk_2022"
    ## [19] "thyroid_mskcc_2016"                "skcm_mskcc_2014"
    ## [21] "tmb_mskcc_2018"                    "rectal_msk_2019"
    ## [23] "skcm_tcga_pub_2015"                "msk_spectrum_tme_2022"
    ## [25] "ucec_ccr_cfdna_msk_2022"           "paired_bladder_2022"
    ## [27] "mtnn_msk_2022"                     "pog570_bcgsc_2020"
    ## [29] "sarcoma_msk_2023"                  "bowel_colitis_msk_2022"
    ## [31] "luad_mskcc_2023_met_organotropism" "coad_silu_2022"
    ## [33] "paac_msk_jco_2023"

We can also have a look at the entirety of the dataset.

    err_api_info

    ## $`Barcodes must start with 'TCGA'`
    ## [1] "blca_msk_tcga_2020"    "nsclc_tcga_broad_2016"
    ##
    ## $`group length is 0 but data length > 0`
    ## [1] "glioma_msk_2018"
    ##
    ## $`Frequency of NA values higher than the cutoff tolerance`
    ## [1] "mixed_selpercatinib_2020" "ucec_ccr_msk_2022"
    ##
    ## $`Inconsistent build numbers found`
    ##  [1] "msk_ch_2020"                       "msk_access_2021"
    ##  [3] "mixed_msk_tcga_2021"               "mixed_impact_subset_2022"
    ##  [5] "pan_origimed_2020"                 "prad_msk_stopsack_2021"
    ##  [7] "pancan_pcawg_2020"                 "prad_pik3r1_msk_2021"
    ##  [9] "skcm_tcga"                         "stad_tcga"
    ## [11] "stad_tcga_pub"                     "skcm_tcga_pan_can_atlas_2018"
    ## [13] "stad_tcga_pan_can_atlas_2018"      "stes_tcga_pub"
    ## [15] "summit_2018"                       "cfdna_msk_2019"
    ## [17] "blca_bcan_hcrn_2022"               "nsclc_ctdx_msk_2022"
    ## [19] "thyroid_mskcc_2016"                "skcm_mskcc_2014"
    ## [21] "tmb_mskcc_2018"                    "rectal_msk_2019"
    ## [23] "skcm_tcga_pub_2015"                "msk_spectrum_tme_2022"
    ## [25] "ucec_ccr_cfdna_msk_2022"           "paired_bladder_2022"
    ## [27] "mtnn_msk_2022"                     "pog570_bcgsc_2020"
    ## [29] "sarcoma_msk_2023"                  "bowel_colitis_msk_2022"
    ## [31] "luad_mskcc_2023_met_organotropism" "coad_silu_2022"
    ## [33] "paac_msk_jco_2023"
    ##
    ## $``n` must be a single number, not an integer `NA`.`
    ## [1] "msk_met_2021"
    ##
    ## $`Argument 1 must be a data frame or a named atomic vector.`
    ## [1] "makeanimpact_ccr_2023"

## Packaged data from `cBioDataPack()`

Now let’s look at the errors in the packaged datasets that are used for `cBioDataPack`:

    pack_errs <- system.file(
        "extdata", "pack", "err_pack_info.json",
        package = "cBioPortalData", mustWork = TRUE
    )
    err_pack_info <- fromJSON(pack_errs)

We can do the same for this data:

    length(err_pack_info)

    ## [1] 5

    lengths(err_pack_info)

    ##                                         more columns than column names
    ##                                                                     12
    ##                Frequency of NA values higher than the cutoff tolerance
    ##                                                                      5
    ## invalid class "ExperimentList" object: \n    Non-unique names provided
    ##                                                                      2
    ##                                                 non-character argument
    ##                                                                      2
    ##                                    'wget' call had nonzero exit status
    ##                                                                     13

We can get a list of all the errors present:

    names(err_pack_info)

    ## [1] "more columns than column names"
    ## [2] "Frequency of NA values higher than the cutoff tolerance"
    ## [3] "invalid class \"ExperimentList\" object: \n    Non-unique names provided"
    ## [4] "non-character argument"
    ## [5] "'wget' call had nonzero exit status"

And finally the full list of errors:

    err_pack_info

    ## $`more columns than column names`
    ##  [1] "ccrcc_utokyo_2013"                "gbm_cptac_2021"
    ##  [3] "luad_mskimpact_2021"              "mbl_dkfz_2017"
    ##  [5] "pan_origimed_2020"                "sarcoma_msk_2022"
    ##  [7] "bowel_colitis_msk_2022"           "prad_msk_mdanderson_2023"
    ##  [9] "brca_tcga_pan_can_atlas_2018"     "coadread_tcga_pan_can_atlas_2018"
    ## [11] "ov_tcga_pan_can_atlas_2018"       "sarc_tcga_pan_can_atlas_2018"
    ##
    ## $`Frequency of NA values higher than the cutoff tolerance`
    ## [1] "ihch_mskcc_2020"          "mixed_selpercatinib_2020"
    ## [3] "ucec_ccr_msk_2022"        "mixed_msk_tcga_2021"
    ## [5] "ihch_msk_2021"
    ##
    ## $`invalid class "ExperimentList" object: \n    Non-unique names provided`
    ## [1] "mpnst_mskcc"   "stad_tcga_pub"
    ##
    ## $`non-character argument`
    ## [1] "pcpg_tcga_pub"  "mbn_mdacc_2013"
    ##
    ## $`'wget' call had nonzero exit status`
    ##  [1] "braf_msk_impact_2024"  "braf_msk_archer_2024"  "prostate_msk_2024"
    ##  [4] "pcnsl_msk_2024"        "pdac_msk_2024"         "ucs_msk_2024"
    ##  [7] "asclc_msk_2024"        "lms_msk_2024"          "crc_orion_2024"
    ## [10] "brca_aurora_2023"      "hcc_msk_2024"          "pancreas_msk_2024"
    ## [13] "pancan_mimsi_msk_2024"

# sessionInfo

    sessionInfo()

    ## R version 4.6.0 Patched (2026-05-01 r89994)
    ## Platform: aarch64-apple-darwin23
    ## Running under: macOS Tahoe 26.3.1
    ##
    ## Matrix products: default
    ## BLAS:   /Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libRblas.0.dylib
    ## LAPACK: /Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.1
    ##
    ## locale:
    ## [1] C/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
    ##
    ## time zone: America/New_York
    ## tzcode source: internal
    ##
    ## attached base packages:
    ## [1] stats4    stats     graphics  grDevices utils     datasets  methods
    ## [8] base
    ##
    ## other attached packages:
    ##  [1] jsonlite_2.0.0              survminer_0.5.2
    ##  [3] ggpubr_0.6.3                ggplot2_4.0.3
    ##  [5] survival_3.8-6              cBioPortalData_2.25.1
    ##  [7] MultiAssayExperiment_1.39.0 SummarizedExperiment_1.43.0
    ##  [9] Biobase_2.73.1              GenomicRanges_1.65.0
    ## [11] Seqinfo_1.3.0               IRanges_2.47.1
    ## [13] S4Vectors_0.51.2            BiocGenerics_0.59.2
    ## [15] generics_0.1.4              MatrixGenerics_1.25.0
    ## [17] matrixStats_1.5.0           AnVIL_1.25.1
    ## [19] AnVILBase_1.7.0             dplyr_1.2.1
    ## [21] BiocStyle_2.41.0
    ##
    ## loaded via a namespace (and not attached):
    ##   [1] RColorBrewer_1.1-3        magrittr_2.0.5
    ##   [3] magick_2.9.1              GenomicFeatures_1.65.0
    ##   [5] farver_2.1.2              rmarkdown_2.31
    ##   [7] BiocIO_1.23.3             vctrs_0.7.3
    ##   [9] memoise_2.0.1             Rsamtools_2.29.0
    ##  [11] RCurl_1.98-1.18           tinytex_0.59
    ##  [13] rstatix_0.7.3             htmltools_0.5.9
    ##  [15] S4Arrays_1.13.0           BiocBaseUtils_1.15.1
    ##  [17] lambda.r_1.2.4            curl_7.1.0
    ##  [19] broom_1.0.13              Formula_1.2-5
    ##  [21] SparseArray_1.13.2        sass_0.4.10
    ##  [23] bslib_0.11.0              htmlwidgets_1.6.4
    ##  [25] keyring_1.4.1             httr2_1.2.2
    ##  [27] futile.options_1.0.1      cachem_1.1.0
    ##  [29] commonmark_2.0.0          GenomicAlignments_1.49.0
    ##  [31] mime_0.13                 lifecycle_1.0.5
    ##  [33] pkgconfig_2.0.3           Matrix_1.7-5
    ##  [35] R6_2.6.1                  fastmap_1.2.0
    ##  [37] shiny_1.13.0              digest_0.6.39
    ##  [39] GCPtools_1.3.0            RaggedExperiment_1.37.0
    ##  [41] AnnotationDbi_1.75.0      RSQLite_3.52.0
    ##  [43] labeling_0.4.3            filelock_1.0.3
    ##  [45] RTCGAToolbox_2.43.0       RJSONIO_2.0.5
    ##  [47] httr_1.4.8                abind_1.4-8
    ##  [49] compiler_4.6.0            bit64_4.8.0
    ##  [51] withr_3.0.2               backports_1.5.1
    ##  [53] S7_0.2.2                  BiocParallel_1.47.0
    ##  [55] carData_3.0-6             DBI_1.3.0
    ##  [57] ggsignif_0.6.4            rappdirs_0.3.4
    ##  [59] DelayedArray_0.39.2       rjson_0.2.23
    ##  [61] tools_4.6.0               chromote_0.5.1
    ##  [63] otel_0.2.0                httpuv_1.6.17
    ##  [65] glue_1.8.1                restfulr_0.0.16
    ##  [67] promises_1.5.0            gridtext_0.1.6
    ##  [69] grid_4.6.0                gtable_0.3.6
    ##  [71] tzdb_0.5.0                tidyr_1.3.2
    ##  [73] websocket_1.4.4           data.table_1.18.4
    ##  [75] hms_1.1.4                 car_3.1-5
    ##  [77] xml2_1.5.2                utf8_1.2.6
    ##  [79] XVector_0.53.0            markdown_2.0
    ##  [81] pillar_1.11.1             stringr_1.6.0
    ##  [83] later_1.4.8               splines_4.6.0
    ##  [85] ggtext_0.1.2              BiocFileCache_3.3.0
    ##  [87] lattice_0.22-9            rtracklayer_1.73.0
    ##  [89] bit_4.6.0                 tidyselect_1.2.1
    ##  [91] Biostrings_2.81.1         miniUI_0.1.2
    ##  [93] knitr_1.51                gridExtra_2.3
    ##  [95] litedown_0.9              bookdown_0.46
    ##  [97] futile.logger_1.4.9       xfun_0.57
    ##  [99] DT_0.34.0                 stringi_1.8.7
    ## [101] UCSC.utils_1.9.0          yaml_2.3.12
    ## [103] evaluate_1.0.5            codetools_0.2-20
    ## [105] cigarillo_1.3.0           tibble_3.3.1
    ## [107] BiocManager_1.30.27       cli_3.6.6
    ## [109] xtable_1.8-8              processx_3.9.0
    ## [111] jquerylib_0.1.4           dichromat_2.0-0.1
    ## [113] Rcpp_1.1.1-1.1            GenomeInfoDb_1.49.0
    ## [115] GenomicDataCommons_1.37.0 dbplyr_2.5.2
    ## [117] png_0.1-9                 XML_3.99-0.23
    ## [119] rapiclient_0.1.8          parallel_4.6.0
    ## [121] TCGAutils_1.33.1          readr_2.2.0
    ## [123] blob_1.3.0                bitops_1.0-9
    ## [125] scales_1.4.0              purrr_1.2.2
    ## [127] crayon_1.5.3              rlang_1.2.0
    ## [129] KEGGREST_1.53.0           rvest_1.0.5
    ## [131] formatR_1.14