library(cBioPortalData)
library(AnVIL)This document serves as a reporting tool for errors that occur when running our utility functions on the cBioPortal datasets.
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.rda",
package = "cBioPortalData", mustWork = TRUE
)
load(api_errs)We can now inspect the contents of the data:
class(err_api_info)## [1] "list"length(err_api_info)## [1] 4lengths(err_api_info)## Barcodes must start with 'TCGA'
## 2
## Empty reply from server
## 1
## Frequency of NA values higher than the cutoff tolerance
## 1
## replacement has length zero
## 1There were about 4 unique errors during the last build run.
names(err_api_info)## [1] "Barcodes must start with 'TCGA'"
## [2] "Empty reply from server"
## [3] "Frequency of NA values higher than the cutoff tolerance"
## [4] "replacement has length zero"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']]## NULLWe can also have a look at the entirety of the dataset.
err_api_info## $`Barcodes must start with 'TCGA'`
## [1] "nsclc_tcga_broad_2016" "blca_msk_tcga_2020"
##
## $`Empty reply from server`
## [1] "ccle_broad_2019"
##
## $`Frequency of NA values higher than the cutoff tolerance`
## [1] "mixed_msk_tcga_2021"
##
## $`replacement has length zero`
## [1] "glioma_msk_2018"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.rda",
package = "cBioPortalData", mustWork = TRUE
)
load(pack_errs)We can do the same for this data:
length(err_pack_info)## [1] 42lengths(err_pack_info)## failed to create directory '/tmp/RtmpzXtVhu/3249cd7a0f6245_laml_tcga'
## 1
## no lines available in input
## 12
## failed to create directory '/tmp/RtmpzXtVhu/3249dc7a0f6245_cesc_tcga'
## 1
## failed to create directory '/tmp/RtmpzXtVhu/3249dd7a0f6245_chol_tcga'
## 1
## failed to create directory '/tmp/RtmpzXtVhu/3249f02adae78d_kich_tcga'
## 1
## failed to create directory '/tmp/RtmpzXtVhu/3249e0108540f3_coadread_tcga'
## 1
## failed to create directory '/tmp/RtmpzXtVhu/3249f77ab68a7d_dlbc_tcga'
## 1
## failed to create directory '/tmp/RtmpzXtVhu/3249d62adae78d_lgg_tcga'
## 1
## object 'clindata' not found
## 7
## attempt to set 'colnames' on an object with less than two dimensions
## 8
## cannot coerce type 'closure' to vector of type 'character'
## 19
## non-character argument
## 2
## failed to create directory '/tmp/RtmpzXtVhu/3249d4108540f3_blca_dfarber_mskcc_2014'
## 1
## failed to create directory '/tmp/RtmpzXtVhu/3249d9108540f3_brca_sanger'
## 1
## more columns than column names
## 2
## failed to create directory '/tmp/RtmpzXtVhu/3249e57a0f6245_esca_broad'
## 1
## failed to create directory '/tmp/RtmpzXtVhu/3249f37a0f6245_lihc_riken'
## 1
## failed to create directory '/tmp/RtmpzXtVhu/3249f47ab68a7d_luad_mskcc_2015'
## 1
## failed to create directory '/tmp/RtmpzXtVhu/3249cc2adae78d_paac_jhu_2014'
## 1
## replacement has 1 row, data has 0
## 1
## invalid class "ExperimentList" object: \n Non-unique names provided
## 1
## failed to create directory '/tmp/RtmpzXtVhu/324a037ab68a7d_nepc_wcm_2016'
## 1
## failed to create directory '/tmp/RtmpzXtVhu/3249de2adae78d_lcll_broad_2013'
## 1
## failed to create directory '/tmp/RtmpzXtVhu/3249f8108540f3_mixed_allen_2018'
## 1
## failed to create directory '/tmp/RtmpzXtVhu/324a142adae78d_rectal_msk_2019'
## 1
## failed to create directory '/tmp/RtmpzXtVhu/324a007a0f6245_prad_mcspc_mskcc_2020'
## 1
## failed to create directory '/tmp/RtmpzXtVhu/3249d82adae78d_brca_smc_2018'
## 1
## failed to create directory '/tmp/RtmpzXtVhu/324a007ab68a7d_mixed_cfdna_msk_2020'
## 1
## failed to create directory '/tmp/RtmpzXtVhu/3249f6108540f3_lung_smc_2016'
## 1
## failed to create directory '/tmp/RtmpzXtVhu/324a017a0f6245_mds_tokyo_2011'
## 1
## failed to create directory '/tmp/RtmpzXtVhu/3249e27ab68a7d_pact_jhu_2011'
## 1
## failed to create directory '/tmp/RtmpzXtVhu/176b15456c3cf_utuc_mskcc_2015'
## 1
## failed to create directory '/tmp/RtmpzXtVhu/324a037a0f6245_nbl_broad_2013'
## 1
## failed to create directory '/tmp/RtmpzXtVhu/3249fd108540f3_egc_msk_2017'
## 1
## failed to create directory '/tmp/RtmpzXtVhu/3249fd7a0f6245_crc_msk_2017'
## 1
## failed to create directory '/tmp/RtmpzXtVhu/3249fe108540f3_mel_ucla_2016'
## 1
## failed to create directory '/tmp/RtmpzXtVhu/3249e47a0f6245_dlbc_tcga_pan_can_atlas_2018'
## 1
## failed to create directory '/tmp/RtmpzXtVhu/3249d8108540f3_bfn_duke_nus_2015'
## 1
## failed to create directory '/tmp/RtmpzXtVhu/3249eb7a0f6245_glioma_mskcc_2019'
## 1
## failed to create directory '/tmp/RtmpzXtVhu/1769344c0b9fb_vsc_cuk_2018'
## 1
## failed to create directory '/tmp/RtmpzXtVhu/7a1a5a6a8099_lung_msk_pdx'
## 1
## failed to create directory '/tmp/RtmpzXtVhu/3249ee2adae78d_histiocytosis_cobi_msk_2019'
## 1We can get a list of all the errors present:
names(err_pack_info)## [1] "failed to create directory '/tmp/RtmpzXtVhu/3249cd7a0f6245_laml_tcga'"
## [2] "no lines available in input"
## [3] "failed to create directory '/tmp/RtmpzXtVhu/3249dc7a0f6245_cesc_tcga'"
## [4] "failed to create directory '/tmp/RtmpzXtVhu/3249dd7a0f6245_chol_tcga'"
## [5] "failed to create directory '/tmp/RtmpzXtVhu/3249f02adae78d_kich_tcga'"
## [6] "failed to create directory '/tmp/RtmpzXtVhu/3249e0108540f3_coadread_tcga'"
## [7] "failed to create directory '/tmp/RtmpzXtVhu/3249f77ab68a7d_dlbc_tcga'"
## [8] "failed to create directory '/tmp/RtmpzXtVhu/3249d62adae78d_lgg_tcga'"
## [9] "object 'clindata' not found"
## [10] "attempt to set 'colnames' on an object with less than two dimensions"
## [11] "cannot coerce type 'closure' to vector of type 'character'"
## [12] "non-character argument"
## [13] "failed to create directory '/tmp/RtmpzXtVhu/3249d4108540f3_blca_dfarber_mskcc_2014'"
## [14] "failed to create directory '/tmp/RtmpzXtVhu/3249d9108540f3_brca_sanger'"
## [15] "more columns than column names"
## [16] "failed to create directory '/tmp/RtmpzXtVhu/3249e57a0f6245_esca_broad'"
## [17] "failed to create directory '/tmp/RtmpzXtVhu/3249f37a0f6245_lihc_riken'"
## [18] "failed to create directory '/tmp/RtmpzXtVhu/3249f47ab68a7d_luad_mskcc_2015'"
## [19] "failed to create directory '/tmp/RtmpzXtVhu/3249cc2adae78d_paac_jhu_2014'"
## [20] "replacement has 1 row, data has 0"
## [21] "invalid class \"ExperimentList\" object: \n Non-unique names provided"
## [22] "failed to create directory '/tmp/RtmpzXtVhu/324a037ab68a7d_nepc_wcm_2016'"
## [23] "failed to create directory '/tmp/RtmpzXtVhu/3249de2adae78d_lcll_broad_2013'"
## [24] "failed to create directory '/tmp/RtmpzXtVhu/3249f8108540f3_mixed_allen_2018'"
## [25] "failed to create directory '/tmp/RtmpzXtVhu/324a142adae78d_rectal_msk_2019'"
## [26] "failed to create directory '/tmp/RtmpzXtVhu/324a007a0f6245_prad_mcspc_mskcc_2020'"
## [27] "failed to create directory '/tmp/RtmpzXtVhu/3249d82adae78d_brca_smc_2018'"
## [28] "failed to create directory '/tmp/RtmpzXtVhu/324a007ab68a7d_mixed_cfdna_msk_2020'"
## [29] "failed to create directory '/tmp/RtmpzXtVhu/3249f6108540f3_lung_smc_2016'"
## [30] "failed to create directory '/tmp/RtmpzXtVhu/324a017a0f6245_mds_tokyo_2011'"
## [31] "failed to create directory '/tmp/RtmpzXtVhu/3249e27ab68a7d_pact_jhu_2011'"
## [32] "failed to create directory '/tmp/RtmpzXtVhu/176b15456c3cf_utuc_mskcc_2015'"
## [33] "failed to create directory '/tmp/RtmpzXtVhu/324a037a0f6245_nbl_broad_2013'"
## [34] "failed to create directory '/tmp/RtmpzXtVhu/3249fd108540f3_egc_msk_2017'"
## [35] "failed to create directory '/tmp/RtmpzXtVhu/3249fd7a0f6245_crc_msk_2017'"
## [36] "failed to create directory '/tmp/RtmpzXtVhu/3249fe108540f3_mel_ucla_2016'"
## [37] "failed to create directory '/tmp/RtmpzXtVhu/3249e47a0f6245_dlbc_tcga_pan_can_atlas_2018'"
## [38] "failed to create directory '/tmp/RtmpzXtVhu/3249d8108540f3_bfn_duke_nus_2015'"
## [39] "failed to create directory '/tmp/RtmpzXtVhu/3249eb7a0f6245_glioma_mskcc_2019'"
## [40] "failed to create directory '/tmp/RtmpzXtVhu/1769344c0b9fb_vsc_cuk_2018'"
## [41] "failed to create directory '/tmp/RtmpzXtVhu/7a1a5a6a8099_lung_msk_pdx'"
## [42] "failed to create directory '/tmp/RtmpzXtVhu/3249ee2adae78d_histiocytosis_cobi_msk_2019'"And finally the full list of errors:
err_pack_info## $`failed to create directory '/tmp/RtmpzXtVhu/3249cd7a0f6245_laml_tcga'`
## [1] "laml_tcga"
##
## $`no lines available in input`
## [1] "blca_tcga" "brca_tcga"
## [3] "skcm_tcga" "prad_tcga"
## [5] "laml_tcga_pub" "lgggbm_tcga_pub"
## [7] "luad_tcga_pub" "brca_metabric"
## [9] "lihc_tcga_pan_can_atlas_2018" "brca_mbcproject_wagle_2017"
## [11] "angs_painter_2020" "paad_qcmg_uq_2016"
##
## $`failed to create directory '/tmp/RtmpzXtVhu/3249dc7a0f6245_cesc_tcga'`
## [1] "cesc_tcga"
##
## $`failed to create directory '/tmp/RtmpzXtVhu/3249dd7a0f6245_chol_tcga'`
## [1] "chol_tcga"
##
## $`failed to create directory '/tmp/RtmpzXtVhu/3249f02adae78d_kich_tcga'`
## [1] "kich_tcga"
##
## $`failed to create directory '/tmp/RtmpzXtVhu/3249e0108540f3_coadread_tcga'`
## [1] "coadread_tcga"
##
## $`failed to create directory '/tmp/RtmpzXtVhu/3249f77ab68a7d_dlbc_tcga'`
## [1] "dlbc_tcga"
##
## $`failed to create directory '/tmp/RtmpzXtVhu/3249d62adae78d_lgg_tcga'`
## [1] "lgg_tcga"
##
## $`object 'clindata' not found`
## [1] "luad_tcga" "hnsc_tcga_pub" "luad_broad"
## [4] "thca_tcga_pub" "msk_impact_2017" "nbl_target_2018_pub"
## [7] "skcm_dfci_2015"
##
## $`attempt to set 'colnames' on an object with less than two dimensions`
## [1] "lusc_tcga" "ampca_bcm_2016"
## [3] "skcm_tcga_pub_2015" "thym_tcga_pan_can_atlas_2018"
## [5] "msk_ch_2020" "cll_broad_2015"
## [7] "cscc_hgsc_bcm_2014" "ucs_tcga_pan_can_atlas_2018"
##
## $`cannot coerce type 'closure' to vector of type 'character'`
## [1] "bcc_unige_2016" "brca_bccrc_xenograft_2014"
## [3] "chol_jhu_2013" "luad_tsp"
## [5] "mbl_broad_2012" "sarc_mskcc"
## [7] "ctcl_columbia_2015" "mds_mskcc_2020"
## [9] "rbl_cfdna_msk_2020" "mcl_idibips_2013"
## [11] "cllsll_icgc_2011" "nsclc_unito_2016"
## [13] "hcc_msk_venturaa_2018" "mpn_cimr_2013"
## [15] "brca_jup_msk_2020" "utuc_igbmc_2021"
## [17] "dlbc_broad_2012" "mixed_msk_tcga_2021"
## [19] "ihch_mskcc_2020"
##
## $`non-character argument`
## [1] "prad_fhcrc" "mbn_mdacc_2013"
##
## $`failed to create directory '/tmp/RtmpzXtVhu/3249d4108540f3_blca_dfarber_mskcc_2014'`
## [1] "blca_dfarber_mskcc_2014"
##
## $`failed to create directory '/tmp/RtmpzXtVhu/3249d9108540f3_brca_sanger'`
## [1] "brca_sanger"
##
## $`more columns than column names`
## [1] "ccrcc_utokyo_2013" "acyc_fmi_2014"
##
## $`failed to create directory '/tmp/RtmpzXtVhu/3249e57a0f6245_esca_broad'`
## [1] "esca_broad"
##
## $`failed to create directory '/tmp/RtmpzXtVhu/3249f37a0f6245_lihc_riken'`
## [1] "lihc_riken"
##
## $`failed to create directory '/tmp/RtmpzXtVhu/3249f47ab68a7d_luad_mskcc_2015'`
## [1] "luad_mskcc_2015"
##
## $`failed to create directory '/tmp/RtmpzXtVhu/3249cc2adae78d_paac_jhu_2014'`
## [1] "paac_jhu_2014"
##
## $`replacement has 1 row, data has 0`
## [1] "prad_su2c_2015"
##
## $`invalid class "ExperimentList" object: \n Non-unique names provided`
## [1] "stad_tcga_pub"
##
## $`failed to create directory '/tmp/RtmpzXtVhu/324a037ab68a7d_nepc_wcm_2016'`
## [1] "nepc_wcm_2016"
##
## $`failed to create directory '/tmp/RtmpzXtVhu/3249de2adae78d_lcll_broad_2013'`
## [1] "lcll_broad_2013"
##
## $`failed to create directory '/tmp/RtmpzXtVhu/3249f8108540f3_mixed_allen_2018'`
## [1] "mixed_allen_2018"
##
## $`failed to create directory '/tmp/RtmpzXtVhu/324a142adae78d_rectal_msk_2019'`
## [1] "rectal_msk_2019"
##
## $`failed to create directory '/tmp/RtmpzXtVhu/324a007a0f6245_prad_mcspc_mskcc_2020'`
## [1] "prad_mcspc_mskcc_2020"
##
## $`failed to create directory '/tmp/RtmpzXtVhu/3249d82adae78d_brca_smc_2018'`
## [1] "brca_smc_2018"
##
## $`failed to create directory '/tmp/RtmpzXtVhu/324a007ab68a7d_mixed_cfdna_msk_2020'`
## [1] "mixed_cfdna_msk_2020"
##
## $`failed to create directory '/tmp/RtmpzXtVhu/3249f6108540f3_lung_smc_2016'`
## [1] "lung_smc_2016"
##
## $`failed to create directory '/tmp/RtmpzXtVhu/324a017a0f6245_mds_tokyo_2011'`
## [1] "mds_tokyo_2011"
##
## $`failed to create directory '/tmp/RtmpzXtVhu/3249e27ab68a7d_pact_jhu_2011'`
## [1] "pact_jhu_2011"
##
## $`failed to create directory '/tmp/RtmpzXtVhu/176b15456c3cf_utuc_mskcc_2015'`
## [1] "utuc_mskcc_2015"
##
## $`failed to create directory '/tmp/RtmpzXtVhu/324a037a0f6245_nbl_broad_2013'`
## [1] "nbl_broad_2013"
##
## $`failed to create directory '/tmp/RtmpzXtVhu/3249fd108540f3_egc_msk_2017'`
## [1] "egc_msk_2017"
##
## $`failed to create directory '/tmp/RtmpzXtVhu/3249fd7a0f6245_crc_msk_2017'`
## [1] "crc_msk_2017"
##
## $`failed to create directory '/tmp/RtmpzXtVhu/3249fe108540f3_mel_ucla_2016'`
## [1] "mel_ucla_2016"
##
## $`failed to create directory '/tmp/RtmpzXtVhu/3249e47a0f6245_dlbc_tcga_pan_can_atlas_2018'`
## [1] "dlbc_tcga_pan_can_atlas_2018"
##
## $`failed to create directory '/tmp/RtmpzXtVhu/3249d8108540f3_bfn_duke_nus_2015'`
## [1] "bfn_duke_nus_2015"
##
## $`failed to create directory '/tmp/RtmpzXtVhu/3249eb7a0f6245_glioma_mskcc_2019'`
## [1] "glioma_mskcc_2019"
##
## $`failed to create directory '/tmp/RtmpzXtVhu/1769344c0b9fb_vsc_cuk_2018'`
## [1] "vsc_cuk_2018"
##
## $`failed to create directory '/tmp/RtmpzXtVhu/7a1a5a6a8099_lung_msk_pdx'`
## [1] "lung_msk_pdx"
##
## $`failed to create directory '/tmp/RtmpzXtVhu/3249ee2adae78d_histiocytosis_cobi_msk_2019'`
## [1] "histiocytosis_cobi_msk_2019"sessionInfo()## R version 4.3.0 RC (2023-04-13 r84269)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 22.04.2 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.17-bioc/R/lib/libRblas.so
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_GB LC_COLLATE=C
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## time zone: America/New_York
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats4 stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] survminer_0.4.9 ggpubr_0.6.0
## [3] ggplot2_3.4.2 survival_3.5-5
## [5] cBioPortalData_2.12.0 MultiAssayExperiment_1.26.0
## [7] SummarizedExperiment_1.30.0 Biobase_2.60.0
## [9] GenomicRanges_1.52.0 GenomeInfoDb_1.36.0
## [11] IRanges_2.34.0 S4Vectors_0.38.0
## [13] BiocGenerics_0.46.0 MatrixGenerics_1.12.0
## [15] matrixStats_0.63.0 AnVIL_1.12.0
## [17] dplyr_1.1.2 BiocStyle_2.28.0
##
## loaded via a namespace (and not attached):
## [1] jsonlite_1.8.4 magrittr_2.0.3
## [3] magick_2.7.4 GenomicFeatures_1.52.0
## [5] farver_2.1.1 rmarkdown_2.21
## [7] BiocIO_1.10.0 zlibbioc_1.46.0
## [9] vctrs_0.6.2 memoise_2.0.1
## [11] Rsamtools_2.16.0 RCurl_1.98-1.12
## [13] rstatix_0.7.2 BiocBaseUtils_1.2.0
## [15] htmltools_0.5.5 progress_1.2.2
## [17] lambda.r_1.2.4 curl_5.0.0
## [19] broom_1.0.4 sass_0.4.5
## [21] bslib_0.4.2 htmlwidgets_1.6.2
## [23] zoo_1.8-12 futile.options_1.0.1
## [25] cachem_1.0.7 commonmark_1.9.0
## [27] GenomicAlignments_1.36.0 mime_0.12
## [29] lifecycle_1.0.3 pkgconfig_2.0.3
## [31] Matrix_1.5-4 R6_2.5.1
## [33] fastmap_1.1.1 GenomeInfoDbData_1.2.10
## [35] shiny_1.7.4 digest_0.6.31
## [37] colorspace_2.1-0 RaggedExperiment_1.24.0
## [39] AnnotationDbi_1.62.0 RSQLite_2.3.1
## [41] labeling_0.4.2 filelock_1.0.2
## [43] RTCGAToolbox_2.30.0 km.ci_0.5-6
## [45] fansi_1.0.4 RJSONIO_1.3-1.8
## [47] abind_1.4-5 httr_1.4.5
## [49] compiler_4.3.0 bit64_4.0.5
## [51] withr_2.5.0 backports_1.4.1
## [53] BiocParallel_1.34.0 carData_3.0-5
## [55] DBI_1.1.3 highr_0.10
## [57] ggsignif_0.6.4 biomaRt_2.56.0
## [59] rappdirs_0.3.3 DelayedArray_0.26.0
## [61] rjson_0.2.21 tools_4.3.0
## [63] httpuv_1.6.9 glue_1.6.2
## [65] restfulr_0.0.15 promises_1.2.0.1
## [67] gridtext_0.1.5 grid_4.3.0
## [69] generics_0.1.3 gtable_0.3.3
## [71] KMsurv_0.1-5 tzdb_0.3.0
## [73] tidyr_1.3.0 data.table_1.14.8
## [75] hms_1.1.3 car_3.1-2
## [77] xml2_1.3.3 utf8_1.2.3
## [79] XVector_0.40.0 markdown_1.6
## [81] pillar_1.9.0 stringr_1.5.0
## [83] vroom_1.6.1 RCircos_1.2.2
## [85] later_1.3.0 splines_4.3.0
## [87] ggtext_0.1.2 BiocFileCache_2.8.0
## [89] lattice_0.21-8 rtracklayer_1.60.0
## [91] bit_4.0.5 tidyselect_1.2.0
## [93] Biostrings_2.68.0 miniUI_0.1.1.1
## [95] knitr_1.42 gridExtra_2.3
## [97] bookdown_0.33 futile.logger_1.4.3
## [99] xfun_0.39 DT_0.27
## [101] stringi_1.7.12 yaml_2.3.7
## [103] evaluate_0.20 codetools_0.2-19
## [105] archive_1.1.5 tibble_3.2.1
## [107] BiocManager_1.30.20 cli_3.6.1
## [109] xtable_1.8-4 munsell_0.5.0
## [111] jquerylib_0.1.4 survMisc_0.5.6
## [113] Rcpp_1.0.10 GenomicDataCommons_1.24.0
## [115] dbplyr_2.3.2 png_0.1-8
## [117] XML_3.99-0.14 rapiclient_0.1.3
## [119] parallel_4.3.0 TCGAutils_1.20.0
## [121] ellipsis_0.3.2 readr_2.1.4
## [123] blob_1.2.4 prettyunits_1.1.1
## [125] bitops_1.0-7 scales_1.2.1
## [127] purrr_1.0.1 crayon_1.5.2
## [129] rlang_1.1.0 KEGGREST_1.40.0
## [131] rvest_1.0.3 formatR_1.14