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] 4
lengths(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
## 1
There 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']]
## NULL
We 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 letโs 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] 42
lengths(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'
## 1
We 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 4.2.0 (2022-04-22)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.4 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.15-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.15-bioc/R/lib/libRlapack.so
##
## 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
##
## attached base packages:
## [1] stats4 stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] survminer_0.4.9 ggpubr_0.4.0
## [3] ggplot2_3.3.6 survival_3.3-1
## [5] cBioPortalData_2.8.2 MultiAssayExperiment_1.22.0
## [7] SummarizedExperiment_1.26.1 Biobase_2.56.0
## [9] GenomicRanges_1.48.0 GenomeInfoDb_1.32.2
## [11] IRanges_2.30.0 S4Vectors_0.34.0
## [13] BiocGenerics_0.42.0 MatrixGenerics_1.8.0
## [15] matrixStats_0.62.0 AnVIL_1.8.2
## [17] dplyr_1.0.9 BiocStyle_2.24.0
##
## loaded via a namespace (and not attached):
## [1] backports_1.4.1 BiocFileCache_2.4.0
## [3] RCircos_1.2.2 splines_4.2.0
## [5] BiocParallel_1.30.3 TCGAutils_1.16.0
## [7] digest_0.6.29 htmltools_0.5.2
## [9] magick_2.7.3 fansi_1.0.3
## [11] magrittr_2.0.3 memoise_2.0.1
## [13] tzdb_0.3.0 limma_3.52.1
## [15] Biostrings_2.64.0 readr_2.1.2
## [17] vroom_1.5.7 prettyunits_1.1.1
## [19] colorspace_2.0-3 blob_1.2.3
## [21] rvest_1.0.2 rappdirs_0.3.3
## [23] xfun_0.31 crayon_1.5.1
## [25] RCurl_1.98-1.7 jsonlite_1.8.0
## [27] RaggedExperiment_1.20.0 zoo_1.8-10
## [29] glue_1.6.2 GenomicDataCommons_1.20.1
## [31] gtable_0.3.0 zlibbioc_1.42.0
## [33] XVector_0.36.0 DelayedArray_0.22.0
## [35] car_3.1-0 abind_1.4-5
## [37] scales_1.2.0 futile.options_1.0.1
## [39] DBI_1.1.2 rstatix_0.7.0
## [41] Rcpp_1.0.8.3 xtable_1.8-4
## [43] progress_1.2.2 gridtext_0.1.4
## [45] bit_4.0.4 km.ci_0.5-6
## [47] httr_1.4.3 ellipsis_0.3.2
## [49] pkgconfig_2.0.3 XML_3.99-0.10
## [51] rapiclient_0.1.3 farver_2.1.0
## [53] sass_0.4.1 dbplyr_2.2.0
## [55] utf8_1.2.2 RJSONIO_1.3-1.6
## [57] tidyselect_1.1.2 labeling_0.4.2
## [59] rlang_1.0.2 AnnotationDbi_1.58.0
## [61] munsell_0.5.0 tools_4.2.0
## [63] cachem_1.0.6 cli_3.3.0
## [65] generics_0.1.2 RSQLite_2.2.14
## [67] broom_0.8.0 evaluate_0.15
## [69] stringr_1.4.0 fastmap_1.1.0
## [71] yaml_2.3.5 knitr_1.39
## [73] bit64_4.0.5 survMisc_0.5.6
## [75] purrr_0.3.4 KEGGREST_1.36.2
## [77] formatR_1.12 xml2_1.3.3
## [79] biomaRt_2.52.0 compiler_4.2.0
## [81] filelock_1.0.2 curl_4.3.2
## [83] png_0.1-7 ggsignif_0.6.3
## [85] tibble_3.1.7 bslib_0.3.1
## [87] stringi_1.7.6 highr_0.9
## [89] futile.logger_1.4.3 GenomicFeatures_1.48.3
## [91] lattice_0.20-45 Matrix_1.4-1
## [93] markdown_1.1 KMsurv_0.1-5
## [95] RTCGAToolbox_2.26.0 vctrs_0.4.1
## [97] pillar_1.7.0 lifecycle_1.0.1
## [99] BiocManager_1.30.18 jquerylib_0.1.4
## [101] data.table_1.14.2 bitops_1.0-7
## [103] rtracklayer_1.56.0 R6_2.5.1
## [105] BiocIO_1.6.0 bookdown_0.27
## [107] gridExtra_2.3 codetools_0.2-18
## [109] lambda.r_1.2.4 assertthat_0.2.1
## [111] rjson_0.2.21 withr_2.5.0
## [113] GenomicAlignments_1.32.0 Rsamtools_2.12.0
## [115] GenomeInfoDbData_1.2.8 parallel_4.2.0
## [117] hms_1.1.1 ggtext_0.1.1
## [119] grid_4.2.0 tidyr_1.2.0
## [121] rmarkdown_2.14 carData_3.0-5
## [123] restfulr_0.0.15