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", "err_api_info.rda", package = "cBioPortalData", mustWork = TRUE
)
load(api_errs)
err_api_info## $`Inconsistent build numbers found`
## [1] "past_dkfz_heidelberg_2013" "mbl_sickkids_2016"
## [3] "mrt_bcgsc_2016" "acyc_jhu_2016"
## [5] "mpnst_mskcc" "gct_msk_2016"
## [7] "chol_msk_2018" "hcc_mskimpact_2018"
## [9] "hnc_mskcc_2016" "es_dfarber_broad_2014"
## [11] "pptc_2019" "stad_tcga_pub"
## [13] "prad_eururol_2017" "nhl_bcgsc_2011"
## [15] "nhl_bcgsc_2013" "prad_mich"
## [17] "nsclc_tcga_broad_2016" "prad_broad_2013"
## [19] "prad_tcga_pan_can_atlas_2018" "thca_tcga_pan_can_atlas_2018"
## [21] "ucs_tcga_pan_can_atlas_2018" "uvm_tcga_pan_can_atlas_2018"
## [23] "stad_tcga_pan_can_atlas_2018" "prad_su2c_2019"
## [25] "thyroid_mskcc_2016" "prad_msk_2019"
## [27] "acyc_mda_2015" "acyc_mgh_2016"
## [29] "ccrcc_utokyo_2013" "blca_tcga_pub"
## [31] "laml_tcga_pub" "kirc_tcga_pub"
## [33] "hnsc_tcga_pub" "luad_oncosg_2020"
## [35] "luad_tcga_pub" "prad_su2c_2015"
## [37] "prad_tcga_pub" "blca_plasmacytoid_mskcc_2016"
## [39] "thca_tcga_pub" "prad_mskcc_2017"
## [41] "prad_p1000" "tet_nci_2014"
## [43] "acc_tcga_pan_can_atlas_2018" "chol_tcga_pan_can_atlas_2018"
## [45] "dlbc_tcga_pan_can_atlas_2018" "esca_tcga_pan_can_atlas_2018"
## [47] "hnsc_tcga_pan_can_atlas_2018" "kich_tcga_pan_can_atlas_2018"
## [49] "kirc_tcga_pan_can_atlas_2018" "egc_trap_msk_2020"
## [51] "prad_mcspc_mskcc_2020" "laml_tcga_pan_can_atlas_2018"
## [53] "lihc_tcga_pan_can_atlas_2018" "luad_tcga_pan_can_atlas_2018"
## [55] "meso_tcga_pan_can_atlas_2018" "ov_tcga_pan_can_atlas_2018"
## [57] "rbl_mskcc_2020"
##
## $`replacement has length zero`
## [1] "glioma_msk_2018"
##
## $`Frequency of NA values higher than the cutoff tolerance`
## [1] "sarc_tcga_pan_can_atlas_2018" "all_stjude_2015"
##
## $`Only two build types at a time can be used`
## [1] "sclc_jhu"
##
## $`Barcodes must start with 'TCGA'`
## [1] "blca_msk_tcga_2020"We can now inspect the contents of the data:
class(err_api_info)## [1] "list"length(err_api_info)## [1] 5lengths(err_api_info)## Inconsistent build numbers found
## 57
## replacement has length zero
## 1
## Frequency of NA values higher than the cutoff tolerance
## 2
## Only two build types at a time can be used
## 1
## Barcodes must start with 'TCGA'
## 1There were about 5 unique errors during the last build run.
names(err_api_info)## [1] "Inconsistent build numbers found"
## [2] "replacement has length zero"
## [3] "Frequency of NA values higher than the cutoff tolerance"
## [4] "Only two build types at a time can be used"
## [5] "Barcodes must start with 'TCGA'"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] "past_dkfz_heidelberg_2013" "mbl_sickkids_2016"
## [3] "mrt_bcgsc_2016" "acyc_jhu_2016"
## [5] "mpnst_mskcc" "gct_msk_2016"
## [7] "chol_msk_2018" "hcc_mskimpact_2018"
## [9] "hnc_mskcc_2016" "es_dfarber_broad_2014"
## [11] "pptc_2019" "stad_tcga_pub"
## [13] "prad_eururol_2017" "nhl_bcgsc_2011"
## [15] "nhl_bcgsc_2013" "prad_mich"
## [17] "nsclc_tcga_broad_2016" "prad_broad_2013"
## [19] "prad_tcga_pan_can_atlas_2018" "thca_tcga_pan_can_atlas_2018"
## [21] "ucs_tcga_pan_can_atlas_2018" "uvm_tcga_pan_can_atlas_2018"
## [23] "stad_tcga_pan_can_atlas_2018" "prad_su2c_2019"
## [25] "thyroid_mskcc_2016" "prad_msk_2019"
## [27] "acyc_mda_2015" "acyc_mgh_2016"
## [29] "ccrcc_utokyo_2013" "blca_tcga_pub"
## [31] "laml_tcga_pub" "kirc_tcga_pub"
## [33] "hnsc_tcga_pub" "luad_oncosg_2020"
## [35] "luad_tcga_pub" "prad_su2c_2015"
## [37] "prad_tcga_pub" "blca_plasmacytoid_mskcc_2016"
## [39] "thca_tcga_pub" "prad_mskcc_2017"
## [41] "prad_p1000" "tet_nci_2014"
## [43] "acc_tcga_pan_can_atlas_2018" "chol_tcga_pan_can_atlas_2018"
## [45] "dlbc_tcga_pan_can_atlas_2018" "esca_tcga_pan_can_atlas_2018"
## [47] "hnsc_tcga_pan_can_atlas_2018" "kich_tcga_pan_can_atlas_2018"
## [49] "kirc_tcga_pan_can_atlas_2018" "egc_trap_msk_2020"
## [51] "prad_mcspc_mskcc_2020" "laml_tcga_pan_can_atlas_2018"
## [53] "lihc_tcga_pan_can_atlas_2018" "luad_tcga_pan_can_atlas_2018"
## [55] "meso_tcga_pan_can_atlas_2018" "ov_tcga_pan_can_atlas_2018"
## [57] "rbl_mskcc_2020"We can also have a look at the entirety of the dataset.
err_api_info## $`Inconsistent build numbers found`
## [1] "past_dkfz_heidelberg_2013" "mbl_sickkids_2016"
## [3] "mrt_bcgsc_2016" "acyc_jhu_2016"
## [5] "mpnst_mskcc" "gct_msk_2016"
## [7] "chol_msk_2018" "hcc_mskimpact_2018"
## [9] "hnc_mskcc_2016" "es_dfarber_broad_2014"
## [11] "pptc_2019" "stad_tcga_pub"
## [13] "prad_eururol_2017" "nhl_bcgsc_2011"
## [15] "nhl_bcgsc_2013" "prad_mich"
## [17] "nsclc_tcga_broad_2016" "prad_broad_2013"
## [19] "prad_tcga_pan_can_atlas_2018" "thca_tcga_pan_can_atlas_2018"
## [21] "ucs_tcga_pan_can_atlas_2018" "uvm_tcga_pan_can_atlas_2018"
## [23] "stad_tcga_pan_can_atlas_2018" "prad_su2c_2019"
## [25] "thyroid_mskcc_2016" "prad_msk_2019"
## [27] "acyc_mda_2015" "acyc_mgh_2016"
## [29] "ccrcc_utokyo_2013" "blca_tcga_pub"
## [31] "laml_tcga_pub" "kirc_tcga_pub"
## [33] "hnsc_tcga_pub" "luad_oncosg_2020"
## [35] "luad_tcga_pub" "prad_su2c_2015"
## [37] "prad_tcga_pub" "blca_plasmacytoid_mskcc_2016"
## [39] "thca_tcga_pub" "prad_mskcc_2017"
## [41] "prad_p1000" "tet_nci_2014"
## [43] "acc_tcga_pan_can_atlas_2018" "chol_tcga_pan_can_atlas_2018"
## [45] "dlbc_tcga_pan_can_atlas_2018" "esca_tcga_pan_can_atlas_2018"
## [47] "hnsc_tcga_pan_can_atlas_2018" "kich_tcga_pan_can_atlas_2018"
## [49] "kirc_tcga_pan_can_atlas_2018" "egc_trap_msk_2020"
## [51] "prad_mcspc_mskcc_2020" "laml_tcga_pan_can_atlas_2018"
## [53] "lihc_tcga_pan_can_atlas_2018" "luad_tcga_pan_can_atlas_2018"
## [55] "meso_tcga_pan_can_atlas_2018" "ov_tcga_pan_can_atlas_2018"
## [57] "rbl_mskcc_2020"
##
## $`replacement has length zero`
## [1] "glioma_msk_2018"
##
## $`Frequency of NA values higher than the cutoff tolerance`
## [1] "sarc_tcga_pan_can_atlas_2018" "all_stjude_2015"
##
## $`Only two build types at a time can be used`
## [1] "sclc_jhu"
##
## $`Barcodes must start with 'TCGA'`
## [1] "blca_msk_tcga_2020"cBioDataPack()Now letโs look at the errors in the packaged datasets that are used for
cBioDataPack:
pack_errs <- system.file(
"extdata", "err_pack_info.rda", package = "cBioPortalData", mustWork = TRUE
)
load(pack_errs)
err_pack_info## $`cannnot find seqnames column`
## [1] "mel_tsam_liang_2017" "gbm_columbia_2019"
## [3] "glioma_msk_2018" "glioma_mskcc_2019"
## [5] "lgg_ucsf_2014" "nsclc_tcga_broad_2016"
## [7] "thyroid_mskcc_2016" "prad_cdk12_mskcc_2020"
## [9] "sclc_cancercell_gardner_2017" "brca_mbcproject_wagle_2017"
## [11] "prad_mpcproject_2018" "lung_msk_pdx"
## [13] "ntrk_msk_2019"
##
## $`attempt to extract less than one element`
## [1] "laml_tcga_pub" "blca_mskcc_solit_2012" "brca_tcga_pub2015"
## [4] "luad_tcga_pub" "ucec_tcga_pub"
##
## $`more columns than column names`
## [1] "acyc_fmi_2014"
##
## $`cannot coerce type 'closure' to vector of type 'character'`
## [1] "bcc_unige_2016" "brca_bccrc_xenograft_2014"
## [3] "lcll_broad_2013" "cllsll_icgc_2011"
## [5] "ctcl_columbia_2015" "dlbc_broad_2012"
## [7] "chol_jhu_2013" "hcc_msk_venturaa_2018"
## [9] "luad_tsp" "mcl_idibips_2013"
## [11] "mbl_broad_2012" "mds_mskcc_2020"
## [13] "mpn_cimr_2013" "nsclc_unito_2016"
## [15] "sarc_mskcc"
##
## $`'cancer_study_id', blca_msk_tcga_2020, not found. See 'data("studiesTable")'.`
## [1] "blca_msk_tcga_2020"
##
## $`'cancer_study_id', brca_smc_2018, not found. See 'data("studiesTable")'.`
## [1] "brca_smc_2018"
##
## $`'names.field' is not found in 'names(df)'`
## [1] "brca_tcga_pub"
##
## $`'cancer_study_id', msk_ch_2020, not found. See 'data("studiesTable")'.`
## [1] "msk_ch_2020"
##
## $`some values in the "start" column cannot be turned into numeric values`
## [1] "cesc_tcga"
##
## $`'cancer_study_id', gct_msk_2020, not found. See 'data("studiesTable")'.`
## [1] "gct_msk_2020"
##
## $`attempt to set too many names (16325) on IRanges object of length 13957`
## [1] "gbm_tcga_pub2013"
##
## $`'start.field' and 'end.field' suffixes do not match`
## [1] "ihch_smmu_2014"
##
## $`'cancer_study_id', brca_jup_msk_2020, not found. See 'data("studiesTable")'.`
## [1] "brca_jup_msk_2020"
##
## $`'cancer_study_id', luad_oncosg_2020, not found. See 'data("studiesTable")'.`
## [1] "luad_oncosg_2020"
##
## $`'cancer_study_id', lung_smc_2016, not found. See 'data("studiesTable")'.`
## [1] "lung_smc_2016"
##
## $`attempt to set too many names (73018) on IRanges object of length 73010`
## [1] "lusc_tcga_pub"
##
## $`non-character argument`
## [1] "mbn_mdacc_2013" "prad_fhcrc"
##
## $`'cancer_study_id', skcm_tcga_pub_2015, not found. See 'data("studiesTable")'.`
## [1] "skcm_tcga_pub_2015"
##
## $`'cancer_study_id', mel_dfci_2019, not found. See 'data("studiesTable")'.`
## [1] "mel_dfci_2019"
##
## $`replacement has 1 row, data has 0`
## [1] "prad_su2c_2015"
##
## $`'cancer_study_id', mixed_cfdna_msk_2020, not found. See 'data("studiesTable")'.`
## [1] "mixed_cfdna_msk_2020"
##
## $`some values in the "End_Position" column cannot be turned into numeric\n values`
## [1] "nsclc_tracerx_2017"
##
## $`attempt to set too many names (19420) on IRanges object of length 19419`
## [1] "ov_tcga_pub"
##
## $`attempt to set too many names (6736) on IRanges object of length 6734`
## [1] "thca_tcga_pub"
##
## $`NAs are not allowed in subscripted assignments`
## [1] "pediatric_dkfz_2017"
##
## $`'cancer_study_id', rbl_cfdna_msk_2020, not found. See 'data("studiesTable")'.`
## [1] "rbl_cfdna_msk_2020"
##
## $`some values in the "Start_Position" column cannot be turned into\n numeric values`
## [1] "sclc_ucologne_2015"
##
## $`invalid class "ExperimentList" object: \n Non-unique names provided`
## [1] "stad_tcga_pub"
##
## $`'cancer_study_id', angs_painter_2020, not found. See 'data("studiesTable")'.`
## [1] "angs_painter_2020"
##
## $`subscript contains out-of-bounds indices`
## [1] "angs_project_painter_2018"
##
## $`'cancer_study_id', utuc_igbmc_2021, not found. See 'data("studiesTable")'.`
## [1] "utuc_igbmc_2021"
##
## $`invalid [[ subscript type: NULL`
## [1] "um_qimr_2016"We can do the same for this data:
length(err_pack_info)## [1] 32lengths(err_pack_info)## cannnot find seqnames column
## 13
## attempt to extract less than one element
## 5
## more columns than column names
## 1
## cannot coerce type 'closure' to vector of type 'character'
## 15
## 'cancer_study_id', blca_msk_tcga_2020, not found. See 'data("studiesTable")'.
## 1
## 'cancer_study_id', brca_smc_2018, not found. See 'data("studiesTable")'.
## 1
## 'names.field' is not found in 'names(df)'
## 1
## 'cancer_study_id', msk_ch_2020, not found. See 'data("studiesTable")'.
## 1
## some values in the "start" column cannot be turned into numeric values
## 1
## 'cancer_study_id', gct_msk_2020, not found. See 'data("studiesTable")'.
## 1
## attempt to set too many names (16325) on IRanges object of length 13957
## 1
## 'start.field' and 'end.field' suffixes do not match
## 1
## 'cancer_study_id', brca_jup_msk_2020, not found. See 'data("studiesTable")'.
## 1
## 'cancer_study_id', luad_oncosg_2020, not found. See 'data("studiesTable")'.
## 1
## 'cancer_study_id', lung_smc_2016, not found. See 'data("studiesTable")'.
## 1
## attempt to set too many names (73018) on IRanges object of length 73010
## 1
## non-character argument
## 2
## 'cancer_study_id', skcm_tcga_pub_2015, not found. See 'data("studiesTable")'.
## 1
## 'cancer_study_id', mel_dfci_2019, not found. See 'data("studiesTable")'.
## 1
## replacement has 1 row, data has 0
## 1
## 'cancer_study_id', mixed_cfdna_msk_2020, not found. See 'data("studiesTable")'.
## 1
## some values in the "End_Position" column cannot be turned into numeric\n values
## 1
## attempt to set too many names (19420) on IRanges object of length 19419
## 1
## attempt to set too many names (6736) on IRanges object of length 6734
## 1
## NAs are not allowed in subscripted assignments
## 1
## 'cancer_study_id', rbl_cfdna_msk_2020, not found. See 'data("studiesTable")'.
## 1
## some values in the "Start_Position" column cannot be turned into\n numeric values
## 1
## invalid class "ExperimentList" object: \n Non-unique names provided
## 1
## 'cancer_study_id', angs_painter_2020, not found. See 'data("studiesTable")'.
## 1
## subscript contains out-of-bounds indices
## 1
## 'cancer_study_id', utuc_igbmc_2021, not found. See 'data("studiesTable")'.
## 1
## invalid [[ subscript type: NULL
## 1We can get a list of all the errors present:
names(err_pack_info)## [1] "cannnot find seqnames column"
## [2] "attempt to extract less than one element"
## [3] "more columns than column names"
## [4] "cannot coerce type 'closure' to vector of type 'character'"
## [5] "'cancer_study_id', blca_msk_tcga_2020, not found. See 'data(\"studiesTable\")'."
## [6] "'cancer_study_id', brca_smc_2018, not found. See 'data(\"studiesTable\")'."
## [7] "'names.field' is not found in 'names(df)'"
## [8] "'cancer_study_id', msk_ch_2020, not found. See 'data(\"studiesTable\")'."
## [9] "some values in the \"start\" column cannot be turned into numeric values"
## [10] "'cancer_study_id', gct_msk_2020, not found. See 'data(\"studiesTable\")'."
## [11] "attempt to set too many names (16325) on IRanges object of length 13957"
## [12] "'start.field' and 'end.field' suffixes do not match"
## [13] "'cancer_study_id', brca_jup_msk_2020, not found. See 'data(\"studiesTable\")'."
## [14] "'cancer_study_id', luad_oncosg_2020, not found. See 'data(\"studiesTable\")'."
## [15] "'cancer_study_id', lung_smc_2016, not found. See 'data(\"studiesTable\")'."
## [16] "attempt to set too many names (73018) on IRanges object of length 73010"
## [17] "non-character argument"
## [18] "'cancer_study_id', skcm_tcga_pub_2015, not found. See 'data(\"studiesTable\")'."
## [19] "'cancer_study_id', mel_dfci_2019, not found. See 'data(\"studiesTable\")'."
## [20] "replacement has 1 row, data has 0"
## [21] "'cancer_study_id', mixed_cfdna_msk_2020, not found. See 'data(\"studiesTable\")'."
## [22] "some values in the \"End_Position\" column cannot be turned into numeric\n values"
## [23] "attempt to set too many names (19420) on IRanges object of length 19419"
## [24] "attempt to set too many names (6736) on IRanges object of length 6734"
## [25] "NAs are not allowed in subscripted assignments"
## [26] "'cancer_study_id', rbl_cfdna_msk_2020, not found. See 'data(\"studiesTable\")'."
## [27] "some values in the \"Start_Position\" column cannot be turned into\n numeric values"
## [28] "invalid class \"ExperimentList\" object: \n Non-unique names provided"
## [29] "'cancer_study_id', angs_painter_2020, not found. See 'data(\"studiesTable\")'."
## [30] "subscript contains out-of-bounds indices"
## [31] "'cancer_study_id', utuc_igbmc_2021, not found. See 'data(\"studiesTable\")'."
## [32] "invalid [[ subscript type: NULL"And finally the full list of errors:
err_pack_info## $`cannnot find seqnames column`
## [1] "mel_tsam_liang_2017" "gbm_columbia_2019"
## [3] "glioma_msk_2018" "glioma_mskcc_2019"
## [5] "lgg_ucsf_2014" "nsclc_tcga_broad_2016"
## [7] "thyroid_mskcc_2016" "prad_cdk12_mskcc_2020"
## [9] "sclc_cancercell_gardner_2017" "brca_mbcproject_wagle_2017"
## [11] "prad_mpcproject_2018" "lung_msk_pdx"
## [13] "ntrk_msk_2019"
##
## $`attempt to extract less than one element`
## [1] "laml_tcga_pub" "blca_mskcc_solit_2012" "brca_tcga_pub2015"
## [4] "luad_tcga_pub" "ucec_tcga_pub"
##
## $`more columns than column names`
## [1] "acyc_fmi_2014"
##
## $`cannot coerce type 'closure' to vector of type 'character'`
## [1] "bcc_unige_2016" "brca_bccrc_xenograft_2014"
## [3] "lcll_broad_2013" "cllsll_icgc_2011"
## [5] "ctcl_columbia_2015" "dlbc_broad_2012"
## [7] "chol_jhu_2013" "hcc_msk_venturaa_2018"
## [9] "luad_tsp" "mcl_idibips_2013"
## [11] "mbl_broad_2012" "mds_mskcc_2020"
## [13] "mpn_cimr_2013" "nsclc_unito_2016"
## [15] "sarc_mskcc"
##
## $`'cancer_study_id', blca_msk_tcga_2020, not found. See 'data("studiesTable")'.`
## [1] "blca_msk_tcga_2020"
##
## $`'cancer_study_id', brca_smc_2018, not found. See 'data("studiesTable")'.`
## [1] "brca_smc_2018"
##
## $`'names.field' is not found in 'names(df)'`
## [1] "brca_tcga_pub"
##
## $`'cancer_study_id', msk_ch_2020, not found. See 'data("studiesTable")'.`
## [1] "msk_ch_2020"
##
## $`some values in the "start" column cannot be turned into numeric values`
## [1] "cesc_tcga"
##
## $`'cancer_study_id', gct_msk_2020, not found. See 'data("studiesTable")'.`
## [1] "gct_msk_2020"
##
## $`attempt to set too many names (16325) on IRanges object of length 13957`
## [1] "gbm_tcga_pub2013"
##
## $`'start.field' and 'end.field' suffixes do not match`
## [1] "ihch_smmu_2014"
##
## $`'cancer_study_id', brca_jup_msk_2020, not found. See 'data("studiesTable")'.`
## [1] "brca_jup_msk_2020"
##
## $`'cancer_study_id', luad_oncosg_2020, not found. See 'data("studiesTable")'.`
## [1] "luad_oncosg_2020"
##
## $`'cancer_study_id', lung_smc_2016, not found. See 'data("studiesTable")'.`
## [1] "lung_smc_2016"
##
## $`attempt to set too many names (73018) on IRanges object of length 73010`
## [1] "lusc_tcga_pub"
##
## $`non-character argument`
## [1] "mbn_mdacc_2013" "prad_fhcrc"
##
## $`'cancer_study_id', skcm_tcga_pub_2015, not found. See 'data("studiesTable")'.`
## [1] "skcm_tcga_pub_2015"
##
## $`'cancer_study_id', mel_dfci_2019, not found. See 'data("studiesTable")'.`
## [1] "mel_dfci_2019"
##
## $`replacement has 1 row, data has 0`
## [1] "prad_su2c_2015"
##
## $`'cancer_study_id', mixed_cfdna_msk_2020, not found. See 'data("studiesTable")'.`
## [1] "mixed_cfdna_msk_2020"
##
## $`some values in the "End_Position" column cannot be turned into numeric\n values`
## [1] "nsclc_tracerx_2017"
##
## $`attempt to set too many names (19420) on IRanges object of length 19419`
## [1] "ov_tcga_pub"
##
## $`attempt to set too many names (6736) on IRanges object of length 6734`
## [1] "thca_tcga_pub"
##
## $`NAs are not allowed in subscripted assignments`
## [1] "pediatric_dkfz_2017"
##
## $`'cancer_study_id', rbl_cfdna_msk_2020, not found. See 'data("studiesTable")'.`
## [1] "rbl_cfdna_msk_2020"
##
## $`some values in the "Start_Position" column cannot be turned into\n numeric values`
## [1] "sclc_ucologne_2015"
##
## $`invalid class "ExperimentList" object: \n Non-unique names provided`
## [1] "stad_tcga_pub"
##
## $`'cancer_study_id', angs_painter_2020, not found. See 'data("studiesTable")'.`
## [1] "angs_painter_2020"
##
## $`subscript contains out-of-bounds indices`
## [1] "angs_project_painter_2018"
##
## $`'cancer_study_id', utuc_igbmc_2021, not found. See 'data("studiesTable")'.`
## [1] "utuc_igbmc_2021"
##
## $`invalid [[ subscript type: NULL`
## [1] "um_qimr_2016"sessionInfo()## R version 4.1.1 (2021-08-10)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.3 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.13-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.13-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] parallel stats4 stats graphics grDevices utils datasets
## [8] methods base
##
## other attached packages:
## [1] survminer_0.4.9 ggpubr_0.4.0
## [3] ggplot2_3.3.5 survival_3.2-13
## [5] cBioPortalData_2.4.10 MultiAssayExperiment_1.18.0
## [7] SummarizedExperiment_1.22.0 Biobase_2.52.0
## [9] GenomicRanges_1.44.0 GenomeInfoDb_1.28.4
## [11] IRanges_2.26.0 S4Vectors_0.30.2
## [13] BiocGenerics_0.38.0 MatrixGenerics_1.4.3
## [15] matrixStats_0.61.0 AnVIL_1.4.1
## [17] dplyr_1.0.7 BiocStyle_2.20.2
##
## loaded via a namespace (and not attached):
## [1] readxl_1.3.1 backports_1.2.1
## [3] BiocFileCache_2.0.0 RCircos_1.2.1
## [5] splines_4.1.1 BiocParallel_1.26.2
## [7] TCGAutils_1.12.0 digest_0.6.28
## [9] htmltools_0.5.2 magick_2.7.3
## [11] fansi_0.5.0 magrittr_2.0.1
## [13] memoise_2.0.0 tzdb_0.1.2
## [15] openxlsx_4.2.4 limma_3.48.3
## [17] Biostrings_2.60.2 readr_2.0.2
## [19] vroom_1.5.5 prettyunits_1.1.1
## [21] colorspace_2.0-2 blob_1.2.2
## [23] rvest_1.0.1 rappdirs_0.3.3
## [25] haven_2.4.3 xfun_0.26
## [27] crayon_1.4.1 RCurl_1.98-1.5
## [29] jsonlite_1.7.2 RaggedExperiment_1.16.0
## [31] zoo_1.8-9 glue_1.4.2
## [33] GenomicDataCommons_1.16.0 gtable_0.3.0
## [35] zlibbioc_1.38.0 XVector_0.32.0
## [37] DelayedArray_0.18.0 car_3.0-11
## [39] abind_1.4-5 scales_1.1.1
## [41] futile.options_1.0.1 DBI_1.1.1
## [43] rstatix_0.7.0 Rcpp_1.0.7
## [45] gridtext_0.1.4 xtable_1.8-4
## [47] progress_1.2.2 foreign_0.8-81
## [49] bit_4.0.4 km.ci_0.5-2
## [51] httr_1.4.2 ellipsis_0.3.2
## [53] farver_2.1.0 pkgconfig_2.0.3
## [55] XML_3.99-0.8 rapiclient_0.1.3
## [57] sass_0.4.0 dbplyr_2.1.1
## [59] utf8_1.2.2 RJSONIO_1.3-1.6
## [61] labeling_0.4.2 tidyselect_1.1.1
## [63] rlang_0.4.11 AnnotationDbi_1.54.1
## [65] munsell_0.5.0 cellranger_1.1.0
## [67] tools_4.1.1 cachem_1.0.6
## [69] cli_3.0.1 generics_0.1.0
## [71] RSQLite_2.2.8 broom_0.7.9
## [73] evaluate_0.14 stringr_1.4.0
## [75] fastmap_1.1.0 yaml_2.2.1
## [77] knitr_1.36 bit64_4.0.5
## [79] zip_2.2.0 survMisc_0.5.5
## [81] purrr_0.3.4 KEGGREST_1.32.0
## [83] formatR_1.11 xml2_1.3.2
## [85] biomaRt_2.48.3 compiler_4.1.1
## [87] filelock_1.0.2 curl_4.3.2
## [89] png_0.1-7 ggsignif_0.6.3
## [91] tibble_3.1.5 bslib_0.3.1
## [93] stringi_1.7.5 highr_0.9
## [95] futile.logger_1.4.3 GenomicFeatures_1.44.2
## [97] forcats_0.5.1 lattice_0.20-45
## [99] Matrix_1.3-4 markdown_1.1
## [101] KMsurv_0.1-5 RTCGAToolbox_2.22.1
## [103] vctrs_0.3.8 pillar_1.6.3
## [105] lifecycle_1.0.1 BiocManager_1.30.16
## [107] jquerylib_0.1.4 data.table_1.14.2
## [109] bitops_1.0-7 rtracklayer_1.52.1
## [111] R6_2.5.1 BiocIO_1.2.0
## [113] bookdown_0.24 gridExtra_2.3
## [115] rio_0.5.27 codetools_0.2-18
## [117] lambda.r_1.2.4 assertthat_0.2.1
## [119] rjson_0.2.20 withr_2.4.2
## [121] GenomicAlignments_1.28.0 Rsamtools_2.8.0
## [123] GenomeInfoDbData_1.2.6 ggtext_0.1.1
## [125] hms_1.1.1 grid_4.1.1
## [127] tidyr_1.1.4 rmarkdown_2.11
## [129] carData_3.0-4 restfulr_0.0.13