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] 5
lengths(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'
## 1
There 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] 32
lengths(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
## 1
We 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