R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(cBioPortalData)
Loading required package: AnVIL
Loading required package: dplyr

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Loading required package: AnVILBase
Loading required package: MultiAssayExperiment
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'matrixStats'

The following object is masked from 'package:dplyr':

    count


Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following object is masked from 'package:dplyr':

    explain

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following object is masked from 'package:dplyr':

    combine

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:dplyr':

    first, rename

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

The following objects are masked from 'package:dplyr':

    collapse, desc, slice

Loading required package: Seqinfo
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

> 
> test_check("cBioPortalData")
Error in read.table(file = file, header = header, sep = sep, quote = quote,  : 
  more columns than column names
trying URL 'https://datahub.assets.cbioportal.org/brca_msk_2025.tar.gz'
Error in download.file(url = url, destfile = destfile) : 
  cannot open URL 'https://datahub.assets.cbioportal.org/brca_msk_2025.tar.gz'
trying URL 'https://datahub.assets.cbioportal.org/gist_msk_2025.tar.gz'
Error in download.file(url = url, destfile = destfile) : 
  cannot open URL 'https://datahub.assets.cbioportal.org/gist_msk_2025.tar.gz'
trying URL 'https://datahub.assets.cbioportal.org/cllsll_msk_2026.tar.gz'
Error in download.file(url = url, destfile = destfile) : 
  cannot open URL 'https://datahub.assets.cbioportal.org/cllsll_msk_2026.tar.gz'
trying URL 'https://datahub.assets.cbioportal.org/lms_msk_2024.tar.gz'
Error in download.file(url = url, destfile = destfile) : 
  cannot open URL 'https://datahub.assets.cbioportal.org/lms_msk_2024.tar.gz'
trying URL 'https://datahub.assets.cbioportal.org/ccrcc_sjuh_2023.tar.gz'
Error in download.file(url = url, destfile = destfile) : 
  cannot open URL 'https://datahub.assets.cbioportal.org/ccrcc_sjuh_2023.tar.gz'
Error in TCGAutils::uniformBuilds(x[[ncbi]]) : 
  Frequency of NA values higher than the cutoff tolerance
trying URL 'https://datahub.assets.cbioportal.org/pancan_pdmr_2025.tar.gz'
Error in download.file(url = url, destfile = destfile) : 
  cannot open URL 'https://datahub.assets.cbioportal.org/pancan_pdmr_2025.tar.gz'
Error in strsplit(hugos, "|", TRUE) : non-character argument
trying URL 'https://datahub.assets.cbioportal.org/soft_tissue_myod1_msk_2025.tar.gz'
Error in download.file(url = url, destfile = destfile) : 
  cannot open URL 'https://datahub.assets.cbioportal.org/soft_tissue_myod1_msk_2025.tar.gz'
trying URL 'https://datahub.assets.cbioportal.org/prad_msk_2025.tar.gz'
Error in download.file(url = url, destfile = destfile) : 
  cannot open URL 'https://datahub.assets.cbioportal.org/prad_msk_2025.tar.gz'
Error in validObject(.Object) : invalid class "ExperimentList" object: 
    ExperimentList elements must be named
Error in read.table(file = file, header = header, sep = sep, quote = quote,  : 
  more columns than column names
Error in read.table(file = file, header = header, sep = sep, quote = quote,  : 
  more columns than column names
Error in read.table(file = file, header = header, sep = sep, quote = quote,  : 
  more columns than column names
Error in validObject(.Object) : invalid class "ExperimentList" object: 
    ExperimentList elements must be named
trying URL 'https://datahub.assets.cbioportal.org/ovarian_msk_2025.tar.gz'
Error in download.file(url = url, destfile = destfile) : 
  cannot open URL 'https://datahub.assets.cbioportal.org/ovarian_msk_2025.tar.gz'
Error in TCGAutils::uniformBuilds(x[[ncbi]]) : 
  Frequency of NA values higher than the cutoff tolerance
Error in read.table(file = file, header = header, sep = sep, quote = quote,  : 
  more columns than column names
trying URL 'https://datahub.assets.cbioportal.org/brca_aurora_2023.tar.gz'
Error in download.file(url = url, destfile = destfile) : 
  cannot open URL 'https://datahub.assets.cbioportal.org/brca_aurora_2023.tar.gz'
Error in strsplit(hugos, "|", TRUE) : non-character argument
Error in read.table(file = file, header = header, sep = sep, quote = quote,  : 
  more columns than column names
Error in read.table(file = file, header = header, sep = sep, quote = quote,  : 
  more columns than column names
trying URL 'https://datahub.assets.cbioportal.org/breast_msk_cfdna_2026.tar.gz'
Error in download.file(url = url, destfile = destfile) : 
  cannot open URL 'https://datahub.assets.cbioportal.org/breast_msk_cfdna_2026.tar.gz'
trying URL 'https://datahub.assets.cbioportal.org/prad_idhmut_msk_2025.tar.gz'
Error in download.file(url = url, destfile = destfile) : 
  cannot open URL 'https://datahub.assets.cbioportal.org/prad_idhmut_msk_2025.tar.gz'
trying URL 'https://datahub.assets.cbioportal.org/hdcn_msk_2025.tar.gz'
Error in download.file(url = url, destfile = destfile) : 
  cannot open URL 'https://datahub.assets.cbioportal.org/hdcn_msk_2025.tar.gz'
aml_target_gdc/data_mrna_seq_fpkm.txt: Write failed
aml_target_gdc/data_gene_panel_matrix.txt: Write to restore size failed
aml_target_gdc/data_mrna_seq_fpkm_zscores_ref_all_samples.txt: Write to restore size failed
aml_target_gdc/data_mrna_seq_read_counts.txt: Write to restore size failed
aml_target_gdc/data_mrna_seq_read_counts_zscores_ref_all_samples.txt: Write to restore size failed
aml_target_gdc/data_mrna_seq_tpm.txt: Write to restore size failed
tar: Error exit delayed from previous errors.
Error in read.table(file = file, header = header, sep = sep, quote = quote,  : 
  more columns than column names
pancan_pcawg_2020/data_mrna_seq_fpkm_zscores_ref_all_samples.txt: Write failed
pancan_pcawg_2020/data_mirna_zscores.txt: Write to restore size failed
pancan_pcawg_2020/data_mutational_signatures_contribution_ID.txt: Write to restore size failed
pancan_pcawg_2020/data_resource_sample.txt: Write to restore size failed
pancan_pcawg_2020/data_resource_definition.txt: Write to restore size failed
pancan_pcawg_2020/data_clinical_sample.txt: Write to restore size failed
pancan_pcawg_2020/meta_study.txt: Write to restore size failed
pancan_pcawg_2020/data_mutational_signatures_contribution_SBS.txt: Write to restore size failed
pancan_pcawg_2020/data_mutational_signatures_contribution_DBS.txt: Write to restore size failed
pancan_pcawg_2020/data_mutational_signatures_counts_ID.txt: Write to restore size failed
pancan_pcawg_2020/data_mutational_signatures_counts_SBS.txt: Write to restore size failed
pancan_pcawg_2020/data_mirna.txt: Write to restore size failed
pancan_pcawg_2020/data_mutations.txt: Write to restore size failed
pancan_pcawg_2020/data_timeline_status.txt: Write to restore size failed
pancan_pcawg_2020/data_gene_panel_matrix.txt: Write to restore size failed
tar: Error exit delayed from previous errors.
Error in validObject(.Object) : invalid class "ExperimentList" object: 
    ExperimentList elements must be named
Error in validObject(.Object) : invalid class "ExperimentList" object: 
    Non-unique names provided
trying URL 'https://datahub.assets.cbioportal.org/bladder_msk_2024.tar.gz'
Error in download.file(url = url, destfile = destfile) : 
  cannot open URL 'https://datahub.assets.cbioportal.org/bladder_msk_2024.tar.gz'
ccle_broad_2019/data_mutations.txt: Write failed
ccle_broad_2019/data_cna.txt: Write to restore size failed
ccle_broad_2019/data_drug_treatment_auc.txt: Write to restore size failed
ccle_broad_2019/data_gene_panel_matrix.txt: Write to restore size failed
ccle_broad_2019/data_clinical_patient.txt: Write to restore size failed
ccle_broad_2019/data_mrna_seq_rpkm_zscores_ref_diploid_samples.txt: Write to restore size failed
ccle_broad_2019/data_protein_quantification_zscores.txt: Write to restore size failed
ccle_broad_2019/data_protein_quantification.txt: Write to restore size failed
ccle_broad_2019/data_sv.txt: Write to restore size failed
ccle_broad_2019/data_drug_treatment_ic50.txt: Write to restore size failed
ccle_broad_2019/data_cna_hg19.seg: Write to restore size failed
tar: Error exit delayed from previous errors.
trying URL 'https://datahub.assets.cbioportal.org/aml_stjude_2024.tar.gz'
Error in download.file(url = url, destfile = destfile) : 
  cannot open URL 'https://datahub.assets.cbioportal.org/aml_stjude_2024.tar.gz'
trying URL 'https://datahub.assets.cbioportal.org/pancreas_ctdna_msk_2025.tar.gz'
Error in download.file(url = url, destfile = destfile) : 
  cannot open URL 'https://datahub.assets.cbioportal.org/pancreas_ctdna_msk_2025.tar.gz'
trying URL 'https://datahub.assets.cbioportal.org/uec_msk_2024.tar.gz'
Error in download.file(url = url, destfile = destfile) : 
  cannot open URL 'https://datahub.assets.cbioportal.org/uec_msk_2024.tar.gz'
Error in TCGAutils::uniformBuilds(x[[ncbi]]) : 
  Frequency of NA values higher than the cutoff tolerance
trying URL 'https://datahub.assets.cbioportal.org/soft_tissue_msk_2025.tar.gz'
Error in download.file(url = url, destfile = destfile) : 
  cannot open URL 'https://datahub.assets.cbioportal.org/soft_tissue_msk_2025.tar.gz'
Error in read.table(file = file, header = header, sep = sep, quote = quote,  : 
  more columns than column names
Error in read.table(file = file, header = header, sep = sep, quote = quote,  : 
  more columns than column names
trying URL 'https://datahub.assets.cbioportal.org/pancan_hcmi_2025.tar.gz'
Error in download.file(url = url, destfile = destfile) : 
  cannot open URL 'https://datahub.assets.cbioportal.org/pancan_hcmi_2025.tar.gz'
trying URL 'https://datahub.assets.cbioportal.org/blca_msk_2025.tar.gz'
Error in download.file(url = url, destfile = destfile) : 
  cannot open URL 'https://datahub.assets.cbioportal.org/blca_msk_2025.tar.gz'
Error in read.table(file = file, header = header, sep = sep, quote = quote,  : 
  more columns than column names
Error in TCGAutils::uniformBuilds(x[[ncbi]]) : 
  Frequency of NA values higher than the cutoff tolerance
Error in read.table(file = file, header = header, sep = sep, quote = quote,  : 
  more columns than column names
Error in TCGAutils::uniformBuilds(x[[ncbi]]) : 
  Frequency of NA values higher than the cutoff tolerance
Error in read.table(file = file, header = header, sep = sep, quote = quote,  : 
  more columns than column names
Error in read.table(file = file, header = header, sep = sep, quote = quote,  : 
  more columns than column names
brca_metabric/data_methylation_promoters_rrbs.txt: Write failed
brca_metabric/meta_study.txt: Write to restore size failed
brca_metabric/data_clinical_sample.txt: Write to restore size failed
brca_metabric/data_cna.txt: Write to restore size failed
tar: Error exit delayed from previous errors.
Error in file(con, "r") : invalid 'description' argument
trying URL 'https://datahub.assets.cbioportal.org/pancan_ped_mai_msk_2025.tar.gz'
Error in download.file(url = url, destfile = destfile) : 
  cannot open URL 'https://datahub.assets.cbioportal.org/pancan_ped_mai_msk_2025.tar.gz'
brca_tcga/data_methylation_hm450.txt: Write failed
brca_tcga/data_cna_hg19.seg: Can't create 'brca_tcga/data_cna_hg19.seg'
tar: Error exit delayed from previous errors.
brca_tcga_gdc/data_mrna_seq_read_counts.txt: Write failed
brca_tcga_gdc/data_mrna_seq_read_counts_zscores_ref_all_samples.txt: Write to restore size failed
brca_tcga_gdc/data_mrna_seq_tpm.txt: Write to restore size failed
tar: Error exit delayed from previous errors.
trying URL 'https://datahub.assets.cbioportal.org/rectal_radiation_msk_2024.tar.gz'
Error in download.file(url = url, destfile = destfile) : 
  cannot open URL 'https://datahub.assets.cbioportal.org/rectal_radiation_msk_2024.tar.gz'
trying URL 'https://datahub.assets.cbioportal.org/brca_tcga_pub.tar.gz'
Content type 'application/x-tar' length 128997503 bytes (123.0 MB)
==================================================
downloaded 123.0 MB

trying URL 'https://datahub.assets.cbioportal.org/coadread_tcga.tar.gz'
Content type 'application/x-tar' length 143712750 bytes (137.1 MB)
==================================================
downloaded 137.1 MB

trying URL 'https://datahub.assets.cbioportal.org/egc_msk_tp53_ccr_2022.tar.gz'
Content type 'application/x-tar' length 334106 bytes (326 KB)
==================================================
downloaded 326 KB

trying URL 'https://datahub.assets.cbioportal.org/gbm_tcga_gdc.tar.gz'
Content type 'application/x-tar' length 161346652 bytes (153.9 MB)
==================================================
downloaded 153.9 MB

trying URL 'https://datahub.assets.cbioportal.org/heme_msk_impact_2022.tar.gz'
Content type 'application/x-tar' length 1787665 bytes (1.7 MB)
==================================================
downloaded 1.7 MB

trying URL 'https://datahub.assets.cbioportal.org/thym_tcga.tar.gz'
Content type 'application/x-tar' length 39527816 bytes (37.7 MB)
==================================================
downloaded 37.7 MB

trying URL 'https://datahub.assets.cbioportal.org/difg_msk_2023.tar.gz'
Content type 'application/x-tar' length 151926 bytes (148 KB)
==================================================
downloaded 148 KB

trying URL 'https://datahub.assets.cbioportal.org/utuc_msk_2019.tar.gz'
Content type 'application/x-tar' length 240866 bytes (235 KB)
==================================================
downloaded 235 KB

trying URL 'https://datahub.assets.cbioportal.org/crc_hta8_htan_2024.tar.gz'
Content type 'application/x-tar' length 8540414 bytes (8.1 MB)
==================================================
downloaded 8.1 MB

trying URL 'https://datahub.assets.cbioportal.org/dlbc_broad_2012.tar.gz'
Content type 'application/x-tar' length 513841 bytes (501 KB)
==================================================
downloaded 501 KB

trying URL 'https://datahub.assets.cbioportal.org/gct_msk_2020.tar.gz'
Content type 'application/x-tar' length 51405 bytes (50 KB)
==================================================
downloaded 50 KB

trying URL 'https://datahub.assets.cbioportal.org/kirp_tcga_pan_can_atlas_2018.tar.gz'
Content type 'application/x-tar' length 127693093 bytes (121.8 MB)
==================================================
downloaded 121.8 MB

trying URL 'https://datahub.assets.cbioportal.org/lgggbm_tcga_pub.tar.gz'
Content type 'application/x-tar' length 29588494 bytes (28.2 MB)
==================================================
downloaded 28.2 MB

trying URL 'https://datahub.assets.cbioportal.org/luad_cas_2020.tar.gz'
Content type 'application/x-tar' length 7282624 bytes (6.9 MB)
==================================================
downloaded 6.9 MB

trying URL 'https://datahub.assets.cbioportal.org/asclc_msk_2024.tar.gz'
Content type 'application/x-tar' length 2652903 bytes (2.5 MB)
==================================================
downloaded 2.5 MB

trying URL 'https://datahub.assets.cbioportal.org/ptad_msk_2024.tar.gz'
Content type 'application/x-tar' length 140496 bytes (137 KB)
==================================================
downloaded 137 KB

trying URL 'https://datahub.assets.cbioportal.org/ctcl_columbia_2015.tar.gz'
Content type 'application/x-tar' length 124249 bytes (121 KB)
==================================================
downloaded 121 KB

trying URL 'https://datahub.assets.cbioportal.org/crc_dd_2022.tar.gz'
Content type 'application/x-tar' length 137574 bytes (134 KB)
==================================================
downloaded 134 KB

trying URL 'https://datahub.assets.cbioportal.org/brca_tcga_pub2015.tar.gz'
Content type 'application/x-tar' length 254833483 bytes (243.0 MB)
==================================================
downloaded 243.0 MB

brca_tcga_pub2015/data_mrna_seq_v2_rsem_zscores_ref_diploid_samples.txt: Write failed
brca_tcga_pub2015/data_mutations.txt: Write to restore size failed
brca_tcga_pub2015/data_cna.txt: Write to restore size failed
brca_tcga_pub2015/data_mrna_seq_v2_rsem_zscores_ref_all_samples.txt: Write to restore size failed
brca_tcga_pub2015/data_rppa_zscores.txt: Write to restore size failed
brca_tcga_pub2015/data_mrna_seq_v2_rsem.txt: Write to restore size failed
brca_tcga_pub2015/data_rppa.txt: Write to restore size failed
brca_tcga_pub2015/data_clinical_patient.txt: Write to restore size failed
brca_tcga_pub2015/data_methylation_hm27.txt: Write to restore size failed
brca_tcga_pub2015/data_mrna_agilent_microarray.txt: Write to restore size failed
brca_tcga_pub2015/data_methylation_hm450.txt: Write to restore size failed
brca_tcga_pub2015/data_cna_hg19.seg: Write to restore size failed
tar: Error exit delayed from previous errors.
trying URL 'https://datahub.assets.cbioportal.org/gbm_columbia_2019.tar.gz'
Content type 'application/x-tar' length 52214 bytes (50 KB)
==================================================
downloaded 50 KB

trying URL 'https://datahub.assets.cbioportal.org/mbl_pcgp.tar.gz'
Content type 'application/x-tar' length 32784 bytes (32 KB)
==================================================
downloaded 32 KB

trying URL 'https://datahub.assets.cbioportal.org/sarcoma_msk_2026.tar.gz'
Error in download.file(url = url, destfile = destfile) : 
  cannot open URL 'https://datahub.assets.cbioportal.org/sarcoma_msk_2026.tar.gz'
trying URL 'https://datahub.assets.cbioportal.org/ucs_msk_2024.tar.gz'
Error in download.file(url = url, destfile = destfile) : 
  cannot open URL 'https://datahub.assets.cbioportal.org/ucs_msk_2024.tar.gz'
trying URL 'https://datahub.assets.cbioportal.org/aml_tcga_gdc.tar.gz'
Content type 'application/x-tar' length 68549821 bytes (65.4 MB)
==================================================
downloaded 65.4 MB

trying URL 'https://datahub.assets.cbioportal.org/tgct_tcga.tar.gz'
Content type 'application/x-tar' length 53005524 bytes (50.6 MB)
==================================================
downloaded 50.6 MB

trying URL 'https://datahub.assets.cbioportal.org/dlbcl_dfci_2018.tar.gz'
Content type 'application/x-tar' length 4606377 bytes (4.4 MB)
==================================================
downloaded 4.4 MB

trying URL 'https://datahub.assets.cbioportal.org/hcc_msk_venturaa_2018.tar.gz'
Content type 'application/x-tar' length 20098 bytes (19 KB)
==================================================
downloaded 19 KB

trying URL 'https://datahub.assets.cbioportal.org/pdac_msk_2024.tar.gz'
Content type 'application/x-tar' length 1936157 bytes (1.8 MB)
==================================================
downloaded 1.8 MB

trying URL 'https://datahub.assets.cbioportal.org/cervix_msk_2023.tar.gz'
Content type 'application/x-tar' length 203061 bytes (198 KB)
==================================================
downloaded 198 KB

trying URL 'https://datahub.assets.cbioportal.org/msk_met_2021.tar.gz'
Content type 'application/x-tar' length 34487450 bytes (32.9 MB)
==================================================
downloaded 32.9 MB

msk_met_2021/data_cna_hg19.seg: Write failed
msk_met_2021/data_gene_panel_matrix.txt: Write to restore size failed
msk_met_2021/data_sv.txt: Write to restore size failed
msk_met_2021/data_clinical_sample.txt: Write to restore size failed
msk_met_2021/data_timeline_sequencing.txt: Write to restore size failed
tar: Error exit delayed from previous errors.
Error in loadStudy(exdir, names.field, cleanup) : 
  Experiment data could not be mapped to colData
trying URL 'https://datahub.assets.cbioportal.org/laml_tcga_pub.tar.gz'
Content type 'application/x-tar' length 46025813 bytes (43.9 MB)
==================================================
downloaded 43.9 MB

laml_tcga_pub/data_mrna_seq_v2_rsem.txt: Write failed
laml_tcga_pub/data_cna_hg19.seg: Can't create 'laml_tcga_pub/data_cna_hg19.seg'
laml_tcga_pub/data_clinical_sample.txt: Write failed
laml_tcga_pub/data_mrna_seq_v2_rsem_zscores_ref_all_samples.txt: Can't create 'laml_tcga_pub/data_mrna_seq_v2_rsem_zscores_ref_all_samples.txt'
tar: Error exit delayed from previous errors.
Error in cbioportal2clinicaldf(clinicalfiles) : 
  object 'clindata' not found
trying URL 'https://datahub.assets.cbioportal.org/brca_broad.tar.gz'
Content type 'application/x-tar' length 1210508 bytes (1.2 MB)
==================================================
downloaded 1.2 MB

trying URL 'https://datahub.assets.cbioportal.org/esca_broad.tar.gz'
Content type 'application/x-tar' length 8200490 bytes (7.8 MB)
==================================================
downloaded 7.8 MB

trying URL 'https://datahub.assets.cbioportal.org/hcc_meric_2021.tar.gz'
Content type 'application/x-tar' length 5704997 bytes (5.4 MB)
==================================================
downloaded 5.4 MB

trying URL 'https://datahub.assets.cbioportal.org/nbl_ucologne_2015.tar.gz'
Content type 'application/x-tar' length 50803 bytes (49 KB)
==================================================
downloaded 49 KB

trying URL 'https://datahub.assets.cbioportal.org/sarc_tcga.tar.gz'
Content type 'application/x-tar' length 72857686 bytes (69.5 MB)
==================================================
downloaded 69.5 MB

sarc_tcga/data_mutations.txt: Write failed
sarc_tcga/data_rppa.txt: Write to restore size failed
sarc_tcga/normals/data_methylation_hm450_normals.txt: Write to restore size failed
sarc_tcga/data_linear_cna.txt: Write to restore size failed
sarc_tcga/LICENSE: Write to restore size failed
sarc_tcga/data_mrna_seq_v2_rsem_zscores_ref_diploid_samples.txt: Write to restore size failed
sarc_tcga/data_clinical_patient.txt: Write to restore size failed
sarc_tcga/data_gistic_genes_amp.txt: Write to restore size failed
sarc_tcga/meta_study.txt: Write to restore size failed
sarc_tcga/data_methylation_hm450.txt: Write to restore size failed
sarc_tcga/data_mutsig.txt: Write to restore size failed
sarc_tcga/data_mrna_seq_v2_rsem.txt: Write to restore size failed
sarc_tcga/data_cna_hg19.seg: Write to restore size failed
sarc_tcga/data_clinical_sample.txt: Write to restore size failed
sarc_tcga/data_rppa_zscores.txt: Write to restore size failed
sarc_tcga/data_mrna_seq_v2_rsem_zscores_ref_all_samples.txt: Write to restore size failed
tar: Error exit delayed from previous errors.
Error in if (length(x) > 1 || grepl("\n", x)) { : 
  missing value where TRUE/FALSE needed
trying URL 'https://datahub.assets.cbioportal.org/brca_hta9_htan_2022.tar.gz'
Content type 'application/x-tar' length 134786 bytes (131 KB)
==================================================
downloaded 131 KB

trying URL 'https://datahub.assets.cbioportal.org/blca_bcan_hcrn_2022.tar.gz'
Content type 'application/x-tar' length 20165817 bytes (19.2 MB)
==================================================
downloaded 19.2 MB

blca_bcan_hcrn_2022/data_RNA_Seq_v2_mRNA_median_Zscores.txt: Write failed
blca_bcan_hcrn_2022/data_mutations.txt: Write to restore size failed
blca_bcan_hcrn_2022/data_clinical_patient.txt: Write to restore size failed
tar: Error exit delayed from previous errors.
trying URL 'https://datahub.assets.cbioportal.org/plmeso_nyu_2015.tar.gz'
Content type 'application/x-tar' length 31287 bytes (30 KB)
==================================================
downloaded 30 KB

trying URL 'https://datahub.assets.cbioportal.org/sft_sysucc_2023.tar.gz'
Content type 'application/x-tar' length 79925 bytes (78 KB)
==================================================
downloaded 78 KB

trying URL 'https://datahub.assets.cbioportal.org/panet_shanghai_2013.tar.gz'
Content type 'application/x-tar' length 7353 bytes
==================================================
downloaded 7353 bytes

trying URL 'https://datahub.assets.cbioportal.org/gbc_shanghai_2014.tar.gz'
Content type 'application/x-tar' length 1230379 bytes (1.2 MB)
==================================================
downloaded 1.2 MB

gbc_shanghai_2014/data_mutations.txt: Write failed
gbc_shanghai_2014/data_clinical_patient.txt: Can't create 'gbc_shanghai_2014/data_clinical_patient.txt'
tar: Error exit delayed from previous errors.
trying URL 'https://datahub.assets.cbioportal.org/mnm_washu_2016.tar.gz'
Content type 'application/x-tar' length 57553 bytes (56 KB)
==================================================
downloaded 56 KB

Error : unable to open database file
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/RtmpQ2fwda/file12b024c01131a.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/RtmpQ2fwda/file12b025a8d36f1.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/RtmpQ2fwda/file12b026d1236a8.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/RtmpQ2fwda/file12b0246c28789.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/RtmpQ2fwda/file12b02d5057aa.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/RtmpQ2fwda/file12b0215ab60ba.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/RtmpQ2fwda/file12b02265b5e73.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/RtmpQ2fwda/file12b023895e3b1.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/RtmpQ2fwda/file12b027897967c.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/RtmpQ2fwda/file12b022818e4be.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/RtmpQ2fwda/file12b027a518a82.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/RtmpQ2fwda/file12b027f5c9b8a.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/RtmpQ2fwda/file12b0218e7c259.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/RtmpQ2fwda/file12b0217886dd5.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/RtmpQ2fwda/file12b027de2c704.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/RtmpQ2fwda/file12b023378182d.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/RtmpQ2fwda/file12b02117b4cc1.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/RtmpQ2fwda/file12b0235ec1bde.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/RtmpQ2fwda/file12b022019a77a.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/RtmpQ2fwda/file12b0274424b0c.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/RtmpQ2fwda/file12b022c4d3c75.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/RtmpQ2fwda/file12b022bc3c0c.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/RtmpQ2fwda/file12b02140a393b.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/RtmpQ2fwda/file12b022b335ac4.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/RtmpQ2fwda/file12b02388c1004.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/RtmpQ2fwda/file12b02736f939c.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/RtmpQ2fwda/file12b02224421f9.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/RtmpQ2fwda/file12b0227127402.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/RtmpQ2fwda/file12b022c7e4358.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/RtmpQ2fwda/file12b0215775d3a.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/RtmpQ2fwda/file12b024f8995d8.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/RtmpQ2fwda/file12b0251ccc0b3.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/RtmpQ2fwda/file12b02597f51b9.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/RtmpQ2fwda/file12b0235ce7696.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/RtmpQ2fwda/file12b025cb8d73.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/RtmpQ2fwda/file12b0276b37bfd.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/RtmpQ2fwda/file12b021915bed.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/RtmpQ2fwda/file12b026e2a2568.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/RtmpQ2fwda/file12b0210fe0759.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/RtmpQ2fwda/file12b0215946cc6.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/RtmpQ2fwda/file12b024371463b.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/RtmpQ2fwda/file12b0241b9ee14.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/RtmpQ2fwda/file12b0215bd84c2.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/RtmpQ2fwda/file12b024d56e7b4.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/RtmpQ2fwda/file12b024860217.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/RtmpQ2fwda/file12b0279f33652.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/RtmpQ2fwda/file12b024e73800a.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/RtmpQ2fwda/file12b02db38c3.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/RtmpQ2fwda/file12b02386b8aa5.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/RtmpQ2fwda/file12b021c5b7393.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/RtmpQ2fwda/file12b023800c670.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/RtmpQ2fwda/file12b023ae3ffc9.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/RtmpQ2fwda/file12b024eae0353.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/RtmpQ2fwda/file12b0225c6680.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/RtmpQ2fwda/file12b024d5eb6.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/RtmpQ2fwda/file12b025784fee1.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/RtmpQ2fwda/file12b025c7992aa.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/RtmpQ2fwda/file12b02318c0654.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/RtmpQ2fwda/file12b025ff38e35.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/RtmpQ2fwda/file12b026efd6ac9.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/RtmpQ2fwda/file12b023f6deb0c.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/RtmpQ2fwda/file12b024962815c.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/RtmpQ2fwda/file12b02621ae4a7.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/RtmpQ2fwda/file12b025399c242.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/RtmpQ2fwda/file12b0213a0a5ef.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/RtmpQ2fwda/file12b0217edf7fa.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/RtmpQ2fwda/file12b028334a5c.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/RtmpQ2fwda/file12b025f56e238.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/RtmpQ2fwda/file12b02411dfb6e.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/RtmpQ2fwda/file12b0217661428.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/RtmpQ2fwda/file12b022eb55a18.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/RtmpQ2fwda/file12b0242df59d.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/RtmpQ2fwda/file12b026558188f.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/RtmpQ2fwda/file12b027ab48843.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/RtmpQ2fwda/file12b02625e25a4.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/RtmpQ2fwda/file12b0212f96470.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/RtmpQ2fwda/file12b023330fecb.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/RtmpQ2fwda/file12b0255a7dbae.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/RtmpQ2fwda/file12b027f47a870.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/RtmpQ2fwda/file12b0239839258.
Saving _problems/test_cBioDataPack-19.R
Saving _problems/test_cBioPortalData-3.R
[ FAIL 2 | WARN 306 | SKIP 0 | PASS 6 ]

Error in gzfile(file, mode) : cannot open the connection
Calls: test_check ... o_apply -> lapply -> FUN -> <Anonymous> -> saveRDS -> gzfile
In addition: Warning message:
In gzfile(file, mode) :
  cannot open compressed file 'testthat-problems.rds', probable reason 'No space left on device'
Execution halted

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no cBioPortalData_2.22.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc-longtests/meat/cBioPortalData.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘cBioPortalData/DESCRIPTION’ ... OK
* this is package ‘cBioPortalData’ version ‘2.22.3’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘cBioPortalData’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘longtests/testthat.R’ failed.
Last 13 lines of output:
    Failed to open file /tmp/RtmpQ2fwda/file12b0255a7dbae.
  Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
    Failed to open file /tmp/RtmpQ2fwda/file12b027f47a870.
  Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
    Failed to open file /tmp/RtmpQ2fwda/file12b0239839258.
  Saving _problems/test_cBioDataPack-19.R
  Saving _problems/test_cBioPortalData-3.R
  [ FAIL 2 | WARN 306 | SKIP 0 | PASS 6 ]
  
  Error in gzfile(file, mode) : cannot open the connection
  Calls: test_check ... o_apply -> lapply -> FUN -> <Anonymous> -> saveRDS -> gzfile
  In addition: Warning message:
  In gzfile(file, mode) :
    cannot open compressed file 'testthat-problems.rds', probable reason 'No space left on device'
  Execution halted
* DONE

Status: 1 ERROR
See
  ‘/Users/biocbuild/bbs-3.22-bioc-longtests/meat/cBioPortalData.Rcheck/00check.log’
for details.

* installing *source* package ‘cBioPortalData’ ...
** this is package ‘cBioPortalData’ version ‘2.22.3’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (cBioPortalData)