Back to Long Tests report for BioC 3.22

This page was generated on 2026-04-04 23:55 -0400 (Sat, 04 Apr 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4897
merida1macOS 12.7.6 Montereyx86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4691
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 10/31HostnameOS / ArchCHECK
cBioPortalData 2.22.3  (landing page)
Marcel Ramos
Snapshot Date: 2026-04-04 09:55 -0400 (Sat, 04 Apr 2026)
git_url: https://git.bioconductor.org/packages/cBioPortalData
git_branch: RELEASE_3_22
git_last_commit: 612b93e
git_last_commit_date: 2026-02-23 21:08:36 -0400 (Mon, 23 Feb 2026)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  ERROR  
merida1macOS 12.7.6 Monterey / x86_64  ERROR  

CHECK results for cBioPortalData on merida1

To the developers/maintainers of the cBioPortalData package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: cBioPortalData
Version: 2.22.3
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
StartedAt: 2026-04-04 16:01:13 -0400 (Sat, 04 Apr 2026)
EndedAt: 2026-04-04 19:10:06 -0400 (Sat, 04 Apr 2026)
EllapsedTime: 11332.2 seconds
RetCode: 1
Status:   ERROR  
CheckDir: cBioPortalData.Rcheck
Warnings: NA

Tests output

cBioPortalData.Rcheck/tests/testthat.Rout.fail


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/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
blca_tcga_gdc/data_mrna_seq_read_counts_zscores_ref_all_samples.txt: Write failed
blca_tcga_gdc/data_mrna_seq_tpm.txt: Can't create 'blca_tcga_gdc/data_mrna_seq_tpm.txt'
tar: Error exit delayed from previous errors.
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'
difg_glass/data_mutations.txt: Write failed
difg_glass/data_cna.txt: Can't create 'difg_glass/data_cna.txt'
difg_glass/data_mrna_seq_tpm_zscores_ref_all_samples.txt: Can't create 'difg_glass/data_mrna_seq_tpm_zscores_ref_all_samples.txt'
difg_glass/data_resource_definition.txt: Write failed
difg_glass/data_clinical_patient.txt: Can't create 'difg_glass/data_clinical_patient.txt'
difg_glass/data_cna_hg19.seg: Can't create 'difg_glass/data_cna_hg19.seg'
tar: Error exit delayed from previous errors.
Error in read.table(file = file, header = header, sep = sep, quote = quote,  : 
  empty beginning of file
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_tpm_zscores_ref_all_samples.txt: Write failed
aml_target_gdc/data_mrna_seq_fpkm.txt: Write to restore size 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_cna.txt: Write failed
pancan_pcawg_2020/data_mrna_seq_fpkm_zscores_ref_all_samples.txt: Can't create 'pancan_pcawg_2020/data_mrna_seq_fpkm_zscores_ref_all_samples.txt'
pancan_pcawg_2020/data_mirna_zscores.txt: Can't create 'pancan_pcawg_2020/data_mirna_zscores.txt'
pancan_pcawg_2020/data_mutational_signatures_contribution_ID.txt: Can't create 'pancan_pcawg_2020/data_mutational_signatures_contribution_ID.txt'
pancan_pcawg_2020/data_resource_sample.txt: Write failed
pancan_pcawg_2020/data_resource_definition.txt: Can't create 'pancan_pcawg_2020/data_resource_definition.txt'
pancan_pcawg_2020/data_clinical_sample.txt: Can't create 'pancan_pcawg_2020/data_clinical_sample.txt'
pancan_pcawg_2020/meta_study.txt: Can't create 'pancan_pcawg_2020/meta_study.txt'
pancan_pcawg_2020/data_mutational_signatures_contribution_SBS.txt: Can't create 'pancan_pcawg_2020/data_mutational_signatures_contribution_SBS.txt'
pancan_pcawg_2020/data_mutational_signatures_contribution_DBS.txt: Can't create 'pancan_pcawg_2020/data_mutational_signatures_contribution_DBS.txt'
pancan_pcawg_2020/data_mutational_signatures_counts_ID.txt: Can't create 'pancan_pcawg_2020/data_mutational_signatures_counts_ID.txt'
pancan_pcawg_2020/data_mutational_signatures_counts_SBS.txt: Can't create 'pancan_pcawg_2020/data_mutational_signatures_counts_SBS.txt'
pancan_pcawg_2020/data_mirna.txt: Can't create 'pancan_pcawg_2020/data_mirna.txt'
pancan_pcawg_2020/data_mutations.txt: Can't create 'pancan_pcawg_2020/data_mutations.txt'
pancan_pcawg_2020/data_timeline_status.txt: Write failed
pancan_pcawg_2020/data_gene_panel_matrix.txt: Can't create 'pancan_pcawg_2020/data_gene_panel_matrix.txt'
tar: Error exit delayed from previous errors.
Error in read.table(file = file, header = header, sep = sep, quote = quote,  : 
  empty beginning of file
Error in validObject(.Object) : invalid class "ExperimentList" object: 
    Non-unique names provided
ccrcc_tcga_gdc/data_mrna_seq_read_counts_zscores_ref_all_samples.txt: Write failed
ccrcc_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/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_mrna_seq_rpkm.txt: Write failed
ccle_broad_2019/data_mutations.txt: Can't create 'ccle_broad_2019/data_mutations.txt'
ccle_broad_2019/data_cna.txt: Can't create 'ccle_broad_2019/data_cna.txt'
ccle_broad_2019/data_drug_treatment_auc.txt: Can't create 'ccle_broad_2019/data_drug_treatment_auc.txt'
ccle_broad_2019/data_gene_panel_matrix.txt: Can't create 'ccle_broad_2019/data_gene_panel_matrix.txt'
ccle_broad_2019/data_clinical_patient.txt: Can't create 'ccle_broad_2019/data_clinical_patient.txt'
ccle_broad_2019/data_mrna_seq_rpkm_zscores_ref_diploid_samples.txt: Write failed
ccle_broad_2019/data_protein_quantification_zscores.txt: Can't create 'ccle_broad_2019/data_protein_quantification_zscores.txt'
ccle_broad_2019/data_protein_quantification.txt: Can't create 'ccle_broad_2019/data_protein_quantification.txt'
ccle_broad_2019/data_sv.txt: Can't create 'ccle_broad_2019/data_sv.txt'
ccle_broad_2019/data_drug_treatment_ic50.txt: Can't create 'ccle_broad_2019/data_drug_treatment_ic50.txt'
ccle_broad_2019/data_cna_hg19.seg: Can't create 'ccle_broad_2019/data_cna_hg19.seg'
tar: Error exit delayed from previous errors.
Error in read.table(file = file, header = header, sep = sep, quote = quote,  : 
  empty beginning of file
ov_tcga/data_methylation_hm27.txt: Write failed
ov_tcga/data_gistic_genes_amp.txt: Can't create 'ov_tcga/data_gistic_genes_amp.txt'
ov_tcga/data_protein_quantification.txt: Write failed
ov_tcga/meta_study.txt: Write to restore size failed
ov_tcga/data_mrna_seq_v2_rsem.txt: Can't create 'ov_tcga/data_mrna_seq_v2_rsem.txt'
ov_tcga/data_mrna_affymetrix_microarray_zscores_ref_all_samples.txt: Can't create 'ov_tcga/data_mrna_affymetrix_microarray_zscores_ref_all_samples.txt'
ov_tcga/data_cna_hg19.seg: Can't create 'ov_tcga/data_cna_hg19.seg'
ov_tcga/data_clinical_sample.txt: Can't create 'ov_tcga/data_clinical_sample.txt'
ov_tcga/data_rppa_zscores.txt: Can't create 'ov_tcga/data_rppa_zscores.txt'
ov_tcga/data_mrna_seq_v2_rsem_zscores_ref_all_samples.txt: Can't create 'ov_tcga/data_mrna_seq_v2_rsem_zscores_ref_all_samples.txt'
tar: Error exit delayed from previous errors.
Error in file(con, "r") : invalid 'description' argument
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'
thpa_tcga_gdc/data_cna.txt: Write failed
thpa_tcga_gdc/data_mrna_seq_tpm.txt: Write to restore size failed
tar: Error exit delayed from previous errors.
hnsc_tcga_gdc/data_mrna_seq_read_counts_zscores_ref_all_samples.txt: Write failed
hnsc_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/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
cellline_ccle_broad/data_cna_hg19.seg: Write failed
tar: Error exit delayed from previous errors.
difg_tcga_gdc/data_mrna_seq_read_counts_zscores_ref_all_samples.txt: Write failed
difg_tcga_gdc/data_mrna_seq_tpm.txt: Can't create 'difg_tcga_gdc/data_mrna_seq_tpm.txt'
tar: Error exit delayed from previous errors.
Error in TCGAutils::uniformBuilds(x[[ncbi]]) : 
  Frequency of NA values higher than the cutoff tolerance
bll_target_gdc/data_mrna_seq_read_counts_zscores_ref_all_samples.txt: Write failed
bll_target_gdc/data_mrna_seq_tpm.txt: Write to restore size failed
tar: Error exit delayed from previous errors.
coad_tcga_gdc/data_mrna_seq_fpkm.txt: Write failed
coad_tcga_gdc/data_gene_panel_matrix.txt: Can't create 'coad_tcga_gdc/data_gene_panel_matrix.txt'
coad_tcga_gdc/data_mrna_seq_fpkm_zscores_ref_all_samples.txt: Write failed
coad_tcga_gdc/data_mrna_seq_read_counts.txt: Can't create 'coad_tcga_gdc/data_mrna_seq_read_counts.txt'
coad_tcga_gdc/data_mrna_seq_read_counts_zscores_ref_all_samples.txt: Can't create 'coad_tcga_gdc/data_mrna_seq_read_counts_zscores_ref_all_samples.txt'
coad_tcga_gdc/data_mrna_seq_tpm.txt: Can't create 'coad_tcga_gdc/data_mrna_seq_tpm.txt'
tar: Error exit delayed from previous errors.
Error in read.table(file = file, header = header, sep = sep, quote = quote,  : 
  empty beginning of file
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
luad_tcga_gdc/data_mrna_seq_fpkm_zscores_ref_all_samples.txt: Write failed
luad_tcga_gdc/data_mrna_seq_read_counts.txt: Can't create 'luad_tcga_gdc/data_mrna_seq_read_counts.txt'
luad_tcga_gdc/data_mrna_seq_read_counts_zscores_ref_all_samples.txt: Can't create 'luad_tcga_gdc/data_mrna_seq_read_counts_zscores_ref_all_samples.txt'
luad_tcga_gdc/data_mrna_seq_tpm.txt: Can't create 'luad_tcga_gdc/data_mrna_seq_tpm.txt'
tar: Error exit delayed from previous errors.
Error in read.table(file = file, header = header, sep = sep, quote = quote,  : 
  more columns than column names
brca_metabric/data_mrna_illumina_microarray.txt: Write failed
brca_metabric/data_clinical_patient.txt: Write to restore size failed
brca_metabric/data_gene_panel_matrix.txt: Write to restore size failed
brca_metabric/data_methylation_promoters_rrbs.txt: Write to restore size 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'
nsclc_tcga_broad_2016/data_mutations.txt: Write failed
nsclc_tcga_broad_2016/data_timeline_treatment.txt: Can't create 'nsclc_tcga_broad_2016/data_timeline_treatment.txt'
nsclc_tcga_broad_2016/data_gene_panel_matrix.txt: Write failed
nsclc_tcga_broad_2016/LICENSE: Can't create 'nsclc_tcga_broad_2016/LICENSE'
nsclc_tcga_broad_2016/data_clinical_patient.txt: Write failed
nsclc_tcga_broad_2016/meta_study.txt: Can't create 'nsclc_tcga_broad_2016/meta_study.txt'
nsclc_tcga_broad_2016/data_cna_hg19.seg: Can't create 'nsclc_tcga_broad_2016/data_cna_hg19.seg'
nsclc_tcga_broad_2016/data_clinical_sample.txt: Can't create 'nsclc_tcga_broad_2016/data_clinical_sample.txt'
tar: Error exit delayed from previous errors.
Error in `colnames<-`(`*tmp*`, value = c("column", "definition")) : 
  attempt to set 'colnames' on an object with less than two dimensions
brca_tcga/data_mrna_seq_v2_rsem_zscores_ref_all_samples.txt: Write failed
brca_tcga/data_rppa_zscores.txt: Can't create 'brca_tcga/data_rppa_zscores.txt'
brca_tcga/data_mrna_seq_v2_rsem.txt: Can't create 'brca_tcga/data_mrna_seq_v2_rsem.txt'
brca_tcga/data_rppa.txt: Can't create 'brca_tcga/data_rppa.txt'
brca_tcga/data_clinical_patient.txt: Can't create 'brca_tcga/data_clinical_patient.txt'
brca_tcga/data_protein_quantification_zscores.txt: Can't create 'brca_tcga/data_protein_quantification_zscores.txt'
brca_tcga/data_mrna_agilent_microarray.txt: Can't create 'brca_tcga/data_mrna_agilent_microarray.txt'
brca_tcga/data_protein_quantification.txt: Can't create 'brca_tcga/data_protein_quantification.txt'
brca_tcga/data_methylation_hm450.txt: Can't create 'brca_tcga/data_methylation_hm450.txt'
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_fpkm.txt: Write failed
brca_tcga_gdc/data_gene_panel_matrix.txt: Write to restore size failed
brca_tcga_gdc/data_mrna_seq_fpkm_zscores_ref_all_samples.txt: Write to restore size failed
brca_tcga_gdc/data_mrna_seq_read_counts.txt: Write to restore size 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/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'
brca_tcga_pub2015/data_mrna_seq_v2_rsem.txt: Write 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/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/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'
stad_tcga_gdc/data_mrna_seq_read_counts_zscores_ref_all_samples.txt: Write failed
stad_tcga_gdc/data_mrna_seq_fpkm_zscores_ref_all_samples.txt: Can't create 'stad_tcga_gdc/data_mrna_seq_fpkm_zscores_ref_all_samples.txt'
stad_tcga_gdc/data_cna.txt: Can't create 'stad_tcga_gdc/data_cna.txt'
stad_tcga_gdc/data_mrna_seq_tpm.txt: Can't create 'stad_tcga_gdc/data_mrna_seq_tpm.txt'
tar: Error exit delayed from previous errors.
trying URL 'https://datahub.assets.cbioportal.org/ucec_msk_dacruzpaula_2025.tar.gz'
Error in download.file(url = url, destfile = destfile) : 
  cannot open URL 'https://datahub.assets.cbioportal.org/ucec_msk_dacruzpaula_2025.tar.gz'
trying URL 'https://datahub.assets.cbioportal.org/brca_tcga_pan_can_atlas_2018.tar.gz'
Content type 'application/x-tar' length 491659217 bytes (468.9 MB)
==================================================
downloaded 468.9 MB

brca_tcga_pan_can_atlas_2018/data_methylation_hm27_hm450_merged.txt: Write failed
brca_tcga_pan_can_atlas_2018/data_armlevel_cna.txt: Write to restore size failed
brca_tcga_pan_can_atlas_2018/data_mrna_seq_v2_rsem_zscores_ref_diploid_samples.txt: Write to restore size failed
brca_tcga_pan_can_atlas_2018/normals/data_mrna_seq_v2_rsem_normal_samples.txt: Write to restore size failed
brca_tcga_pan_can_atlas_2018/normals/data_mrna_seq_v2_rsem_normal_samples_zscores_ref_normal_samples.txt: Write to restore size failed
brca_tcga_pan_can_atlas_2018/data_mutations.txt: Write to restore size failed
brca_tcga_pan_can_atlas_2018/data_cna.txt: Write to restore size failed
brca_tcga_pan_can_atlas_2018/data_mrna_seq_v2_rsem_zscores_ref_all_samples.txt: Write to restore size failed
brca_tcga_pan_can_atlas_2018/data_mrna_seq_v2_rsem_zscores_ref_normal_samples.txt: Write to restore size failed
brca_tcga_pan_can_atlas_2018/data_rppa_zscores.txt: Write to restore size failed
brca_tcga_pan_can_atlas_2018/data_resource_definition.txt: Write to restore size failed
brca_tcga_pan_can_atlas_2018/data_timeline_sample_acquisition.txt: Write to restore size failed
brca_tcga_pan_can_atlas_2018/data_mrna_seq_v2_rsem.txt: Write to restore size failed
brca_tcga_pan_can_atlas_2018/data_gene_panel_matrix.txt: Write to restore size failed
brca_tcga_pan_can_atlas_2018/data_rppa.txt: Write to restore size failed
brca_tcga_pan_can_atlas_2018/data_clinical_patient.txt: Write to restore size failed
brca_tcga_pan_can_atlas_2018/data_protein_quantification_zscores.txt: Write to restore size failed
brca_tcga_pan_can_atlas_2018/data_protein_quantification.txt: Write to restore size failed
brca_tcga_pan_can_atlas_2018/data_sv.txt: Write to restore size failed
brca_tcga_pan_can_atlas_2018/data_cna_hg19.seg: Write to restore size failed
tar: Error exit delayed from previous errors.
trying URL 'https://datahub.assets.cbioportal.org/tet_nci_2014.tar.gz'
Content type 'application/x-tar' length 135206 bytes (132 KB)
==================================================
downloaded 132 KB

trying URL 'https://datahub.assets.cbioportal.org/all_stjude_2015.tar.gz'
Content type 'application/x-tar' length 10070 bytes
==================================================
downloaded 10070 bytes

trying URL 'https://datahub.assets.cbioportal.org/gbm_mayo_pdx_sarkaria_2019.tar.gz'
Content type 'application/x-tar' length 67852585 bytes (64.7 MB)
==================================================
downloaded 64.7 MB

trying URL 'https://datahub.assets.cbioportal.org/wt_target_gdc.tar.gz'
Content type 'application/x-tar' length 61129093 bytes (58.3 MB)
==================================================
downloaded 58.3 MB

trying URL 'https://datahub.assets.cbioportal.org/brca_dldccc_2022.tar.gz'
Content type 'application/x-tar' length 10554354 bytes (10.1 MB)
==================================================
downloaded 10.1 MB

trying URL 'https://datahub.assets.cbioportal.org/prcc_tcga_gdc.tar.gz'
Content type 'application/x-tar' length 126453925 bytes (120.6 MB)
==================================================
downloaded 120.6 MB

prcc_tcga_gdc/data_mrna_seq_fpkm_zscores_ref_all_samples.txt: Write failed
prcc_tcga_gdc/data_mrna_seq_read_counts.txt: Write to restore size failed
prcc_tcga_gdc/data_mrna_seq_read_counts_zscores_ref_all_samples.txt: Write to restore size failed
prcc_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/paad_utsw_2015.tar.gz'
Content type 'application/x-tar' length 1585270 bytes (1.5 MB)
==================================================
downloaded 1.5 MB

trying URL 'https://datahub.assets.cbioportal.org/brca_mbcproject_wagle_2017.tar.gz'
Content type 'application/x-tar' length 40198284 bytes (38.3 MB)
==================================================
downloaded 38.3 MB

trying URL 'https://datahub.assets.cbioportal.org/ov_tcga_pub.tar.gz'
Content type 'application/x-tar' length 313808154 bytes (299.3 MB)
==============================
downloaded 181.5 MB

Error in download.file(url = url, destfile = destfile) : 
  download from 'https://datahub.assets.cbioportal.org/ov_tcga_pub.tar.gz' failed
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/Rtmp3RWlri/file94a173a1edb3.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/Rtmp3RWlri/file94a1bfcbe14.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/Rtmp3RWlri/file94a17e231931.
Saving _problems/test_cBioDataPack-19.R
Saving _problems/test_cBioPortalData-3.R
[ FAIL 2 | WARN 350 | SKIP 0 | PASS 6 ]

'R CMD check' output

##############################################################################
##############################################################################
###
### 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:
  ==============================
  downloaded 181.5 MB
  
  Error in download.file(url = url, destfile = destfile) : 
    download from 'https://datahub.assets.cbioportal.org/ov_tcga_pub.tar.gz' failed
  Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
    Failed to open file /tmp/Rtmp3RWlri/file94a173a1edb3.
  Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
    Failed to open file /tmp/Rtmp3RWlri/file94a1bfcbe14.
  Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
    Failed to open file /tmp/Rtmp3RWlri/file94a17e231931.
  Saving _problems/test_cBioDataPack-19.R
  Saving _problems/test_cBioPortalData-3.R
  [ FAIL 2 | WARN 350 | SKIP 0 | PASS 6 ]
  
* DONE

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

Installation output

cBioPortalData.Rcheck/00install.out

* 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)