Long Tests report for BioC 3.22 - CHECK results for cBioPortalData on merida1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"	4891
merida1	macOS 12.7.6 Monterey	x86_64	4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"	4681
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*

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: 2026-02-28 16:01:22 -0500 (Sat, 28 Feb 2026)

EndedAt: 2026-02-28 18:54:24 -0500 (Sat, 28 Feb 2026)

EllapsedTime: 10382.0 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")
trying URL 'https://datahub.assets.cbioportal.org/mixed_cfdna_msk_2020.tar.gz'
Content type 'application/x-tar' length 275450 bytes (268 KB)
==================================================
downloaded 268 KB

trying URL 'https://datahub.assets.cbioportal.org/uec_cptac_gdc.tar.gz'
Content type 'application/x-tar' length 278896067 bytes (266.0 MB)
==================================================
downloaded 266.0 MB

trying URL 'https://datahub.assets.cbioportal.org/mcl_idibips_2013.tar.gz'
Content type 'application/x-tar' length 38953 bytes (38 KB)
==================================================
downloaded 38 KB

trying URL 'https://datahub.assets.cbioportal.org/thyroid_gatci_2024.tar.gz'
Content type 'application/x-tar' length 1786272 bytes (1.7 MB)
==================================================
downloaded 1.7 MB

trying URL 'https://datahub.assets.cbioportal.org/stad_pfizer_uhongkong.tar.gz'
Content type 'application/x-tar' length 1042124 bytes (1017 KB)
==================================================
downloaded 1017 KB

trying URL 'https://datahub.assets.cbioportal.org/nsclc_mskcc_2015.tar.gz'
Content type 'application/x-tar' length 232303 bytes (226 KB)
==================================================
downloaded 226 KB

trying URL 'https://datahub.assets.cbioportal.org/cellline_nci60.tar.gz'
Content type 'application/x-tar' length 20204413 bytes (19.3 MB)
==================================================
downloaded 19.3 MB

trying URL 'https://datahub.assets.cbioportal.org/thca_tcga.tar.gz'
Content type 'application/x-tar' length 157092509 bytes (149.8 MB)
==================================================
downloaded 149.8 MB

trying URL 'https://datahub.assets.cbioportal.org/rbl_cfdna_msk_2020.tar.gz'
Content type 'application/x-tar' length 2332190 bytes (2.2 MB)
==================================================
downloaded 2.2 MB

trying URL 'https://datahub.assets.cbioportal.org/mbn_msk_2024.tar.gz'
Content type 'application/x-tar' length 641073 bytes (626 KB)
==================================================
downloaded 626 KB

trying URL 'https://datahub.assets.cbioportal.org/es_dsrct_msk_2023.tar.gz'
Content type 'application/x-tar' length 183428 bytes (179 KB)
==================================================
downloaded 179 KB

trying URL 'https://datahub.assets.cbioportal.org/sarc_mskcc.tar.gz'
Content type 'application/x-tar' length 23614078 bytes (22.5 MB)
==================================================
downloaded 22.5 MB

trying URL 'https://datahub.assets.cbioportal.org/kich_tcga_pub.tar.gz'
Content type 'application/x-tar' length 21449055 bytes (20.5 MB)
==================================================
downloaded 20.5 MB

trying URL 'https://datahub.assets.cbioportal.org/makeanimpact_ccr_2023.tar.gz'
Content type 'application/x-tar' length 126368 bytes (123 KB)
==================================================
downloaded 123 KB

trying URL 'https://datahub.assets.cbioportal.org/paad_qcmg_uq_2016.tar.gz'
Content type 'application/x-tar' length 14841658 bytes (14.2 MB)
==================================================
downloaded 14.2 MB

trying URL 'https://datahub.assets.cbioportal.org/meso_tcga_pan_can_atlas_2018.tar.gz'
Content type 'application/x-tar' length 33295818 bytes (31.8 MB)
==================================================
downloaded 31.8 MB

trying URL 'https://datahub.assets.cbioportal.org/acbc_mskcc_2015.tar.gz'
Content type 'application/x-tar' length 34488 bytes (33 KB)
==================================================
downloaded 33 KB

trying URL 'https://datahub.assets.cbioportal.org/hcc_mskimpact_2018.tar.gz'
Content type 'application/x-tar' length 136419 bytes (133 KB)
==================================================
downloaded 133 KB

trying URL 'https://datahub.assets.cbioportal.org/msk_access_2021.tar.gz'
Content type 'application/x-tar' length 926028 bytes (904 KB)
==================================================
downloaded 904 KB

trying URL 'https://datahub.assets.cbioportal.org/nsclc_tracerx_2017.tar.gz'
Content type 'application/x-tar' length 21698939 bytes (20.7 MB)
==================================================
downloaded 20.7 MB

trying URL 'https://datahub.assets.cbioportal.org/mbl_icgc.tar.gz'
Content type 'application/x-tar' length 257453 bytes (251 KB)
==================================================
downloaded 251 KB

trying URL 'https://datahub.assets.cbioportal.org/mixed_msk_tcga_2021.tar.gz'
Content type 'application/x-tar' length 143819 bytes (140 KB)
==================================================
downloaded 140 KB

trying URL 'https://datahub.assets.cbioportal.org/prad_broad_2013.tar.gz'
Content type 'application/x-tar' length 2633299 bytes (2.5 MB)
==================================================
downloaded 2.5 MB

trying URL 'https://datahub.assets.cbioportal.org/lung_msk_pdx.tar.gz'
Content type 'application/x-tar' length 547120 bytes (534 KB)
==================================================
downloaded 534 KB

trying URL 'https://datahub.assets.cbioportal.org/braf_msk_impact_2024.tar.gz'
Content type 'application/x-tar' length 141484 bytes (138 KB)
==================================================
downloaded 138 KB

trying URL 'https://datahub.assets.cbioportal.org/gbm_cptac_2021.tar.gz'
Content type 'application/x-tar' length 675568726 bytes (644.3 MB)
==================================================
downloaded 644.3 MB

Error in read.table(file = file, header = header, sep = sep, quote = quote,  : 
  more columns than column names
trying URL 'https://datahub.assets.cbioportal.org/nst_nfosi_ntap.tar.gz'
Content type 'application/x-tar' length 160182 bytes (156 KB)
==================================================
downloaded 156 KB

trying URL 'https://datahub.assets.cbioportal.org/dlbc_tcga_pan_can_atlas_2018.tar.gz'
Content type 'application/x-tar' length 19997908 bytes (19.1 MB)
==================================================
downloaded 19.1 MB

trying URL 'https://datahub.assets.cbioportal.org/pediatric_dkfz_2017.tar.gz'
Content type 'application/x-tar' length 4603466 bytes (4.4 MB)
==================================================
downloaded 4.4 MB

trying URL 'https://datahub.assets.cbioportal.org/brca_bccrc.tar.gz'
Content type 'application/x-tar' length 645819 bytes (630 KB)
==================================================
downloaded 630 KB

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/prostate_msk_2024.tar.gz'
Content type 'application/x-tar' length 2776699 bytes (2.6 MB)
==================================================
downloaded 2.6 MB

trying URL 'https://datahub.assets.cbioportal.org/mel_mskimpact_2020.tar.gz'
Content type 'application/x-tar' length 1510156 bytes (1.4 MB)
==================================================
downloaded 1.4 MB

trying URL 'https://datahub.assets.cbioportal.org/crc_hta11_htan_2021.tar.gz'
Content type 'application/x-tar' length 11121923 bytes (10.6 MB)
==================================================
downloaded 10.6 MB

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/rt_target_2018_pub.tar.gz'
Content type 'application/x-tar' length 8658447 bytes (8.3 MB)
==================================================
downloaded 8.3 MB

trying URL 'https://datahub.assets.cbioportal.org/mel_iatlas_liu_2019.tar.gz'
Content type 'application/x-tar' length 37046530 bytes (35.3 MB)
==================================================
downloaded 35.3 MB

trying URL 'https://datahub.assets.cbioportal.org/mds_mskcc_2020.tar.gz'
Content type 'application/x-tar' length 13769623 bytes (13.1 MB)
==================================================
downloaded 13.1 MB

trying URL 'https://datahub.assets.cbioportal.org/prad_pik3r1_msk_2021.tar.gz'
Content type 'application/x-tar' length 1534087 bytes (1.5 MB)
==================================================
downloaded 1.5 MB

trying URL 'https://datahub.assets.cbioportal.org/nhl_bcgsc_2011.tar.gz'
Content type 'application/x-tar' length 39263 bytes (38 KB)
==================================================
downloaded 38 KB

trying URL 'https://datahub.assets.cbioportal.org/brca_mbcproject_2022.tar.gz'
Content type 'application/x-tar' length 35202713 bytes (33.6 MB)
==================================================
downloaded 33.6 MB

trying URL 'https://datahub.assets.cbioportal.org/sarcoma_msk_2023.tar.gz'
Content type 'application/x-tar' length 98053 bytes (95 KB)
==================================================
downloaded 95 KB

trying URL 'https://datahub.assets.cbioportal.org/kirc_tcga_pan_can_atlas_2018.tar.gz'
Content type 'application/x-tar' length 223980145 bytes (213.6 MB)
==================================================
downloaded 213.6 MB

trying URL 'https://datahub.assets.cbioportal.org/ccrcc_iatlas_choueiri_2016.tar.gz'
Content type 'application/x-tar' length 4860144 bytes (4.6 MB)
==================================================
downloaded 4.6 MB

trying URL 'https://datahub.assets.cbioportal.org/breast_msk_2018.tar.gz'
Content type 'application/x-tar' length 2238155 bytes (2.1 MB)
==================================================
downloaded 2.1 MB

trying URL 'https://datahub.assets.cbioportal.org/prad_msk_2019.tar.gz'
Content type 'application/x-tar' length 16356 bytes (15 KB)
==================================================
downloaded 15 KB

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/lihc_tcga.tar.gz'
Content type 'application/x-tar' length 119101476 bytes (113.6 MB)
==================================================
downloaded 113.6 MB

trying URL 'https://datahub.assets.cbioportal.org/prad_organoids_msk_2022.tar.gz'
Content type 'application/x-tar' length 3497560 bytes (3.3 MB)
==================================================
downloaded 3.3 MB

trying URL 'https://datahub.assets.cbioportal.org/read_tcga_gdc.tar.gz'
Content type 'application/x-tar' length 87118481 bytes (83.1 MB)
==================================================
downloaded 83.1 MB

trying URL 'https://datahub.assets.cbioportal.org/cesc_tcga_pan_can_atlas_2018.tar.gz'
Content type 'application/x-tar' length 127010521 bytes (121.1 MB)
==================================================
downloaded 121.1 MB

trying URL 'https://datahub.assets.cbioportal.org/cscc_dfarber_2015.tar.gz'
Content type 'application/x-tar' length 138535 bytes (135 KB)
==================================================
downloaded 135 KB

trying URL 'https://datahub.assets.cbioportal.org/brca_mapk_hp_msk_2021.tar.gz'
Content type 'application/x-tar' length 210076 bytes (205 KB)
==================================================
downloaded 205 KB

trying URL 'https://datahub.assets.cbioportal.org/crc_apc_impact_2020.tar.gz'
Content type 'application/x-tar' length 591332 bytes (577 KB)
==================================================
downloaded 577 KB

trying URL 'https://datahub.assets.cbioportal.org/brca_dfci_2020.tar.gz'
Content type 'application/x-tar' length 831320 bytes (811 KB)
==================================================
downloaded 811 KB

trying URL 'https://datahub.assets.cbioportal.org/pact_jhu_2011.tar.gz'
Content type 'application/x-tar' length 26638 bytes (26 KB)
==================================================
downloaded 26 KB

trying URL 'https://datahub.assets.cbioportal.org/skcm_tcga_gdc.tar.gz'
Content type 'application/x-tar' length 300602257 bytes (286.7 MB)
==================================================
downloaded 286.7 MB

trying URL 'https://datahub.assets.cbioportal.org/mel_iatlas_gide_2019.tar.gz'
Content type 'application/x-tar' length 23488658 bytes (22.4 MB)
==================================================
downloaded 22.4 MB

trying URL 'https://datahub.assets.cbioportal.org/meso_tcga.tar.gz'
Content type 'application/x-tar' length 29638617 bytes (28.3 MB)
==================================================
downloaded 28.3 MB

trying URL 'https://datahub.assets.cbioportal.org/chl_sccc_2023.tar.gz'
Content type 'application/x-tar' length 424725 bytes (414 KB)
==================================================
downloaded 414 KB

trying URL 'https://datahub.assets.cbioportal.org/soft_tissue_msk_2023.tar.gz'
Content type 'application/x-tar' length 44097 bytes (43 KB)
==================================================
downloaded 43 KB

trying URL 'https://datahub.assets.cbioportal.org/chol_nus_2012.tar.gz'
Content type 'application/x-tar' length 16777 bytes (16 KB)
==================================================
downloaded 16 KB

trying URL 'https://datahub.assets.cbioportal.org/ovary_cptac_gdc.tar.gz'
Content type 'application/x-tar' length 49596978 bytes (47.3 MB)
==================================================
downloaded 47.3 MB

trying URL 'https://datahub.assets.cbioportal.org/lusc_tcga_pan_can_atlas_2018.tar.gz'
Content type 'application/x-tar' length 256992991 bytes (245.1 MB)
==================================================
downloaded 245.1 MB

trying URL 'https://datahub.assets.cbioportal.org/gbm_tcga_pan_can_atlas_2018.tar.gz'
Content type 'application/x-tar' length 125292019 bytes (119.5 MB)
==================================================
downloaded 119.5 MB

trying URL 'https://datahub.assets.cbioportal.org/paad_tcga.tar.gz'
Content type 'application/x-tar' length 72147923 bytes (68.8 MB)
==================================================
downloaded 68.8 MB

trying URL 'https://datahub.assets.cbioportal.org/stad_tcga_pan_can_atlas_2018.tar.gz'
Content type 'application/x-tar' length 270708573 bytes (258.2 MB)
==================================================
downloaded 258.2 MB

trying URL 'https://datahub.assets.cbioportal.org/chrcc_tcga_gdc.tar.gz'
Content type 'application/x-tar' length 28588327 bytes (27.3 MB)
==================================================
downloaded 27.3 MB

trying URL 'https://datahub.assets.cbioportal.org/bcc_unige_2016.tar.gz'
Content type 'application/x-tar' length 19376348 bytes (18.5 MB)
==================================================
downloaded 18.5 MB

trying URL 'https://datahub.assets.cbioportal.org/mixed_selpercatinib_2020.tar.gz'
Content type 'application/x-tar' length 31809 bytes (31 KB)
==================================================
downloaded 31 KB

Error in TCGAutils::uniformBuilds(x[[ncbi]]) : 
  Frequency of NA values higher than the cutoff tolerance
trying URL 'https://datahub.assets.cbioportal.org/nsgct_tcga_gdc.tar.gz'
Content type 'application/x-tar' length 70175719 bytes (66.9 MB)
==================================================
downloaded 66.9 MB

trying URL 'https://datahub.assets.cbioportal.org/es_iocurie_2014.tar.gz'
Content type 'application/x-tar' length 207153 bytes (202 KB)
==================================================
downloaded 202 KB

trying URL 'https://datahub.assets.cbioportal.org/paac_msk_jco_2023.tar.gz'
Content type 'application/x-tar' length 65564 bytes (64 KB)
==================================================
downloaded 64 KB

trying URL 'https://datahub.assets.cbioportal.org/egc_trap_msk_2020.tar.gz'
Content type 'application/x-tar' length 3021026 bytes (2.9 MB)
==================================================
downloaded 2.9 MB

trying URL 'https://datahub.assets.cbioportal.org/ohnca_cptac_gdc.tar.gz'
Content type 'application/x-tar' length 92464941 bytes (88.2 MB)
==================================================
downloaded 88.2 MB

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'
trying URL 'https://datahub.assets.cbioportal.org/liad_inserm_fr_2014.tar.gz'
Content type 'application/x-tar' length 63840 bytes (62 KB)
==================================================
downloaded 62 KB

trying URL 'https://datahub.assets.cbioportal.org/acyc_sanger_2013.tar.gz'
Content type 'application/x-tar' length 27619 bytes (26 KB)
==================================================
downloaded 26 KB

trying URL 'https://datahub.assets.cbioportal.org/pan_origimed_2020.tar.gz'
Content type 'application/x-tar' length 5674094 bytes (5.4 MB)
==================================================
downloaded 5.4 MB

trying URL 'https://datahub.assets.cbioportal.org/sarc_tcga_pub.tar.gz'
Content type 'application/x-tar' length 38576662 bytes (36.8 MB)
==================================================
downloaded 36.8 MB

trying URL 'https://datahub.assets.cbioportal.org/mpcproject_broad_2021.tar.gz'
Content type 'application/x-tar' length 22961713 bytes (21.9 MB)
==================================================
downloaded 21.9 MB

trying URL 'https://datahub.assets.cbioportal.org/blca_tcga_pub.tar.gz'
Content type 'application/x-tar' length 43486958 bytes (41.5 MB)
==================================================
downloaded 41.5 MB

trying URL 'https://datahub.assets.cbioportal.org/coad_silu_2022.tar.gz'
Content type 'application/x-tar' length 71077306 bytes (67.8 MB)
==================================================
downloaded 67.8 MB

trying URL 'https://datahub.assets.cbioportal.org/pcpg_tcga_pub.tar.gz'
Content type 'application/x-tar' length 152458279 bytes (145.4 MB)
==================================================
downloaded 145.4 MB

Error in strsplit(hugos, "|", TRUE) : non-character argument
trying URL 'https://datahub.assets.cbioportal.org/hcc_jcopo_msk_2023.tar.gz'
Content type 'application/x-tar' length 33817 bytes (33 KB)
==================================================
downloaded 33 KB

trying URL 'https://datahub.assets.cbioportal.org/egc_mskcc_2020.tar.gz'
Content type 'application/x-tar' length 633574 bytes (618 KB)
==================================================
downloaded 618 KB

trying URL 'https://datahub.assets.cbioportal.org/breast_msk_2025.tar.gz'
Content type 'application/x-tar' length 5240562 bytes (5.0 MB)
==================================================
downloaded 5.0 MB

trying URL 'https://datahub.assets.cbioportal.org/braf_msk_archer_2024.tar.gz'
Content type 'application/x-tar' length 8123 bytes
==================================================
downloaded 8123 bytes

Error in validObject(.Object) : invalid class "ExperimentList" object: 
    ExperimentList elements must be named
trying URL 'https://datahub.assets.cbioportal.org/thca_tcga_pub.tar.gz'
Content type 'application/x-tar' length 127147346 bytes (121.3 MB)
==================================================
downloaded 121.3 MB

trying URL 'https://datahub.assets.cbioportal.org/rcc_iatlas_immotion150_2018.tar.gz'
Content type 'application/x-tar' length 82354111 bytes (78.5 MB)
==================================================
downloaded 78.5 MB

trying URL 'https://datahub.assets.cbioportal.org/skcm_tcga_pan_can_atlas_2018.tar.gz'
Content type 'application/x-tar' length 218772681 bytes (208.6 MB)
==================================================
downloaded 208.6 MB

trying URL 'https://datahub.assets.cbioportal.org/mtnn_msk_2022.tar.gz'
Content type 'application/x-tar' length 124936 bytes (122 KB)
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downloaded 122 KB

trying URL 'https://datahub.assets.cbioportal.org/msk_chord_2024.tar.gz'
Content type 'application/x-tar' length 46915983 bytes (44.7 MB)
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downloaded 44.7 MB

trying URL 'https://datahub.assets.cbioportal.org/blca_bgi.tar.gz'
Content type 'application/x-tar' length 495098 bytes (483 KB)
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trying URL 'https://datahub.assets.cbioportal.org/nsclc_mskcc_2018.tar.gz'
Content type 'application/x-tar' length 3117122 bytes (3.0 MB)
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trying URL 'https://datahub.assets.cbioportal.org/prad_mskcc_2017.tar.gz'
Content type 'application/x-tar' length 545973 bytes (533 KB)
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trying URL 'https://datahub.assets.cbioportal.org/normal_skin_fibroblast_2024.tar.gz'
Content type 'application/x-tar' length 1672068 bytes (1.6 MB)
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downloaded 1.6 MB

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_ink4_msk_2021.tar.gz'
Content type 'application/x-tar' length 1683716 bytes (1.6 MB)
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downloaded 1.6 MB

trying URL 'https://datahub.assets.cbioportal.org/paac_jhu_2014.tar.gz'
Content type 'application/x-tar' length 137290 bytes (134 KB)
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trying URL 'https://datahub.assets.cbioportal.org/brca_igr_2015.tar.gz'
Content type 'application/x-tar' length 2003379 bytes (1.9 MB)
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downloaded 1.9 MB

trying URL 'https://datahub.assets.cbioportal.org/ntrk_msk_2019.tar.gz'
Content type 'application/x-tar' length 81584 bytes (79 KB)
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trying URL 'https://datahub.assets.cbioportal.org/pog570_bcgsc_2020.tar.gz'
Content type 'application/x-tar' length 386747698 bytes (368.8 MB)
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downloaded 368.8 MB

trying URL 'https://datahub.assets.cbioportal.org/thyroid_mskcc_2016.tar.gz'
Content type 'application/x-tar' length 100365 bytes (98 KB)
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trying URL 'https://datahub.assets.cbioportal.org/lusc_cptac_2021.tar.gz'
Content type 'application/x-tar' length 45704228 bytes (43.6 MB)
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downloaded 43.6 MB

trying URL 'https://datahub.assets.cbioportal.org/coadread_tcga_pan_can_atlas_2018.tar.gz'
Content type 'application/x-tar' length 284181333 bytes (271.0 MB)
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downloaded 271.0 MB

Error in read.table(file = file, header = header, sep = sep, quote = quote,  : 
  more columns than column names
trying URL 'https://datahub.assets.cbioportal.org/normal_skin_melanocytes_2024.tar.gz'
Content type 'application/x-tar' length 15123623 bytes (14.4 MB)
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downloaded 14.4 MB

Error in read.table(file = file, header = header, sep = sep, quote = quote,  : 
  more columns than column names
trying URL 'https://datahub.assets.cbioportal.org/mng_utoronto_2021.tar.gz'
Content type 'application/x-tar' length 44694607 bytes (42.6 MB)
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downloaded 42.6 MB

trying URL 'https://datahub.assets.cbioportal.org/luad_mskcc_2020.tar.gz'
Content type 'application/x-tar' length 605977 bytes (591 KB)
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downloaded 591 KB

trying URL 'https://datahub.assets.cbioportal.org/coadread_tcga_pub.tar.gz'
Content type 'application/x-tar' length 110633024 bytes (105.5 MB)
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downloaded 105.5 MB

trying URL 'https://datahub.assets.cbioportal.org/gbm_tcga.tar.gz'
Content type 'application/x-tar' length 220899601 bytes (210.7 MB)
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downloaded 210.7 MB

trying URL 'https://datahub.assets.cbioportal.org/tmb_mskcc_2018.tar.gz'
Content type 'application/x-tar' length 1254634 bytes (1.2 MB)
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downloaded 1.2 MB

trying URL 'https://datahub.assets.cbioportal.org/stad_uhongkong.tar.gz'
Content type 'application/x-tar' length 445180 bytes (434 KB)
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trying URL 'https://datahub.assets.cbioportal.org/ucec_tcga_gdc.tar.gz'
Content type 'application/x-tar' length 417421960 bytes (398.1 MB)
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downloaded 398.1 MB

trying URL 'https://datahub.assets.cbioportal.org/usarc_msk_2020.tar.gz'
Content type 'application/x-tar' length 150080 bytes (146 KB)
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trying URL 'https://datahub.assets.cbioportal.org/hcc_clca_2024.tar.gz'
Content type 'application/x-tar' length 34520708 bytes (32.9 MB)
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downloaded 32.9 MB

trying URL 'https://datahub.assets.cbioportal.org/os_target_gdc.tar.gz'
Content type 'application/x-tar' length 42543240 bytes (40.6 MB)
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downloaded 40.6 MB

trying URL 'https://datahub.assets.cbioportal.org/nbl_msk_2023.tar.gz'
Content type 'application/x-tar' length 175868 bytes (171 KB)
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trying URL 'https://datahub.assets.cbioportal.org/luad_cptac_2020.tar.gz'
Content type 'application/x-tar' length 45542042 bytes (43.4 MB)
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downloaded 43.4 MB

trying URL 'https://datahub.assets.cbioportal.org/laml_tcga_pan_can_atlas_2018.tar.gz'
Content type 'application/x-tar' length 78883535 bytes (75.2 MB)
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downloaded 75.2 MB

trying URL 'https://datahub.assets.cbioportal.org/mixed_allen_2018.tar.gz'
Content type 'application/x-tar' length 15178602 bytes (14.5 MB)
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downloaded 14.5 MB

trying URL 'https://datahub.assets.cbioportal.org/prad_tcga_pan_can_atlas_2018.tar.gz'
Content type 'application/x-tar' length 218752976 bytes (208.6 MB)
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downloaded 208.6 MB

trying URL 'https://datahub.assets.cbioportal.org/brca_cptac_2020.tar.gz'
Content type 'application/x-tar' length 47075229 bytes (44.9 MB)
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trying URL 'https://datahub.assets.cbioportal.org/ucec_ccr_cfdna_msk_2022.tar.gz'
Content type 'application/x-tar' length 33313 bytes (32 KB)
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Error in validObject(.Object) : invalid class "ExperimentList" object: 
    ExperimentList elements must be named
trying URL 'https://datahub.assets.cbioportal.org/coadread_dfci_2016.tar.gz'
Content type 'application/x-tar' length 11317552 bytes (10.8 MB)
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downloaded 10.8 MB

trying URL 'https://datahub.assets.cbioportal.org/rectal_msk_2022.tar.gz'
Content type 'application/x-tar' length 23429205 bytes (22.3 MB)
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downloaded 22.3 MB

trying URL 'https://datahub.assets.cbioportal.org/hgsoc_tcga_gdc.tar.gz'
Content type 'application/x-tar' length 211821119 bytes (202.0 MB)
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downloaded 202.0 MB

trying URL 'https://datahub.assets.cbioportal.org/stad_oncosg_2018.tar.gz'
Content type 'application/x-tar' length 33886486 bytes (32.3 MB)
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downloaded 32.3 MB

trying URL 'https://datahub.assets.cbioportal.org/angs_painter_2025.tar.gz'
Content type 'application/x-tar' length 31304139 bytes (29.9 MB)
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downloaded 29.9 MB

trying URL 'https://datahub.assets.cbioportal.org/appendiceal_msk_2022.tar.gz'
Content type 'application/x-tar' length 210728 bytes (205 KB)
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trying URL 'https://datahub.assets.cbioportal.org/msk_impact_2017.tar.gz'
Content type 'application/x-tar' length 12191399 bytes (11.6 MB)
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downloaded 11.6 MB

trying URL 'https://datahub.assets.cbioportal.org/ucs_tcga.tar.gz'
Content type 'application/x-tar' length 22789494 bytes (21.7 MB)
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downloaded 21.7 MB

trying URL 'https://datahub.assets.cbioportal.org/luad_mskcc_2023_met_organotropism.tar.gz'
Content type 'application/x-tar' length 7644760 bytes (7.3 MB)
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downloaded 7.3 MB

trying URL 'https://datahub.assets.cbioportal.org/mel_iatlas_hugo_ucla_2016.tar.gz'
Content type 'application/x-tar' length 21247668 bytes (20.3 MB)
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downloaded 20.3 MB

trying URL 'https://datahub.assets.cbioportal.org/coadread_cass_2020.tar.gz'
Content type 'application/x-tar' length 3150297 bytes (3.0 MB)
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downloaded 3.0 MB

trying URL 'https://datahub.assets.cbioportal.org/summit_2018.tar.gz'
Content type 'application/x-tar' length 79597 bytes (77 KB)
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trying URL 'https://datahub.assets.cbioportal.org/csf_msk_2024.tar.gz'
Content type 'application/x-tar' length 757119 bytes (739 KB)
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downloaded 739 KB

trying URL 'https://datahub.assets.cbioportal.org/lusc_tcga_pub.tar.gz'
Content type 'application/x-tar' length 117841866 bytes (112.4 MB)
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downloaded 112.4 MB

trying URL 'https://datahub.assets.cbioportal.org/prad_mskcc.tar.gz'
Content type 'application/x-tar' length 45795952 bytes (43.7 MB)
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downloaded 43.7 MB

trying URL 'https://datahub.assets.cbioportal.org/nsclc_ctdx_msk_2022.tar.gz'
Content type 'application/x-tar' length 1272554 bytes (1.2 MB)
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downloaded 1.2 MB

trying URL 'https://datahub.assets.cbioportal.org/pancreas_cptac_gdc.tar.gz'
Content type 'application/x-tar' length 85058664 bytes (81.1 MB)
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downloaded 81.1 MB

trying URL 'https://datahub.assets.cbioportal.org/blca_msk_2024.tar.gz'
Content type 'application/x-tar' length 372245 bytes (363 KB)
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trying URL 'https://datahub.assets.cbioportal.org/all_stjude_2013.tar.gz'
Content type 'application/x-tar' length 62814 bytes (61 KB)
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trying URL 'https://datahub.assets.cbioportal.org/gbc_msk_2018.tar.gz'
Content type 'application/x-tar' length 126352 bytes (123 KB)
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trying URL 'https://datahub.assets.cbioportal.org/lihc_riken.tar.gz'
Content type 'application/x-tar' length 16573 bytes (16 KB)
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trying URL 'https://datahub.assets.cbioportal.org/crc_eo_2020.tar.gz'
Content type 'application/x-tar' length 2105865 bytes (2.0 MB)
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downloaded 2.0 MB

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'
trying URL 'https://datahub.assets.cbioportal.org/egc_trap_ccr_msk_2023.tar.gz'
Content type 'application/x-tar' length 5990917 bytes (5.7 MB)
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downloaded 5.7 MB

trying URL 'https://datahub.assets.cbioportal.org/ccle_genentech_2014.tar.gz'
Content type 'application/x-tar' length 120534760 bytes (115.0 MB)
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downloaded 115.0 MB

trying URL 'https://datahub.assets.cbioportal.org/nbl_amc_2012.tar.gz'
Content type 'application/x-tar' length 90355 bytes (88 KB)
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downloaded 88 KB

trying URL 'https://datahub.assets.cbioportal.org/esca_tcga_pan_can_atlas_2018.tar.gz'
Content type 'application/x-tar' length 101583697 bytes (96.9 MB)
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downloaded 96.9 MB

trying URL 'https://datahub.assets.cbioportal.org/lusc_tcga_gdc.tar.gz'
Content type 'application/x-tar' length 272163713 bytes (259.6 MB)
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downloaded 259.6 MB

trying URL 'https://datahub.assets.cbioportal.org/luad_mskcc_2015.tar.gz'
Content type 'application/x-tar' length 3941189 bytes (3.8 MB)
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downloaded 3.8 MB

trying URL 'https://datahub.assets.cbioportal.org/skcm_dfci_2015.tar.gz'
Content type 'application/x-tar' length 12103909 bytes (11.5 MB)
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downloaded 11.5 MB

trying URL 'https://datahub.assets.cbioportal.org/hcc_inserm_fr_2015.tar.gz'
Content type 'application/x-tar' length 1292710 bytes (1.2 MB)
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downloaded 1.2 MB

trying URL 'https://datahub.assets.cbioportal.org/ucec_ccr_msk_2022.tar.gz'
Content type 'application/x-tar' length 155091 bytes (151 KB)
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Error in TCGAutils::uniformBuilds(x[[ncbi]]) : 
  Frequency of NA values higher than the cutoff tolerance
trying URL 'https://datahub.assets.cbioportal.org/mel_tsam_liang_2017.tar.gz'
Content type 'application/x-tar' length 8344418 bytes (8.0 MB)
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downloaded 8.0 MB

trying URL 'https://datahub.assets.cbioportal.org/ccrcc_utokyo_2013.tar.gz'
Content type 'application/x-tar' length 6566959 bytes (6.3 MB)
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downloaded 6.3 MB

Error in read.table(file = file, header = header, sep = sep, quote = quote,  : 
  more columns than column names
trying URL 'https://datahub.assets.cbioportal.org/paad_iatlas_prince_2022.tar.gz'
Content type 'application/x-tar' length 32787199 bytes (31.3 MB)
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downloaded 31.3 MB

trying URL 'https://datahub.assets.cbioportal.org/skcm_broad_brafresist_2012.tar.gz'
Content type 'application/x-tar' length 6477729 bytes (6.2 MB)
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downloaded 6.2 MB

trying URL 'https://datahub.assets.cbioportal.org/coad_cptac_gdc.tar.gz'
Content type 'application/x-tar' length 66418383 bytes (63.3 MB)
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downloaded 63.3 MB

trying URL 'https://datahub.assets.cbioportal.org/aml_ohsu_2022.tar.gz'
Content type 'application/x-tar' length 150212379 bytes (143.3 MB)
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downloaded 143.3 MB

trying URL 'https://datahub.assets.cbioportal.org/panet_arcnet_2017.tar.gz'
Content type 'application/x-tar' length 264230 bytes (258 KB)
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trying URL 'https://datahub.assets.cbioportal.org/um_tcga_gdc.tar.gz'
Content type 'application/x-tar' length 31584013 bytes (30.1 MB)
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downloaded 30.1 MB

trying URL 'https://datahub.assets.cbioportal.org/ucec_cptac_2020.tar.gz'
Content type 'application/x-tar' length 67227470 bytes (64.1 MB)
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downloaded 64.1 MB

trying URL 'https://datahub.assets.cbioportal.org/cscc_ranson_2022.tar.gz'
Content type 'application/x-tar' length 8781606 bytes (8.4 MB)
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downloaded 8.4 MB

trying URL 'https://datahub.assets.cbioportal.org/prad_tcga_gdc.tar.gz'
Content type 'application/x-tar' length 213279394 bytes (203.4 MB)
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downloaded 203.4 MB

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'
trying URL 'https://datahub.assets.cbioportal.org/coad_caseccc_2015.tar.gz'
Content type 'application/x-tar' length 193176 bytes (188 KB)
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trying URL 'https://datahub.assets.cbioportal.org/kirp_tcga.tar.gz'
Content type 'application/x-tar' length 92933854 bytes (88.6 MB)
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downloaded 88.6 MB

trying URL 'https://datahub.assets.cbioportal.org/brain_cptac_gdc.tar.gz'
Content type 'application/x-tar' length 120111850 bytes (114.5 MB)
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downloaded 114.5 MB

trying URL 'https://datahub.assets.cbioportal.org/aml_ohsu_2018.tar.gz'
Content type 'application/x-tar' length 157510971 bytes (150.2 MB)
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downloaded 150.2 MB

trying URL 'https://datahub.assets.cbioportal.org/paad_cptac_2021.tar.gz'
Content type 'application/x-tar' length 105401424 bytes (100.5 MB)
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downloaded 100.5 MB

trying URL 'https://datahub.assets.cbioportal.org/dlbcl_duke_2017.tar.gz'
Content type 'application/x-tar' length 462249 bytes (451 KB)
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downloaded 451 KB

trying URL 'https://datahub.assets.cbioportal.org/mbn_mdacc_2013.tar.gz'
Content type 'application/x-tar' length 58172468 bytes (55.5 MB)
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downloaded 55.5 MB

Error in strsplit(hugos, "|", TRUE) : non-character argument
trying URL 'https://datahub.assets.cbioportal.org/mds_iwg_2022.tar.gz'
Content type 'application/x-tar' length 1006604 bytes (983 KB)
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downloaded 983 KB

trying URL 'https://datahub.assets.cbioportal.org/npc_nusingapore.tar.gz'
Content type 'application/x-tar' length 423385 bytes (413 KB)
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downloaded 413 KB

trying URL 'https://datahub.assets.cbioportal.org/prad_su2c_2019.tar.gz'
Content type 'application/x-tar' length 102584661 bytes (97.8 MB)
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downloaded 97.8 MB

trying URL 'https://datahub.assets.cbioportal.org/ucec_tcga_pub.tar.gz'
Content type 'application/x-tar' length 115467080 bytes (110.1 MB)
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downloaded 110.1 MB

trying URL 'https://datahub.assets.cbioportal.org/esca_tcga.tar.gz'
Content type 'application/x-tar' length 68338816 bytes (65.2 MB)
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downloaded 65.2 MB

trying URL 'https://datahub.assets.cbioportal.org/urcc_mskcc_2016.tar.gz'
Content type 'application/x-tar' length 52322 bytes (51 KB)
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downloaded 51 KB

trying URL 'https://datahub.assets.cbioportal.org/pancan_mimsi_msk_2024.tar.gz'
Content type 'application/x-tar' length 9118524 bytes (8.7 MB)
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downloaded 8.7 MB

trying URL 'https://datahub.assets.cbioportal.org/hgsoc_msk_2021.tar.gz'
Content type 'application/x-tar' length 88469 bytes (86 KB)
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downloaded 86 KB

trying URL 'https://datahub.assets.cbioportal.org/panet_msk_2018.tar.gz'
Content type 'application/x-tar' length 122677 bytes (119 KB)
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downloaded 119 KB

trying URL 'https://datahub.assets.cbioportal.org/sarcoma_msk_2022.tar.gz'
Content type 'application/x-tar' length 814179 bytes (795 KB)
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downloaded 795 KB

Error in read.table(file = file, header = header, sep = sep, quote = quote,  : 
  more columns than column names
trying URL 'https://datahub.assets.cbioportal.org/bowel_colitis_msk_2022.tar.gz'
Content type 'application/x-tar' length 260215 bytes (254 KB)
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downloaded 254 KB

Error in read.table(file = file, header = header, sep = sep, quote = quote,  : 
  more columns than column names
trying URL 'https://datahub.assets.cbioportal.org/blca_tcga_gdc.tar.gz'
Content type 'application/x-tar' length 207706218 bytes (198.1 MB)
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downloaded 198.1 MB

trying URL 'https://datahub.assets.cbioportal.org/blca_mskcc_solit_2014.tar.gz'
Content type 'application/x-tar' length 209265 bytes (204 KB)
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downloaded 204 KB

trying URL 'https://datahub.assets.cbioportal.org/luad_tcga.tar.gz'
Content type 'application/x-tar' length 159353112 bytes (152.0 MB)
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downloaded 152.0 MB

trying URL 'https://datahub.assets.cbioportal.org/angs_project_painter_2018.tar.gz'
Content type 'application/x-tar' length 2470899 bytes (2.4 MB)
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downloaded 2.4 MB

trying URL 'https://datahub.assets.cbioportal.org/rcc_cptac_gdc.tar.gz'
Content type 'application/x-tar' length 177374640 bytes (169.2 MB)
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downloaded 169.2 MB

trying URL 'https://datahub.assets.cbioportal.org/plmeso_tcga_gdc.tar.gz'
Content type 'application/x-tar' length 38373054 bytes (36.6 MB)
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downloaded 36.6 MB

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/rms_nih_2014.tar.gz'
Content type 'application/x-tar' length 161152 bytes (157 KB)
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downloaded 157 KB

trying URL 'https://datahub.assets.cbioportal.org/stad_tcga.tar.gz'
Content type 'application/x-tar' length 144072474 bytes (137.4 MB)
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downloaded 137.4 MB

trying URL 'https://datahub.assets.cbioportal.org/ampca_bcm_2016.tar.gz'
Content type 'application/x-tar' length 1534661 bytes (1.5 MB)
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downloaded 1.5 MB

trying URL 'https://datahub.assets.cbioportal.org/brca_jup_msk_2020.tar.gz'
Content type 'application/x-tar' length 10553 bytes (10 KB)
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downloaded 10 KB

trying URL 'https://datahub.assets.cbioportal.org/ovary_geomx_gray_foundation_2024.tar.gz'
Content type 'application/x-tar' length 24494221 bytes (23.4 MB)
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downloaded 23.4 MB

trying URL 'https://datahub.assets.cbioportal.org/stmyec_wcm_2022.tar.gz'
Content type 'application/x-tar' length 195645 bytes (191 KB)
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downloaded 191 KB

trying URL 'https://datahub.assets.cbioportal.org/es_dfarber_broad_2014.tar.gz'
Content type 'application/x-tar' length 683740 bytes (667 KB)
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downloaded 667 KB

trying URL 'https://datahub.assets.cbioportal.org/sclc_ucologne_2015.tar.gz'
Content type 'application/x-tar' length 16207409 bytes (15.5 MB)
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downloaded 15.5 MB

trying URL 'https://datahub.assets.cbioportal.org/difg_glass.tar.gz'
Content type 'application/x-tar' length 285585705 bytes (272.4 MB)
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downloaded 272.4 MB

trying URL 'https://datahub.assets.cbioportal.org/stes_tcga_pub.tar.gz'
Content type 'application/x-tar' length 15252036 bytes (14.5 MB)
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downloaded 14.5 MB

trying URL 'https://datahub.assets.cbioportal.org/prad_mskcc_cheny1_organoids_2014.tar.gz'
Content type 'application/x-tar' length 1917982 bytes (1.8 MB)
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downloaded 1.8 MB

trying URL 'https://datahub.assets.cbioportal.org/bfn_duke_nus_2015.tar.gz'
Content type 'application/x-tar' length 28911 bytes (28 KB)
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downloaded 28 KB

trying URL 'https://datahub.assets.cbioportal.org/luad_oncosg_2020.tar.gz'
Content type 'application/x-tar' length 20021513 bytes (19.1 MB)
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downloaded 19.1 MB

trying URL 'https://datahub.assets.cbioportal.org/ihch_ismms_2015.tar.gz'
Content type 'application/x-tar' length 18563 bytes (18 KB)
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trying URL 'https://datahub.assets.cbioportal.org/blca_mskcc_solit_2012.tar.gz'
Content type 'application/x-tar' length 19719150 bytes (18.8 MB)
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downloaded 18.8 MB

trying URL 'https://datahub.assets.cbioportal.org/pancreas_msk_2024.tar.gz'
Content type 'application/x-tar' length 305369 bytes (298 KB)
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downloaded 298 KB

trying URL 'https://datahub.assets.cbioportal.org/msk_ch_2020.tar.gz'
Content type 'application/x-tar' length 1125467 bytes (1.1 MB)
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downloaded 1.1 MB

trying URL 'https://datahub.assets.cbioportal.org/lusc_tcga.tar.gz'
Content type 'application/x-tar' length 185572508 bytes (177.0 MB)
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downloaded 177.0 MB

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'
trying URL 'https://datahub.assets.cbioportal.org/skcm_tcga_pub_2015.tar.gz'
Content type 'application/x-tar' length 82325817 bytes (78.5 MB)
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downloaded 78.5 MB

trying URL 'https://datahub.assets.cbioportal.org/aml_target_gdc.tar.gz'
Content type 'application/x-tar' length 1087601896 bytes (1037.2 MB)
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downloaded 1037.2 MB

trying URL 'https://datahub.assets.cbioportal.org/sarc_tcga_pan_can_atlas_2018.tar.gz'
Content type 'application/x-tar' length 98851051 bytes (94.3 MB)
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downloaded 94.3 MB

Error in read.table(file = file, header = header, sep = sep, quote = quote,  : 
  more columns than column names
trying URL 'https://datahub.assets.cbioportal.org/kirc_tcga.tar.gz'
Content type 'application/x-tar' length 153629154 bytes (146.5 MB)
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downloaded 146.5 MB

trying URL 'https://datahub.assets.cbioportal.org/blca_nmibc_2017.tar.gz'
Content type 'application/x-tar' length 163700 bytes (159 KB)
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downloaded 159 KB

trying URL 'https://datahub.assets.cbioportal.org/pancan_pcawg_2020.tar.gz'
Content type 'application/x-tar' length 427692970 bytes (407.9 MB)
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downloaded 407.9 MB

trying URL 'https://datahub.assets.cbioportal.org/uccc_nih_2017.tar.gz'
Content type 'application/x-tar' length 110516 bytes (107 KB)
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downloaded 107 KB

trying URL 'https://datahub.assets.cbioportal.org/sclc_clcgp.tar.gz'
Content type 'application/x-tar' length 383551 bytes (374 KB)
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downloaded 374 KB

trying URL 'https://datahub.assets.cbioportal.org/past_dkfz_heidelberg_2013.tar.gz'
Content type 'application/x-tar' length 18990 bytes (18 KB)
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downloaded 18 KB

trying URL 'https://datahub.assets.cbioportal.org/all_stjude_2016.tar.gz'
Content type 'application/x-tar' length 72089 bytes (70 KB)
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downloaded 70 KB

trying URL 'https://datahub.assets.cbioportal.org/chol_tcga.tar.gz'
Content type 'application/x-tar' length 12150308 bytes (11.6 MB)
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downloaded 11.6 MB

trying URL 'https://datahub.assets.cbioportal.org/acyc_mgh_2016.tar.gz'
Content type 'application/x-tar' length 125181 bytes (122 KB)
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downloaded 122 KB

trying URL 'https://datahub.assets.cbioportal.org/esca_tcga_gdc.tar.gz'
Content type 'application/x-tar' length 100881992 bytes (96.2 MB)
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downloaded 96.2 MB

trying URL 'https://datahub.assets.cbioportal.org/dlbc_tcga.tar.gz'
Content type 'application/x-tar' length 17803981 bytes (17.0 MB)
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downloaded 17.0 MB

trying URL 'https://datahub.assets.cbioportal.org/utuc_pdx_msk_2019.tar.gz'
Content type 'application/x-tar' length 191029 bytes (186 KB)
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downloaded 186 KB

trying URL 'https://datahub.assets.cbioportal.org/skcm_vanderbilt_mskcc_2015.tar.gz'
Content type 'application/x-tar' length 39131 bytes (38 KB)
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downloaded 38 KB

trying URL 'https://datahub.assets.cbioportal.org/prad_mich.tar.gz'
Content type 'application/x-tar' length 16019222 bytes (15.3 MB)
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downloaded 15.3 MB

trying URL 'https://datahub.assets.cbioportal.org/lgg_tcga_pan_can_atlas_2018.tar.gz'
Content type 'application/x-tar' length 191940157 bytes (183.0 MB)
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downloaded 183.0 MB

trying URL 'https://datahub.assets.cbioportal.org/coadread_mskcc.tar.gz'
Content type 'application/x-tar' length 32547 bytes (31 KB)
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trying URL 'https://datahub.assets.cbioportal.org/mbc_msk_2021.tar.gz'
Content type 'application/x-tar' length 29157 bytes (28 KB)
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downloaded 28 KB

trying URL 'https://datahub.assets.cbioportal.org/hnsc_tcga.tar.gz'
Content type 'application/x-tar' length 198078390 bytes (188.9 MB)
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downloaded 188.9 MB

trying URL 'https://datahub.assets.cbioportal.org/chol_icgc_2017.tar.gz'
Content type 'application/x-tar' length 234235 bytes (228 KB)
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downloaded 228 KB

trying URL 'https://datahub.assets.cbioportal.org/cscc_ucsf_2021.tar.gz'
Content type 'application/x-tar' length 4195218 bytes (4.0 MB)
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downloaded 4.0 MB

trying URL 'https://datahub.assets.cbioportal.org/mpnst_mskcc.tar.gz'
Content type 'application/x-tar' length 393934 bytes (384 KB)
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downloaded 384 KB

Error in validObject(.Object) : invalid class "ExperimentList" object: 
    Non-unique names provided
trying URL 'https://datahub.assets.cbioportal.org/glioma_mskcc_2019.tar.gz'
Content type 'application/x-tar' length 1037293 bytes (1012 KB)
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trying URL 'https://datahub.assets.cbioportal.org/pancan_mappyacts_2022.tar.gz'
Content type 'application/x-tar' length 67436 bytes (65 KB)
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downloaded 65 KB

trying URL 'https://datahub.assets.cbioportal.org/ccrcc_tcga_gdc.tar.gz'
Content type 'application/x-tar' length 235708547 bytes (224.8 MB)
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downloaded 224.8 MB

trying URL 'https://datahub.assets.cbioportal.org/uvm_tcga_pan_can_atlas_2018.tar.gz'
Content type 'application/x-tar' length 29476938 bytes (28.1 MB)
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downloaded 28.1 MB

trying URL 'https://datahub.assets.cbioportal.org/pcpg_tcga_pan_can_atlas_2018.tar.gz'
Content type 'application/x-tar' length 64631757 bytes (61.6 MB)
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downloaded 61.6 MB

trying URL 'https://datahub.assets.cbioportal.org/hnsc_a5consortium_2025.tar.gz'
Content type 'application/x-tar' length 36070127 bytes (34.4 MB)
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downloaded 34.4 MB

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'
trying URL 'https://datahub.assets.cbioportal.org/plmeso_msk_2024.tar.gz'
Content type 'application/x-tar' length 25250 bytes (24 KB)
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downloaded 24 KB

trying URL 'https://datahub.assets.cbioportal.org/ccle_broad_2019.tar.gz'
Content type 'application/x-tar' length 501915892 bytes (478.7 MB)
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downloaded 478.7 MB

trying URL 'https://datahub.assets.cbioportal.org/blca_msk_tcga_2020.tar.gz'
Content type 'application/x-tar' length 58209119 bytes (55.5 MB)
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downloaded 55.5 MB

trying URL 'https://datahub.assets.cbioportal.org/ov_tcga.tar.gz'
Content type 'application/x-tar' length 361640252 bytes (344.9 MB)
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downloaded 344.9 MB

trying URL 'https://datahub.assets.cbioportal.org/desm_broad_2015.tar.gz'
Content type 'application/x-tar' length 5783281 bytes (5.5 MB)
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downloaded 5.5 MB

trying URL 'https://datahub.assets.cbioportal.org/lung_smc_2016.tar.gz'
Content type 'application/x-tar' length 1958723 bytes (1.9 MB)
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downloaded 1.9 MB

trying URL 'https://datahub.assets.cbioportal.org/blca_tcga_pan_can_atlas_2018.tar.gz'
Content type 'application/x-tar' length 204289303 bytes (194.8 MB)
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downloaded 194.8 MB

trying URL 'https://datahub.assets.cbioportal.org/pcnsl_mayo_2015.tar.gz'
Content type 'application/x-tar' length 77401 bytes (75 KB)
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downloaded 75 KB

trying URL 'https://datahub.assets.cbioportal.org/rectal_msk_2019.tar.gz'
Content type 'application/x-tar' length 402212 bytes (392 KB)
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downloaded 392 KB

trying URL 'https://datahub.assets.cbioportal.org/cll_iuopa_2015.tar.gz'
Content type 'application/x-tar' length 743917 bytes (726 KB)
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downloaded 726 KB

trying URL 'https://datahub.assets.cbioportal.org/kirc_bgi.tar.gz'
Content type 'application/x-tar' length 30524 bytes (29 KB)
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downloaded 29 KB

trying URL 'https://datahub.assets.cbioportal.org/msk_ch_2023.tar.gz'
Content type 'application/x-tar' length 1665565 bytes (1.6 MB)
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downloaded 1.6 MB

trying URL 'https://datahub.assets.cbioportal.org/chol_nccs_2013.tar.gz'
Content type 'application/x-tar' length 71541 bytes (69 KB)
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downloaded 69 KB

trying URL 'https://datahub.assets.cbioportal.org/kirc_tcga_pub.tar.gz'
Content type 'application/x-tar' length 87150764 bytes (83.1 MB)
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downloaded 83.1 MB

trying URL 'https://datahub.assets.cbioportal.org/egc_msk_2017.tar.gz'
Content type 'application/x-tar' length 432114 bytes (421 KB)
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downloaded 421 KB

trying URL 'https://datahub.assets.cbioportal.org/metastatic_solid_tumors_mich_2017.tar.gz'
Content type 'application/x-tar' length 6638837 bytes (6.3 MB)
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downloaded 6.3 MB

trying URL 'https://datahub.assets.cbioportal.org/lihc_amc_prv.tar.gz'
Content type 'application/x-tar' length 7149875 bytes (6.8 MB)
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downloaded 6.8 MB

trying URL 'https://datahub.assets.cbioportal.org/prad_su2c_2015.tar.gz'
Content type 'application/x-tar' length 66817792 bytes (63.7 MB)
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downloaded 63.7 MB

trying URL 'https://datahub.assets.cbioportal.org/all_phase2_target_2018_pub.tar.gz'
Content type 'application/x-tar' length 115460515 bytes (110.1 MB)
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downloaded 110.1 MB

trying URL 'https://datahub.assets.cbioportal.org/lgg_ucsf_2014.tar.gz'
Content type 'application/x-tar' length 739630 bytes (722 KB)
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downloaded 722 KB

trying URL 'https://datahub.assets.cbioportal.org/biliary_tract_summit_2022.tar.gz'
Content type 'application/x-tar' length 25679 bytes (25 KB)
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downloaded 25 KB

trying URL 'https://datahub.assets.cbioportal.org/chol_tcga_gdc.tar.gz'
Content type 'application/x-tar' length 17030884 bytes (16.2 MB)
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downloaded 16.2 MB

trying URL 'https://datahub.assets.cbioportal.org/blca_cornell_2016.tar.gz'
Content type 'application/x-tar' length 4547068 bytes (4.3 MB)
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downloaded 4.3 MB

trying URL 'https://datahub.assets.cbioportal.org/mixed_impact_subset_2022.tar.gz'
Content type 'application/x-tar' length 97530 bytes (95 KB)
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downloaded 95 KB

trying URL 'https://datahub.assets.cbioportal.org/thpa_tcga_gdc.tar.gz'
Content type 'application/x-tar' length 208409806 bytes (198.8 MB)
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downloaded 198.8 MB

trying URL 'https://datahub.assets.cbioportal.org/hnsc_tcga_gdc.tar.gz'
Content type 'application/x-tar' length 244895860 bytes (233.6 MB)
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downloaded 233.6 MB

trying URL 'https://datahub.assets.cbioportal.org/panet_msk_erc_2023.tar.gz'
Content type 'application/x-tar' length 103569 bytes (101 KB)
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downloaded 101 KB

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/utuc_cornell_baylor_mdacc_2019.tar.gz'
Content type 'application/x-tar' length 4219830 bytes (4.0 MB)
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downloaded 4.0 MB

trying URL 'https://datahub.assets.cbioportal.org/gbm_tcga_pub.tar.gz'
Content type 'application/x-tar' length 63112016 bytes (60.2 MB)
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downloaded 60.2 MB

trying URL 'https://datahub.assets.cbioportal.org/mbl_broad_2012.tar.gz'
Content type 'application/x-tar' length 486612 bytes (475 KB)
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downloaded 475 KB

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'
trying URL 'https://datahub.assets.cbioportal.org/bladder_columbia_msk_2018.tar.gz'
Content type 'application/x-tar' length 256831 bytes (250 KB)
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downloaded 250 KB

trying URL 'https://datahub.assets.cbioportal.org/sarcoma_ucla_2024.tar.gz'
Content type 'application/x-tar' length 33068 bytes (32 KB)
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downloaded 32 KB

trying URL 'https://datahub.assets.cbioportal.org/schw_ctf_synodos_2025.tar.gz'
Content type 'application/x-tar' length 7861775 bytes (7.5 MB)
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downloaded 7.5 MB

trying URL 'https://datahub.assets.cbioportal.org/mixed_pipseq_2017.tar.gz'
Content type 'application/x-tar' length 14150218 bytes (13.5 MB)
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downloaded 13.5 MB

trying URL 'https://datahub.assets.cbioportal.org/ihch_smmu_2014.tar.gz'
Content type 'application/x-tar' length 1006942 bytes (983 KB)
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downloaded 983 KB

trying URL 'https://datahub.assets.cbioportal.org/blca_tcga_pub_2017.tar.gz'
Content type 'application/x-tar' length 208248835 bytes (198.6 MB)
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downloaded 198.6 MB

trying URL 'https://datahub.assets.cbioportal.org/brca_bccrc_xenograft_2014.tar.gz'
Content type 'application/x-tar' length 6179900 bytes (5.9 MB)
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downloaded 5.9 MB

trying URL 'https://datahub.assets.cbioportal.org/msk_impact_50k_2026.tar.gz'
Error in download.file(url = url, destfile = destfile) : 
  cannot open URL 'https://datahub.assets.cbioportal.org/msk_impact_50k_2026.tar.gz'
trying URL 'https://datahub.assets.cbioportal.org/egc_msk_2023.tar.gz'
Content type 'application/x-tar' length 1263268 bytes (1.2 MB)
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downloaded 1.2 MB

trying URL 'https://datahub.assets.cbioportal.org/utuc_mskcc_2015.tar.gz'
Content type 'application/x-tar' length 148774 bytes (145 KB)
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downloaded 145 KB

trying URL 'https://datahub.assets.cbioportal.org/ihch_msk_2021.tar.gz'
Content type 'application/x-tar' length 424675 bytes (414 KB)
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downloaded 414 KB

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'
trying URL 'https://datahub.assets.cbioportal.org/crc_orion_2024.tar.gz'
Content type 'application/x-tar' length 85619 bytes (83 KB)
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downloaded 83 KB

Error in read.table(file = file, header = header, sep = sep, quote = quote,  : 
  more columns than column names
trying URL 'https://datahub.assets.cbioportal.org/luad_broad.tar.gz'
Content type 'application/x-tar' length 9717574 bytes (9.3 MB)
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downloaded 9.3 MB

trying URL 'https://datahub.assets.cbioportal.org/mbl_dkfz_2017.tar.gz'
Content type 'application/x-tar' length 220846 bytes (215 KB)
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downloaded 215 KB

Error in read.table(file = file, header = header, sep = sep, quote = quote,  : 
  more columns than column names
trying URL 'https://datahub.assets.cbioportal.org/paad_tcga_pan_can_atlas_2018.tar.gz'
Content type 'application/x-tar' length 72083290 bytes (68.7 MB)
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downloaded 68.7 MB

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/rms_msk_2023.tar.gz'
Content type 'application/x-tar' length 28000 bytes (27 KB)
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downloaded 27 KB

trying URL 'https://datahub.assets.cbioportal.org/prostate_dkfz_2018.tar.gz'
Content type 'application/x-tar' length 51702492 bytes (49.3 MB)
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downloaded 49.3 MB

trying URL 'https://datahub.assets.cbioportal.org/gbm_iatlas_prins_2019.tar.gz'
Content type 'application/x-tar' length 8609876 bytes (8.2 MB)
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downloaded 8.2 MB

trying URL 'https://datahub.assets.cbioportal.org/blca_tcga.tar.gz'
Content type 'application/x-tar' length 138392661 bytes (132.0 MB)
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downloaded 132.0 MB

trying URL 'https://datahub.assets.cbioportal.org/prostate_pcbm_swiss_2019.tar.gz'
Content type 'application/x-tar' length 7288724 bytes (7.0 MB)
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downloaded 7.0 MB

trying URL 'https://datahub.assets.cbioportal.org/prad_cpcg_2017.tar.gz'
Content type 'application/x-tar' length 349497 bytes (341 KB)
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downloaded 341 KB

trying URL 'https://datahub.assets.cbioportal.org/wt_target_2018_pub.tar.gz'
Content type 'application/x-tar' length 68387363 bytes (65.2 MB)
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downloaded 65.2 MB

trying URL 'https://datahub.assets.cbioportal.org/cesc_tcga_gdc.tar.gz'
Content type 'application/x-tar' length 150760856 bytes (143.8 MB)
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downloaded 143.8 MB

trying URL 'https://datahub.assets.cbioportal.org/nbl_target_2018_pub.tar.gz'
Content type 'application/x-tar' length 87878790 bytes (83.8 MB)
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downloaded 83.8 MB

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'
trying URL 'https://datahub.assets.cbioportal.org/acc_tcga_pan_can_atlas_2018.tar.gz'
Content type 'application/x-tar' length 34724513 bytes (33.1 MB)
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downloaded 33.1 MB

trying URL 'https://datahub.assets.cbioportal.org/skcm_broad_dfarber.tar.gz'
Content type 'application/x-tar' length 2185748 bytes (2.1 MB)
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downloaded 2.1 MB

trying URL 'https://datahub.assets.cbioportal.org/msk_ch_ped_2021.tar.gz'
Content type 'application/x-tar' length 29467 bytes (28 KB)
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downloaded 28 KB

trying URL 'https://datahub.assets.cbioportal.org/bladder_msk_2023.tar.gz'
Content type 'application/x-tar' length 761519 bytes (743 KB)
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downloaded 743 KB

trying URL 'https://datahub.assets.cbioportal.org/prad_msk_mdanderson_2023.tar.gz'
Content type 'application/x-tar' length 11675413 bytes (11.1 MB)
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downloaded 11.1 MB

Error in read.table(file = file, header = header, sep = sep, quote = quote,  : 
  more columns than column names
trying URL 'https://datahub.assets.cbioportal.org/lcll_broad_2013.tar.gz'
Content type 'application/x-tar' length 161283 bytes (157 KB)
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downloaded 157 KB

trying URL 'https://datahub.assets.cbioportal.org/pcnsl_msk_2024.tar.gz'
Content type 'application/x-tar' length 152097 bytes (148 KB)
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downloaded 148 KB

trying URL 'https://datahub.assets.cbioportal.org/nbl_target_gdc.tar.gz'
Content type 'application/x-tar' length 75001383 bytes (71.5 MB)
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downloaded 71.5 MB

trying URL 'https://datahub.assets.cbioportal.org/cellline_ccle_broad.tar.gz'
Content type 'application/x-tar' length 174051684 bytes (166.0 MB)
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downloaded 166.0 MB

trying URL 'https://datahub.assets.cbioportal.org/breast_cptac_gdc.tar.gz'
Content type 'application/x-tar' length 60825008 bytes (58.0 MB)
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downloaded 58.0 MB

trying URL 'https://datahub.assets.cbioportal.org/ucs_tcga_pan_can_atlas_2018.tar.gz'
Content type 'application/x-tar' length 24288596 bytes (23.2 MB)
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downloaded 23.2 MB

trying URL 'https://datahub.assets.cbioportal.org/hnsc_tcga_pub.tar.gz'
Content type 'application/x-tar' length 102302780 bytes (97.6 MB)
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downloaded 97.6 MB

trying URL 'https://datahub.assets.cbioportal.org/difg_tcga_gdc.tar.gz'
Content type 'application/x-tar' length 231989509 bytes (221.2 MB)
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downloaded 221.2 MB

trying URL 'https://datahub.assets.cbioportal.org/blca_pdx_msk_2025.tar.gz'
Content type 'application/x-tar' length 1398900 bytes (1.3 MB)
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downloaded 1.3 MB

Error in TCGAutils::uniformBuilds(x[[ncbi]]) : 
  Frequency of NA values higher than the cutoff tolerance
trying URL 'https://datahub.assets.cbioportal.org/prad_eururol_2017.tar.gz'
Content type 'application/x-tar' length 87327557 bytes (83.3 MB)
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downloaded 83.3 MB

trying URL 'https://datahub.assets.cbioportal.org/pancan_pdx_uthsa_2023.tar.gz'
Content type 'application/x-tar' length 1093021 bytes (1.0 MB)
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downloaded 1.0 MB

trying URL 'https://datahub.assets.cbioportal.org/prad_tcga.tar.gz'
Content type 'application/x-tar' length 167191806 bytes (159.4 MB)
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downloaded 159.4 MB

trying URL 'https://datahub.assets.cbioportal.org/msk_spectrum_tme_2022.tar.gz'
Content type 'application/x-tar' length 1035066 bytes (1010 KB)
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downloaded 1010 KB

trying URL 'https://datahub.assets.cbioportal.org/ucec_msk_2018.tar.gz'
Content type 'application/x-tar' length 299150 bytes (292 KB)
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downloaded 292 KB

trying URL 'https://datahub.assets.cbioportal.org/blca_plasmacytoid_mskcc_2016.tar.gz'
Content type 'application/x-tar' length 63337 bytes (61 KB)
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downloaded 61 KB

trying URL 'https://datahub.assets.cbioportal.org/prad_mskcc_2014.tar.gz'
Content type 'application/x-tar' length 426403 bytes (416 KB)
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downloaded 416 KB

trying URL 'https://datahub.assets.cbioportal.org/uvm_tcga.tar.gz'
Content type 'application/x-tar' length 26265822 bytes (25.0 MB)
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downloaded 25.0 MB

trying URL 'https://datahub.assets.cbioportal.org/brca_mskcc_2019.tar.gz'
Content type 'application/x-tar' length 108290 bytes (105 KB)
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downloaded 105 KB

trying URL 'https://datahub.assets.cbioportal.org/lymphoma_cellline_msk_2020.tar.gz'
Content type 'application/x-tar' length 115395 bytes (112 KB)
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downloaded 112 KB

trying URL 'https://datahub.assets.cbioportal.org/brca_fuscc_2020.tar.gz'
Content type 'application/x-tar' length 38884 bytes (37 KB)
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downloaded 37 KB

trying URL 'https://datahub.assets.cbioportal.org/ucec_msk_2024.tar.gz'
Content type 'application/x-tar' length 126898 bytes (123 KB)
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downloaded 123 KB

trying URL 'https://datahub.assets.cbioportal.org/acc_tcga_gdc.tar.gz'
Content type 'application/x-tar' length 35476261 bytes (33.8 MB)
==================================================
downloaded 33.8 MB

trying URL 'https://datahub.assets.cbioportal.org/luad_tsp.tar.gz'
Content type 'application/x-tar' length 860631 bytes (840 KB)
==================================================
downloaded 840 KB

trying URL 'https://datahub.assets.cbioportal.org/coadread_genentech.tar.gz'
Content type 'application/x-tar' length 9028782 bytes (8.6 MB)
==================================================
downloaded 8.6 MB

trying URL 'https://datahub.assets.cbioportal.org/lung_msk_2017.tar.gz'
Content type 'application/x-tar' length 976128 bytes (953 KB)
==================================================
downloaded 953 KB

trying URL 'https://datahub.assets.cbioportal.org/bll_target_gdc.tar.gz'
Content type 'application/x-tar' length 233486906 bytes (222.7 MB)
==================================================
downloaded 222.7 MB

trying URL 'https://datahub.assets.cbioportal.org/cll_broad_2022.tar.gz'
Content type 'application/x-tar' length 143559394 bytes (136.9 MB)
==================================================
downloaded 136.9 MB

trying URL 'https://datahub.assets.cbioportal.org/alal_target_gdc.tar.gz'
Content type 'application/x-tar' length 63724411 bytes (60.8 MB)
==================================================
downloaded 60.8 MB

trying URL 'https://datahub.assets.cbioportal.org/brca_smc_2018.tar.gz'
Content type 'application/x-tar' length 17174824 bytes (16.4 MB)
==================================================
downloaded 16.4 MB

trying URL 'https://datahub.assets.cbioportal.org/crc_nigerian_2020.tar.gz'
Content type 'application/x-tar' length 131156 bytes (128 KB)
==================================================
downloaded 128 KB

trying URL 'https://datahub.assets.cbioportal.org/thym_tcga_pan_can_atlas_2018.tar.gz'
Content type 'application/x-tar' length 45328632 bytes (43.2 MB)
==================================================
downloaded 43.2 MB

trying URL 'https://datahub.assets.cbioportal.org/coad_tcga_gdc.tar.gz'
Content type 'application/x-tar' length 265790810 bytes (253.5 MB)
==================================================
downloaded 253.5 MB

trying URL 'https://datahub.assets.cbioportal.org/ov_tcga_pan_can_atlas_2018.tar.gz'
Content type 'application/x-tar' length 208995543 bytes (199.3 MB)
==================================================
downloaded 199.3 MB

Error in read.table(file = file, header = header, sep = sep, quote = quote,  : 
  more columns than column names
trying URL 'https://datahub.assets.cbioportal.org/crc_sysucc_2022.tar.gz'
Content type 'application/x-tar' length 85206029 bytes (81.3 MB)
==================================================
downloaded 81.3 MB

trying URL 'https://datahub.assets.cbioportal.org/bm_nsclc_mskcc_2023.tar.gz'
Content type 'application/x-tar' length 565029 bytes (551 KB)
==================================================
downloaded 551 KB

trying URL 'https://datahub.assets.cbioportal.org/brca_sanger.tar.gz'
Content type 'application/x-tar' length 449936 bytes (439 KB)
==================================================
downloaded 439 KB

trying URL 'https://datahub.assets.cbioportal.org/blca_dfarber_mskcc_2014.tar.gz'
Content type 'application/x-tar' length 976299 bytes (953 KB)
==================================================
downloaded 953 KB

trying URL 'https://datahub.assets.cbioportal.org/coad_cptac_2019.tar.gz'
Content type 'application/x-tar' length 66380286 bytes (63.3 MB)
==================================================
downloaded 63.3 MB

trying URL 'https://datahub.assets.cbioportal.org/mbl_sickkids_2016.tar.gz'
Content type 'application/x-tar' length 228143 bytes (222 KB)
==================================================
downloaded 222 KB

trying URL 'https://datahub.assets.cbioportal.org/lung_msk_mind_2020.tar.gz'
Content type 'application/x-tar' length 352867 bytes (344 KB)
==================================================
downloaded 344 KB

trying URL 'https://datahub.assets.cbioportal.org/ucs_tcga_gdc.tar.gz'
Content type 'application/x-tar' length 29160535 bytes (27.8 MB)
==================================================
downloaded 27.8 MB

trying URL 'https://datahub.assets.cbioportal.org/thym_tcga_gdc.tar.gz'
Content type 'application/x-tar' length 52089341 bytes (49.7 MB)
==================================================
downloaded 49.7 MB

trying URL 'https://datahub.assets.cbioportal.org/acyc_mskcc_2013.tar.gz'
Content type 'application/x-tar' length 499835 bytes (488 KB)
==================================================
downloaded 488 KB

trying URL 'https://datahub.assets.cbioportal.org/cscc_hgsc_bcm_2014.tar.gz'
Content type 'application/x-tar' length 6227320 bytes (5.9 MB)
==================================================
downloaded 5.9 MB

trying URL 'https://datahub.assets.cbioportal.org/ihch_mskcc_2020.tar.gz'
Content type 'application/x-tar' length 73028 bytes (71 KB)
==================================================
downloaded 71 KB

Error in TCGAutils::uniformBuilds(x[[ncbi]]) : 
  Frequency of NA values higher than the cutoff tolerance
trying URL 'https://datahub.assets.cbioportal.org/prad_msk_stopsack_2021.tar.gz'
Content type 'application/x-tar' length 2440596 bytes (2.3 MB)
==================================================
downloaded 2.3 MB

trying URL 'https://datahub.assets.cbioportal.org/odg_msk_2017.tar.gz'
Content type 'application/x-tar' length 37462 bytes (36 KB)
==================================================
downloaded 36 KB

trying URL 'https://datahub.assets.cbioportal.org/crc_msk_2017.tar.gz'
Content type 'application/x-tar' length 1775071 bytes (1.7 MB)
==================================================
downloaded 1.7 MB

trying URL 'https://datahub.assets.cbioportal.org/luad_tcga_pub.tar.gz'
Content type 'application/x-tar' length 114291444 bytes (109.0 MB)
==================================================
downloaded 109.0 MB

trying URL 'https://datahub.assets.cbioportal.org/breast_alpelisib_2020.tar.gz'
Content type 'application/x-tar' length 168316 bytes (164 KB)
==================================================
downloaded 164 KB

trying URL 'https://datahub.assets.cbioportal.org/hcc_msk_2024.tar.gz'
Content type 'application/x-tar' length 1342441 bytes (1.3 MB)
==================================================
downloaded 1.3 MB

trying URL 'https://datahub.assets.cbioportal.org/cllsll_icgc_2011.tar.gz'
Content type 'application/x-tar' length 56199 bytes (54 KB)
==================================================
downloaded 54 KB

trying URL 'https://datahub.assets.cbioportal.org/pcpg_tcga.tar.gz'
Content type 'application/x-tar' length 58874051 bytes (56.1 MB)
==================================================
downloaded 56.1 MB

trying URL 'https://datahub.assets.cbioportal.org/prad_p1000.tar.gz'
Content type 'application/x-tar' length 25401209 bytes (24.2 MB)
==================================================
downloaded 24.2 MB

trying URL 'https://datahub.assets.cbioportal.org/hnsc_mdanderson_2013.tar.gz'
Content type 'application/x-tar' length 190943 bytes (186 KB)
==================================================
downloaded 186 KB

trying URL 'https://datahub.assets.cbioportal.org/prad_mcspc_mskcc_2020.tar.gz'
Content type 'application/x-tar' length 553938 bytes (540 KB)
==================================================
downloaded 540 KB

trying URL 'https://datahub.assets.cbioportal.org/ilc_msk_2023.tar.gz'
Content type 'application/x-tar' length 33839 bytes (33 KB)
==================================================
downloaded 33 KB

trying URL 'https://datahub.assets.cbioportal.org/glioma_msk_2018.tar.gz'
Content type 'application/x-tar' length 207838 bytes (202 KB)
==================================================
downloaded 202 KB

trying URL 'https://datahub.assets.cbioportal.org/hnsc_jhu.tar.gz'
Content type 'application/x-tar' length 87004 bytes (84 KB)
==================================================
downloaded 84 KB

trying URL 'https://datahub.assets.cbioportal.org/nbl_broad_2013.tar.gz'
Content type 'application/x-tar' length 1365669 bytes (1.3 MB)
==================================================
downloaded 1.3 MB

trying URL 'https://datahub.assets.cbioportal.org/nhl_bcgsc_2013.tar.gz'
Content type 'application/x-tar' length 522804 bytes (510 KB)
==================================================
downloaded 510 KB

trying URL 'https://datahub.assets.cbioportal.org/normal_skin_keratinocytes_2024.tar.gz'
Content type 'application/x-tar' length 6020346 bytes (5.7 MB)
==================================================
downloaded 5.7 MB

Error in read.table(file = file, header = header, sep = sep, quote = quote,  : 
  more columns than column names
trying URL 'https://datahub.assets.cbioportal.org/luad_tcga_gdc.tar.gz'
Content type 'application/x-tar' length 281018648 bytes (268.0 MB)
==================================================
downloaded 268.0 MB

trying URL 'https://datahub.assets.cbioportal.org/lihc_tcga_pan_can_atlas_2018.tar.gz'
Content type 'application/x-tar' length 168807337 bytes (161.0 MB)
==================================================
downloaded 161.0 MB

trying URL 'https://datahub.assets.cbioportal.org/mm_broad.tar.gz'
Content type 'application/x-tar' length 2742199 bytes (2.6 MB)
==================================================
downloaded 2.6 MB

trying URL 'https://datahub.assets.cbioportal.org/gist_msk_2022.tar.gz'
Content type 'application/x-tar' length 382811 bytes (373 KB)
==================================================
downloaded 373 KB

trying URL 'https://datahub.assets.cbioportal.org/luad_mskimpact_2021.tar.gz'
Content type 'application/x-tar' length 219080 bytes (213 KB)
==================================================
downloaded 213 KB

Error in read.table(file = file, header = header, sep = sep, quote = quote,  : 
  more columns than column names
trying URL 'https://datahub.assets.cbioportal.org/ccle_broad_2025.tar.gz'
Content type 'application/x-tar' length 31416992 bytes (30.0 MB)
==================================================
downloaded 30.0 MB

trying URL 'https://datahub.assets.cbioportal.org/prad_broad.tar.gz'
Content type 'application/x-tar' length 8633911 bytes (8.2 MB)
==================================================
downloaded 8.2 MB

trying URL 'https://datahub.assets.cbioportal.org/mel_iatlas_riaz_nivolumab_2017.tar.gz'
Content type 'application/x-tar' length 38513288 bytes (36.7 MB)
==================================================
downloaded 36.7 MB

trying URL 'https://datahub.assets.cbioportal.org/cll_broad_2015.tar.gz'
Content type 'application/x-tar' length 13847835 bytes (13.2 MB)
==================================================
downloaded 13.2 MB

trying URL 'https://datahub.assets.cbioportal.org/prad_tcga_pub.tar.gz'
Content type 'application/x-tar' length 108340629 bytes (103.3 MB)
==================================================
downloaded 103.3 MB

trying URL 'https://datahub.assets.cbioportal.org/mds_tokyo_2011.tar.gz'
Content type 'application/x-tar' length 16711 bytes (16 KB)
==================================================
downloaded 16 KB

trying URL 'https://datahub.assets.cbioportal.org/brca_metabric.tar.gz'
Content type 'application/x-tar' length 510321901 bytes (486.7 MB)
==================================================
downloaded 486.7 MB

brca_metabric/data_mrna_illumina_microarray_zscores_ref_diploid_samples.txt: Write failed
brca_metabric/data_mrna_illumina_microarray.txt: Can't create 'brca_metabric/data_mrna_illumina_microarray.txt'
brca_metabric/data_clinical_patient.txt: Can't create 'brca_metabric/data_clinical_patient.txt'
brca_metabric/data_gene_panel_matrix.txt: Can't create 'brca_metabric/data_gene_panel_matrix.txt'
brca_metabric/data_methylation_promoters_rrbs.txt: Can't create 'brca_metabric/data_methylation_promoters_rrbs.txt'
brca_metabric/meta_study.txt: Can't create 'brca_metabric/meta_study.txt'
brca_metabric/data_clinical_sample.txt: Write failed
brca_metabric/data_cna.txt: Can't create 'brca_metabric/data_cna.txt'
tar: Error exit delayed from previous errors.
Error in file(con, "r") : invalid 'description' argument
trying URL 'https://datahub.assets.cbioportal.org/lung_nci_2022.tar.gz'
Content type 'application/x-tar' length 615968 bytes (601 KB)
==================================================
downloaded 601 KB

trying URL 'https://datahub.assets.cbioportal.org/brca_iatlas_anders_2022.tar.gz'
Content type 'application/x-tar' length 8955863 bytes (8.5 MB)
==================================================
downloaded 8.5 MB

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'
trying URL 'https://datahub.assets.cbioportal.org/sclc_jhu.tar.gz'
Content type 'application/x-tar' length 343735 bytes (335 KB)
==================================================
downloaded 335 KB

trying URL 'https://datahub.assets.cbioportal.org/acyc_mda_2015.tar.gz'
Content type 'application/x-tar' length 52310 bytes (51 KB)
==================================================
downloaded 51 KB

trying URL 'https://datahub.assets.cbioportal.org/scco_mskcc.tar.gz'
Content type 'application/x-tar' length 5319 bytes
==================================================
downloaded 5319 bytes

trying URL 'https://datahub.assets.cbioportal.org/mpn_cimr_2013.tar.gz'
Content type 'application/x-tar' length 104258 bytes (101 KB)
==================================================
downloaded 101 KB

trying URL 'https://datahub.assets.cbioportal.org/hnsc_broad.tar.gz'
Content type 'application/x-tar' length 3657805 bytes (3.5 MB)
==================================================
downloaded 3.5 MB

trying URL 'https://datahub.assets.cbioportal.org/nsclc_tcga_broad_2016.tar.gz'
Content type 'application/x-tar' length 236596299 bytes (225.6 MB)
==================================================
downloaded 225.6 MB

nsclc_tcga_broad_2016/data_cna.txt: Write failed
nsclc_tcga_broad_2016/data_mutations.txt: Write to restore size failed
nsclc_tcga_broad_2016/data_timeline_treatment.txt: Write to restore size failed
nsclc_tcga_broad_2016/data_gene_panel_matrix.txt: Write to restore size failed
nsclc_tcga_broad_2016/LICENSE: Write to restore size failed
nsclc_tcga_broad_2016/data_clinical_patient.txt: Write to restore size failed
nsclc_tcga_broad_2016/meta_study.txt: Write to restore size failed
nsclc_tcga_broad_2016/data_cna_hg19.seg: Write to restore size failed
nsclc_tcga_broad_2016/data_clinical_sample.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/nsclc_pd1_msk_2018.tar.gz'
Content type 'application/x-tar' length 310725 bytes (303 KB)
==================================================
downloaded 303 KB

trying URL 'https://datahub.assets.cbioportal.org/escc_ucla_2014.tar.gz'
Content type 'application/x-tar' length 740916 bytes (723 KB)
==================================================
downloaded 723 KB

escc_ucla_2014/data_mutations.txt: Write failed
escc_ucla_2014/data_gene_panel_matrix.txt: Write to restore size failed
escc_ucla_2014/LICENSE: Write to restore size failed
escc_ucla_2014/data_clinical_patient.txt: Write to restore size failed
escc_ucla_2014/meta_study.txt: Write to restore size failed
escc_ucla_2014/data_clinical_sample.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/dlbclnos_tcga_gdc.tar.gz'
Content type 'application/x-tar' length 23203886 bytes (22.1 MB)
==
downloaded 1.3 MB

Error in download.file(url = url, destfile = destfile) : 
  download from 'https://datahub.assets.cbioportal.org/dlbclnos_tcga_gdc.tar.gz' failed
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/Rtmp4LWdRF/file83f93e9afa36.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/Rtmp4LWdRF/file83f930a10f56.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/Rtmp4LWdRF/file83f91df5f00b.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/Rtmp4LWdRF/file83f97d62718a.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/Rtmp4LWdRF/file83f94a0c5b55.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/Rtmp4LWdRF/file83f971404f6d.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/Rtmp4LWdRF/file83f9351eb731.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/Rtmp4LWdRF/file83f9738d0d35.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/Rtmp4LWdRF/file83f9315e4dd7.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/Rtmp4LWdRF/file83f926487793.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/Rtmp4LWdRF/file83f95fa26787.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/Rtmp4LWdRF/file83f91f3b011e.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/Rtmp4LWdRF/file83f95ac66896.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/Rtmp4LWdRF/file83f917fc7e69.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/Rtmp4LWdRF/file83f941cf2bcc.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/Rtmp4LWdRF/file83f98447fd5.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/Rtmp4LWdRF/file83f949247d30.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/Rtmp4LWdRF/file83f97a96ffd3.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/Rtmp4LWdRF/file83f94f75b485.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/Rtmp4LWdRF/file83f9389eb084.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/Rtmp4LWdRF/file83f93a56c726.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/Rtmp4LWdRF/file83f9172cadb6.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/Rtmp4LWdRF/file83f97640939c.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/Rtmp4LWdRF/file83f999b236b.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /tmp/Rtmp4LWdRF/file83f928324aba.
Saving _problems/test_cBioDataPack-19.R
Saving _problems/test_cBioPortalData-3.R
[ FAIL 2 | WARN 252 | 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:
    Failed to open file /tmp/Rtmp4LWdRF/file83f9389eb084.
  Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
    Failed to open file /tmp/Rtmp4LWdRF/file83f93a56c726.
  Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
    Failed to open file /tmp/Rtmp4LWdRF/file83f9172cadb6.
  Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
    Failed to open file /tmp/Rtmp4LWdRF/file83f97640939c.
  Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
    Failed to open file /tmp/Rtmp4LWdRF/file83f999b236b.
  Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
    Failed to open file /tmp/Rtmp4LWdRF/file83f928324aba.
  Saving _problems/test_cBioDataPack-19.R
  Saving _problems/test_cBioPortalData-3.R
  [ FAIL 2 | WARN 252 | 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)