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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TCGAutils.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TCGAutils_1.33.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.24-bioc/meat/TCGAutils.Rcheck’
* using R version 4.6.0 Patched (2026-05-01 r89994)
* using platform: aarch64-apple-darwin23
* R was compiled by
    Apple clang version 17.0.0 (clang-1700.3.19.1)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-05-23 02:14:08 UTC
* using option ‘--no-vignettes’
* checking for file ‘TCGAutils/DESCRIPTION’ ... OK
* this is package ‘TCGAutils’ version ‘1.33.1’
* 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 ‘TCGAutils’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 ... NOTE
Unexported object imported by a ':::' call: ‘GenomicRanges:::.normarg_field’
  See the note in ?`:::` about the use of this operator.
* 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 ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
simplifyTCGA            15.631  0.430 104.116
TCGAprimaryTumors        5.405  0.303   6.500
oncoPrintTCGA            5.253  0.284   5.987
trimColData              5.180  0.283   6.303
curatedTCGAData-helpers  4.507  0.304   5.258
imputeAssay              4.228  0.252   5.097
ID-translation           0.648  0.013   7.446
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    5.       ├─GenomicDataCommons::results(response_all(x))
    6.       └─GenomicDataCommons::response_all(x)
    7.         ├─GenomicDataCommons::response(x = x, size = count, from = 0, ...)
    8.         └─GenomicDataCommons:::response.GDCQuery(...)
    9.           ├─jsonlite (local) response_handler(...)
   10.           ├─httr::content(...)
   11.           │ ├─base::stopifnot(is.response(x))
   12.           │ └─httr:::is.response(x)
   13.           └─GenomicDataCommons:::.gdc_post(...)
   14.             └─httr::stop_for_status(response)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 47 ]
  Error:
  ! Test failures.
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.24-bioc/meat/TCGAutils.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL TCGAutils
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’
* installing *source* package ‘TCGAutils’ ...
** this is package ‘TCGAutils’ version ‘1.33.1’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘utils::data’ by ‘BiocGenerics::data’ when loading ‘GenomeInfoDb’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘utils::data’ by ‘BiocGenerics::data’ when loading ‘GenomeInfoDb’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘utils::data’ by ‘BiocGenerics::data’ when loading ‘GenomeInfoDb’
** testing if installed package keeps a record of temporary installation path
* DONE (TCGAutils)

R version 4.6.0 Patched (2026-05-01 r89994) -- "Because it was There"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23

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(TCGAutils)
Warning message:
replacing previous import 'utils::data' by 'BiocGenerics::data' when loading 'GenomeInfoDb' 
> 
> test_check("TCGAutils")
Saving _problems/test-ID-translation-114.R
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 47 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-ID-translation.R:114:5'): UUIDtoBarcode shows multiple entries per file_id ──
<http_500/http_error/error/condition>
Error in `.gdc_post(entity_name(x), body = body, token = NULL, ...)`: Internal Server Error (HTTP 500).
Backtrace:
     ▆
  1. └─base::lapply(file_ids, UUIDtoBarcode, "file_id") at test-ID-translation.R:114:5
  2.   └─TCGAutils (local) FUN(X[[i]], ...)
  3.     ├─GenomicDataCommons::results_all(...)
  4.     └─GenomicDataCommons:::results_all.GDCQuery(...)
  5.       ├─GenomicDataCommons::results(response_all(x))
  6.       └─GenomicDataCommons::response_all(x)
  7.         ├─GenomicDataCommons::response(x = x, size = count, from = 0, ...)
  8.         └─GenomicDataCommons:::response.GDCQuery(...)
  9.           ├─jsonlite (local) response_handler(...)
 10.           ├─httr::content(...)
 11.           │ ├─base::stopifnot(is.response(x))
 12.           │ └─httr:::is.response(x)
 13.           └─GenomicDataCommons:::.gdc_post(...)
 14.             └─httr::stop_for_status(response)

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 47 ]
Error:
! Test failures.
Execution halted