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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_1.30.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/TCGAutils.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TCGAutils/DESCRIPTION’ ... OK
* this is package ‘TCGAutils’ version ‘1.30.0’
* 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 ... ERROR
Running examples in ‘TCGAutils-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: makeGRangesListFromCopyNumber
> ### Title: Make a GRangesList from TCGA Copy Number data
> ### Aliases: makeGRangesListFromCopyNumber
> 
> ### ** Examples
> 
> library(GenomicDataCommons)

Attaching package: ‘GenomicDataCommons’

The following object is masked from ‘package:stats’:

    filter

> 
> manif <- files() |>
+     filter(~ cases.project.project_id == "TCGA-COAD" &
+         data_type == "Copy Number Segment") |>
+     manifest(size = 1)
> 
> fname <- gdcdata(manif$id)
> 
> barcode <- UUIDtoBarcode(names(fname), from_type = "file_id")
> barcode <- barcode[["associated_entities.entity_submitter_id"]]
> 
> cndata <- read.delim(fname[[1L]], nrows = 10L)
> 
> cngrl <- makeGRangesListFromCopyNumber(cndata, split.field = "GDC_Aliquot",
+     keep.extra.columns = TRUE)
Error in makeGRangesListFromDataFrame(df = df, split.field = split.field,  : 
  'split.field' is not in 'names(df)'
Calls: makeGRangesListFromCopyNumber -> makeGRangesListFromDataFrame
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
TCGAprimaryTumors       5.418  0.305   6.551
imputeAssay             4.425  0.269   5.276
curatedTCGAData-helpers 4.371  0.309   5.193
ID-translation          0.704  0.020   9.301
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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-3.22-bioc/meat/TCGAutils.Rcheck/00check.log’
for details.