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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_1.27.6.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/TCGAutils.Rcheck’
* using R Under development (unstable) (2025-03-02 r87868)
* 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 option ‘--no-vignettes’
* checking for file ‘TCGAutils/DESCRIPTION’ ... OK
* this is package ‘TCGAutils’ version ‘1.27.6’
* 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: ID-translation
> ### Title: Translate study identifiers from barcode to UUID and vice versa
> ### Aliases: ID-translation UUIDtoBarcode UUIDtoUUID barcodeToUUID
> ###   filenameToBarcode UUIDhistory
> 
> ### ** Examples
> 
> ## Translate UUIDs >> TCGA Barcode
> 
> uuids <- c("b4bce3ff-7fdc-4849-880b-56f2b348ceac",
+ "5ca9fa79-53bc-4e91-82cd-5715038ee23e",
+ "b7c3e5ad-4ffc-4fc4-acbf-1dfcbd2e5382")
> 
> UUIDtoBarcode(uuids, from_type = "file_id")
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Failure when receiving data from the peer [api.gdc.cancer.gov]: OpenSSL SSL_read: SSL_ERROR_SYSCALL, errno 0
Calls: UUIDtoBarcode ... request_fetch.write_memory -> <Anonymous> -> raise_libcurl_error
Execution halted
* 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:
  Backtrace:
      ▆
   1. ├─base::vapply(...) at test-ID-translation.R:130:5
   2. │ └─TCGAutils (local) FUN(X[[i]], ...)
   3. │   └─TCGAutils::UUIDhistory(x) at test-ID-translation.R:133:13
   4. │     └─httr::GET(qurl)
   5. │       └─httr:::request_perform(req, hu$handle$handle)
   6. │         ├─httr:::request_fetch(req$output, req$url, handle)
   7. │         └─httr:::request_fetch.write_memory(req$output, req$url, handle)
   8. │           └─curl::curl_fetch_memory(url, handle = handle)
   9. └─curl:::raise_libcurl_error(...)
  
  [ FAIL 4 | WARN 0 | SKIP 0 | PASS 33 ]
  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: 2 ERRORs, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/TCGAutils.Rcheck/00check.log’
for details.