##############################################################################
##############################################################################
###
### Running command:
###
###   /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
###
##############################################################################
##############################################################################


* 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: 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) : 
  Timeout was reached [api.gdc.cancer.gov]:
Connection timed out after 10003 milliseconds
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-3.22-bioc/meat/TCGAutils.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL TCGAutils
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘TCGAutils’ ...
** this is package ‘TCGAutils’ version ‘1.30.0’
** using staged installation
** R
** data
** 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 (TCGAutils)

R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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(TCGAutils)
> 
> test_check("TCGAutils")
[ FAIL 4 | WARN 0 | SKIP 0 | PASS 33 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-ID-translation.R:5:5'): barcodeToUUID translates correctly ─────
<curl_error_operation_timedout/curl_error/error/condition>
Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached [api.gdc.cancer.gov]:
Connection timed out after 10002 milliseconds
Backtrace:
     ▆
  1. ├─TCGAutils::barcodeToUUID(pts) at test-ID-translation.R:5:5
  2. │ ├─GenomicDataCommons::results_all(...)
  3. │ ├─base (local) pand(x = filter(cases(), as.formula(paste("~ ", endtargets, "%in% barcodes"))))
  4. │ ├─GenomicDataCommons::filter(...)
  5. │ └─GenomicDataCommons::cases()
  6. │   └─GenomicDataCommons::query("cases", ...)
  7. │     ├─base::structure(...)
  8. │     ├─GenomicDataCommons::default_fields(entity)
  9. │     └─GenomicDataCommons:::default_fields.character(entity)
 10. │       ├─base::subset(mapping(x), defaults)
 11. │       └─GenomicDataCommons::mapping(x)
 12. │         └─GenomicDataCommons:::.get_mapping_json(endpoint)
 13. │           └─GenomicDataCommons:::.gdc_get(sprintf("%s/%s", endpoint, "_mapping"))
 14. │             └─httr::GET(uri, add_headers(`X-Auth-Token` = token), ...)
 15. │               └─httr:::request_perform(req, hu$handle$handle)
 16. │                 ├─httr:::request_fetch(req$output, req$url, handle)
 17. │                 └─httr:::request_fetch.write_memory(req$output, req$url, handle)
 18. │                   └─curl::curl_fetch_memory(url, handle = handle)
 19. └─curl:::raise_libcurl_error(...)
── Error ('test-ID-translation.R:60:5'): UUIDtoBarcode translates correctly ────
<curl_error_operation_timedout/curl_error/error/condition>
Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached [api.gdc.cancer.gov]:
Connection timed out after 10003 milliseconds
Backtrace:
     ▆
  1. ├─TCGAutils::UUIDtoBarcode(file_id, from_type = "file_id") at test-ID-translation.R:60:5
  2. │ └─GenomicDataCommons::files()
  3. │   └─GenomicDataCommons::query("files", ...)
  4. │     ├─base::structure(...)
  5. │     ├─GenomicDataCommons::default_fields(entity)
  6. │     └─GenomicDataCommons:::default_fields.character(entity)
  7. │       ├─base::subset(mapping(x), defaults)
  8. │       └─GenomicDataCommons::mapping(x)
  9. │         └─GenomicDataCommons:::.get_mapping_json(endpoint)
 10. │           └─GenomicDataCommons:::.gdc_get(sprintf("%s/%s", endpoint, "_mapping"))
 11. │             └─httr::GET(uri, add_headers(`X-Auth-Token` = token), ...)
 12. │               └─httr:::request_perform(req, hu$handle$handle)
 13. │                 ├─httr:::request_fetch(req$output, req$url, handle)
 14. │                 └─httr:::request_fetch.write_memory(req$output, req$url, handle)
 15. │                   └─curl::curl_fetch_memory(url, handle = handle)
 16. └─curl:::raise_libcurl_error(...)
── Error ('test-ID-translation.R:114:5'): UUIDtoBarcode shows multiple entries per file_id ──
<curl_error_operation_timedout/curl_error/error/condition>
Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached [api.gdc.cancer.gov]:
Connection timed out after 10003 milliseconds
Backtrace:
     ▆
  1. ├─base::lapply(file_ids, UUIDtoBarcode, "file_id") at test-ID-translation.R:114:5
  2. │ └─TCGAutils (local) FUN(X[[i]], ...)
  3. │   └─GenomicDataCommons::files()
  4. │     └─GenomicDataCommons::query("files", ...)
  5. │       ├─base::structure(...)
  6. │       ├─GenomicDataCommons::default_fields(entity)
  7. │       └─GenomicDataCommons:::default_fields.character(entity)
  8. │         ├─base::subset(mapping(x), defaults)
  9. │         └─GenomicDataCommons::mapping(x)
 10. │           └─GenomicDataCommons:::.get_mapping_json(endpoint)
 11. │             └─GenomicDataCommons:::.gdc_get(sprintf("%s/%s", endpoint, "_mapping"))
 12. │               └─httr::GET(uri, add_headers(`X-Auth-Token` = token), ...)
 13. │                 └─httr:::request_perform(req, hu$handle$handle)
 14. │                   ├─httr:::request_fetch(req$output, req$url, handle)
 15. │                   └─httr:::request_fetch.write_memory(req$output, req$url, handle)
 16. │                     └─curl::curl_fetch_memory(url, handle = handle)
 17. └─curl:::raise_libcurl_error(...)
── Error ('test-ID-translation.R:133:13'): UUIDhistory correctly returns the appropriate identifiers ──
<curl_error_operation_timedout/curl_error/error/condition>
Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached [api.gdc.cancer.gov]:
Connection timed out after 10003 milliseconds
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