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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:TCGAutils.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings TCGAutils_1.25.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/TCGAutils.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TCGAutils/DESCRIPTION’ ... OK
* this is package ‘TCGAutils’ version ‘1.25.1’
* 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 loading without being on the library search path ... 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            51.783  1.156  60.466
TCGAprimaryTumors       18.557  0.665  28.585
trimColData             16.183  0.483  25.070
oncoPrintTCGA           15.441  0.782  52.250
curatedTCGAData-helpers 15.249  0.347  23.854
imputeAssay             15.271  0.290  23.956
ID-translation           2.173  0.065  23.591
* 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:
    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)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 39 ]
  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
  ‘/home/biocbuild/bbs-3.20-bioc/meat/TCGAutils.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL TCGAutils
###
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* installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’
* installing *source* package ‘TCGAutils’ ...
** 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 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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 1 | WARN 0 | SKIP 0 | PASS 39 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-ID-translation.R:5:5'): barcodeToUUID translates correctly ─────
Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached: [api.gdc.cancer.gov] Resolving timed out after 10000 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)

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 39 ]
Error: Test failures
Execution halted