##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:GenomicDataCommons.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings GenomicDataCommons_1.35.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/GenomicDataCommons.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘GenomicDataCommons/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GenomicDataCommons’ version ‘1.35.0’
* 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 ‘GenomicDataCommons’ 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 ... OK
* 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 R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘GenomicDataCommons-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: aggregations
> ### Title: aggregations
> ### Aliases: aggregations aggregations.GDCQuery aggregations.GDCResponse
> 
> ### ** Examples
> 
> # Number of each file type
> res = files() |> facet(c('type','data_type')) |> aggregations()
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached [api.gdc.cancer.gov]:
SSL connection timeout
Calls: aggregations ... 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:
    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(...)
  
  [ FAIL 9 | WARN 0 | SKIP 0 | PASS 8 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘overview.Rmd’ using rmarkdown

Quitting from overview.Rmd:109-111 [statusQS]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `curl::curl_fetch_memory()`:
! Timeout was reached [api.gdc.cancer.gov]:
SSL connection timeout
---
Backtrace:
    ▆
 1. ├─GenomicDataCommons::status()
 2. │ └─GenomicDataCommons:::.gdc_get(...)
 3. │   └─httr::GET(uri, add_headers(`X-Auth-Token` = token), ...)
 4. │     └─httr:::request_perform(req, hu$handle$handle)
 5. │       ├─httr:::request_fetch(req$output, req$url, handle)
 6. │       └─httr:::request_fetch.write_memory(req$output, req$url, handle)
 7. │         └─curl::curl_fetch_memory(url, handle = handle)
 8. └─curl:::raise_libcurl_error(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'overview.Rmd' failed with diagnostics:
Timeout was reached [api.gdc.cancer.gov]:
SSL connection timeout
--- failed re-building ‘overview.Rmd’

--- re-building ‘questions-and-answers.Rmd’ using rmarkdown

Quitting from questions-and-answers.Rmd:31-38 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `curl::curl_fetch_memory()`:
! Timeout was reached [api.gdc.cancer.gov]:
SSL connection timeout
---
Backtrace:
     ▆
  1. ├─GenomicDataCommons::filter(...)
  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: processing vignette 'questions-and-answers.Rmd' failed with diagnostics:
Timeout was reached [api.gdc.cancer.gov]:
SSL connection timeout
--- failed re-building ‘questions-and-answers.Rmd’

--- re-building ‘somatic_mutations.Rmd’ using rmarkdown

Quitting from somatic_mutations.Rmd:31-33 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `curl::curl_fetch_memory()`:
! Timeout was reached [api.gdc.cancer.gov]:
SSL connection timeout
---
Backtrace:
     ▆
  1. ├─GenomicDataCommons::grep_fields("genes", "symbol")
  2. │ ├─base::grep(...)
  3. │ │ └─base::is.factor(x)
  4. │ ├─GenomicDataCommons::available_fields(entity)
  5. │ └─GenomicDataCommons:::available_fields.character(entity)
  6. │   └─GenomicDataCommons::mapping(x)
  7. │     └─GenomicDataCommons:::.get_mapping_json(endpoint)
  8. │       └─GenomicDataCommons:::.gdc_get(sprintf("%s/%s", endpoint, "_mapping"))
  9. │         └─httr::GET(uri, add_headers(`X-Auth-Token` = token), ...)
 10. │           └─httr:::request_perform(req, hu$handle$handle)
 11. │             ├─httr:::request_fetch(req$output, req$url, handle)
 12. │             └─httr:::request_fetch.write_memory(req$output, req$url, handle)
 13. │               └─curl::curl_fetch_memory(url, handle = handle)
 14. └─curl:::raise_libcurl_error(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'somatic_mutations.Rmd' failed with diagnostics:
Timeout was reached [api.gdc.cancer.gov]:
SSL connection timeout
--- failed re-building ‘somatic_mutations.Rmd’

SUMMARY: processing the following files failed:
  ‘overview.Rmd’ ‘questions-and-answers.Rmd’ ‘somatic_mutations.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 3 ERRORs
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/GenomicDataCommons.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL GenomicDataCommons
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘GenomicDataCommons’ ...
** this is package ‘GenomicDataCommons’ version ‘1.35.0’
** using staged installation
** R
** 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 (GenomicDataCommons)

R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-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(GenomicDataCommons)

Attaching package: 'GenomicDataCommons'

The following object is masked from 'package:stats':

    filter

> 
> test_check("GenomicDataCommons")
[ FAIL 9 | WARN 0 | SKIP 0 | PASS 8 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_api.R:4:5'): status returns 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]:
SSL connection timeout
Backtrace:
    ▆
 1. ├─GenomicDataCommons::status() at test_api.R:4:5
 2. │ └─GenomicDataCommons:::.gdc_get(...)
 3. │   └─httr::GET(uri, add_headers(`X-Auth-Token` = token), ...)
 4. │     └─httr:::request_perform(req, hu$handle$handle)
 5. │       ├─httr:::request_fetch(req$output, req$url, handle)
 6. │       └─httr:::request_fetch.write_memory(req$output, req$url, handle)
 7. │         └─curl::curl_fetch_memory(url, handle = handle)
 8. └─curl:::raise_libcurl_error(...)
── Error ('test_api.R:14:5'): query ────────────────────────────────────────────
<curl_error_operation_timedout/curl_error/error/condition>
Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached [api.gdc.cancer.gov]:
SSL connection timeout
Backtrace:
     ▆
  1. ├─GenomicDataCommons::query("cases") at test_api.R:14:5
  2. │ ├─base::structure(...)
  3. │ ├─GenomicDataCommons::default_fields(entity)
  4. │ └─GenomicDataCommons:::default_fields.character(entity)
  5. │   ├─base::subset(mapping(x), defaults)
  6. │   └─GenomicDataCommons::mapping(x)
  7. │     └─GenomicDataCommons:::.get_mapping_json(endpoint)
  8. │       └─GenomicDataCommons:::.gdc_get(sprintf("%s/%s", endpoint, "_mapping"))
  9. │         └─httr::GET(uri, add_headers(`X-Auth-Token` = token), ...)
 10. │           └─httr:::request_perform(req, hu$handle$handle)
 11. │             ├─httr:::request_fetch(req$output, req$url, handle)
 12. │             └─httr:::request_fetch.write_memory(req$output, req$url, handle)
 13. │               └─curl::curl_fetch_memory(url, handle = handle)
 14. └─curl:::raise_libcurl_error(...)
── Error ('test_api.R:34:5'): cases ────────────────────────────────────────────
<curl_error_operation_timedout/curl_error/error/condition>
Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached [api.gdc.cancer.gov]:
SSL connection timeout
Backtrace:
     ▆
  1. ├─GenomicDataCommons::cases() at test_api.R:34:5
  2. │ └─GenomicDataCommons::query("cases", ...)
  3. │   ├─base::structure(...)
  4. │   ├─GenomicDataCommons::default_fields(entity)
  5. │   └─GenomicDataCommons:::default_fields.character(entity)
  6. │     ├─base::subset(mapping(x), defaults)
  7. │     └─GenomicDataCommons::mapping(x)
  8. │       └─GenomicDataCommons:::.get_mapping_json(endpoint)
  9. │         └─GenomicDataCommons:::.gdc_get(sprintf("%s/%s", endpoint, "_mapping"))
 10. │           └─httr::GET(uri, add_headers(`X-Auth-Token` = token), ...)
 11. │             └─httr:::request_perform(req, hu$handle$handle)
 12. │               ├─httr:::request_fetch(req$output, req$url, handle)
 13. │               └─httr:::request_fetch.write_memory(req$output, req$url, handle)
 14. │                 └─curl::curl_fetch_memory(url, handle = handle)
 15. └─curl:::raise_libcurl_error(...)
── Error ('test_api.R:42:5'): files ────────────────────────────────────────────
<curl_error_operation_timedout/curl_error/error/condition>
Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached [api.gdc.cancer.gov]:
SSL connection timeout
Backtrace:
     ▆
  1. ├─GenomicDataCommons::files() at test_api.R:42:5
  2. │ └─GenomicDataCommons::query("files", ...)
  3. │   ├─base::structure(...)
  4. │   ├─GenomicDataCommons::default_fields(entity)
  5. │   └─GenomicDataCommons:::default_fields.character(entity)
  6. │     ├─base::subset(mapping(x), defaults)
  7. │     └─GenomicDataCommons::mapping(x)
  8. │       └─GenomicDataCommons:::.get_mapping_json(endpoint)
  9. │         └─GenomicDataCommons:::.gdc_get(sprintf("%s/%s", endpoint, "_mapping"))
 10. │           └─httr::GET(uri, add_headers(`X-Auth-Token` = token), ...)
 11. │             └─httr:::request_perform(req, hu$handle$handle)
 12. │               ├─httr:::request_fetch(req$output, req$url, handle)
 13. │               └─httr:::request_fetch.write_memory(req$output, req$url, handle)
 14. │                 └─curl::curl_fetch_memory(url, handle = handle)
 15. └─curl:::raise_libcurl_error(...)
── Error ('test_api.R:51:5'): annotations ──────────────────────────────────────
<curl_error_operation_timedout/curl_error/error/condition>
Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached [api.gdc.cancer.gov]:
SSL connection timeout
Backtrace:
     ▆
  1. ├─GenomicDataCommons::annotations() at test_api.R:51:5
  2. │ └─GenomicDataCommons::query("annotations", ...)
  3. │   ├─base::structure(...)
  4. │   ├─GenomicDataCommons::default_fields(entity)
  5. │   └─GenomicDataCommons:::default_fields.character(entity)
  6. │     ├─base::subset(mapping(x), defaults)
  7. │     └─GenomicDataCommons::mapping(x)
  8. │       └─GenomicDataCommons:::.get_mapping_json(endpoint)
  9. │         └─GenomicDataCommons:::.gdc_get(sprintf("%s/%s", endpoint, "_mapping"))
 10. │           └─httr::GET(uri, add_headers(`X-Auth-Token` = token), ...)
 11. │             └─httr:::request_perform(req, hu$handle$handle)
 12. │               ├─httr:::request_fetch(req$output, req$url, handle)
 13. │               └─httr:::request_fetch.write_memory(req$output, req$url, handle)
 14. │                 └─curl::curl_fetch_memory(url, handle = handle)
 15. └─curl:::raise_libcurl_error(...)
── Error ('test_api.R:60:5'): mapping ──────────────────────────────────────────
<curl_error_operation_timedout/curl_error/error/condition>
Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached [api.gdc.cancer.gov]:
SSL connection timeout
Backtrace:
    ▆
 1. ├─GenomicDataCommons::mapping("files") at test_api.R:60:5
 2. │ └─GenomicDataCommons:::.get_mapping_json(endpoint)
 3. │   └─GenomicDataCommons:::.gdc_get(sprintf("%s/%s", endpoint, "_mapping"))
 4. │     └─httr::GET(uri, add_headers(`X-Auth-Token` = token), ...)
 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(...)
── Error ('test_api.R:67:5'): projects ─────────────────────────────────────────
<curl_error_operation_timedout/curl_error/error/condition>
Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached [api.gdc.cancer.gov]:
SSL connection timeout
Backtrace:
     ▆
  1. ├─GenomicDataCommons::projects() at test_api.R:67:5
  2. │ └─GenomicDataCommons::query("projects", ...)
  3. │   ├─base::structure(...)
  4. │   ├─GenomicDataCommons::default_fields(entity)
  5. │   └─GenomicDataCommons:::default_fields.character(entity)
  6. │     ├─base::subset(mapping(x), defaults)
  7. │     └─GenomicDataCommons::mapping(x)
  8. │       └─GenomicDataCommons:::.get_mapping_json(endpoint)
  9. │         └─GenomicDataCommons:::.gdc_get(sprintf("%s/%s", endpoint, "_mapping"))
 10. │           └─httr::GET(uri, add_headers(`X-Auth-Token` = token), ...)
 11. │             └─httr:::request_perform(req, hu$handle$handle)
 12. │               ├─httr:::request_fetch(req$output, req$url, handle)
 13. │               └─httr:::request_fetch.write_memory(req$output, req$url, handle)
 14. │                 └─curl::curl_fetch_memory(url, handle = handle)
 15. └─curl:::raise_libcurl_error(...)
── Error ('test_clinical.R:3:5'): clinical data is structured properly ─────────
<curl_error_operation_timedout/curl_error/error/condition>
Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached [api.gdc.cancer.gov]:
SSL connection timeout
Backtrace:
     ▆
  1. ├─GenomicDataCommons::ids(results(cases(), size = sizen)) at test_clinical.R:3:5
  2. ├─GenomicDataCommons::results(cases(), size = sizen)
  3. ├─GenomicDataCommons::cases()
  4. │ └─GenomicDataCommons::query("cases", ...)
  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_data.R:4:1'): (code run outside of `test_that()`) ──────────────
<curl_error_operation_timedout/curl_error/error/condition>
Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached [api.gdc.cancer.gov]:
SSL connection timeout
Backtrace:
     ▆
  1. ├─GenomicDataCommons::ids(results(cases(), size = 10)) at test_data.R:4:1
  2. ├─GenomicDataCommons::results(cases(), size = 10)
  3. ├─GenomicDataCommons::cases()
  4. │ └─GenomicDataCommons::query("cases", ...)
  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(...)

[ FAIL 9 | WARN 0 | SKIP 0 | PASS 8 ]
Error: Test failures
Execution halted