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### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:gypsum.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings gypsum_1.5.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/gypsum.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gypsum/DESCRIPTION’ ... OK
* this is package ‘gypsum’ version ‘1.5.0’
* 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 ‘gypsum’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
fetchMetadataDatabase 0.015      0   9.914
* 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:
  Error in `req_perform(req, path = tmp)`: Failed to perform HTTP request.
  Caused by error in `curl::curl_fetch_disk()`:
  ! Timeout was reached [artifactdb.github.io]:
  Connection timed out after 10001 milliseconds
  Backtrace:
      ▆
   1. └─gypsum::fetchMetadataSchema(cache = cache) at test-metadata.R:7:5
   2.   └─gypsum:::download_and_rename_file(url, cache.path)
   3.     └─httr2::req_perform(req, path = tmp)
   4.       └─httr2:::handle_resp(req, resp, error_call = error_call)
   5.         └─rlang::cnd_signal(resp)
  
  [ FAIL 1 | WARN 0 | SKIP 13 | PASS 248 ]
  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-3.22-bioc/meat/gypsum.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL gypsum
###
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* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘gypsum’ ...
** this is package ‘gypsum’ version ‘1.5.0’
** 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 (gypsum)

R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 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(gypsum)
> test_check("gypsum")
[ FAIL 1 | WARN 0 | SKIP 13 | PASS 248 ]

══ Skipped tests (13) ══════════════════════════════════════════════════════════
• is.na(gh_token) is TRUE (13): 'test-accessToken.R:5:5', 'test-latest.R:5:5',
  'test-permissions.R:5:5', 'test-probation.R:5:5', 'test-probation.R:28:5',
  'test-quota.R:5:5', 'test-quota.R:23:5', 'test-remove.R:5:5',
  'test-unlockProject.R:5:5', 'test-upload.R:5:5', 'test-upload.R:55:5',
  'test-upload.R:89:5', 'test-upload.R:107:5'

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-metadata.R:7:5'): fetchMetadataSchema works as expected ────────
<httr2_failure/httr2_error/rlang_error/error/condition>
Error in `req_perform(req, path = tmp)`: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_disk()`:
! Timeout was reached [artifactdb.github.io]:
Connection timed out after 10001 milliseconds
Backtrace:
    ▆
 1. └─gypsum::fetchMetadataSchema(cache = cache) at test-metadata.R:7:5
 2.   └─gypsum:::download_and_rename_file(url, cache.path)
 3.     └─httr2::req_perform(req, path = tmp)
 4.       └─httr2:::handle_resp(req, resp, error_call = error_call)
 5.         └─rlang::cnd_signal(resp)

[ FAIL 1 | WARN 0 | SKIP 13 | PASS 248 ]
Error: Test failures
Execution halted