##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:CuratedAtlasQueryR.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings CuratedAtlasQueryR_1.9.0.tar.gz
###
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##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/CuratedAtlasQueryR.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 ‘CuratedAtlasQueryR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CuratedAtlasQueryR’ version ‘1.9.0’
* 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 ‘CuratedAtlasQueryR’ 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘spelling.R’
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
   10. │     └─CuratedAtlasQueryR (local) .f(.x[[i]], ...)
   11. │       └─httr::HEAD(url)
   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(...)
   17. │ └─base::stop(e)
   18. └─purrr (local) `<fn>`(`<crl_rr__>`)
   19.   └─cli::cli_abort(...)
   20.     └─rlang::abort(...)
  
  [ FAIL 3 | WARN 2 | SKIP 0 | PASS 19 ]
  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 ‘Introduction.Rmd’ using rmarkdown
Could not fetch https://img.shields.io/badge/lifecycle-maturing-blue.svg
HttpExceptionRequest Request {
  host                 = "img.shields.io"
  port                 = 443
  secure               = True
  requestHeaders       = []
  path                 = "/badge/lifecycle-maturing-blue.svg"
  queryString          = ""
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
}
 ConnectionTimeout
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
pandoc document conversion failed with error 61
--- failed re-building ‘Introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘Introduction.Rmd’

Error: Vignette re-building failed.
Execution halted

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

Status: 2 ERRORs
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/CuratedAtlasQueryR.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL CuratedAtlasQueryR
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘CuratedAtlasQueryR’ ...
** this is package ‘CuratedAtlasQueryR’ version ‘1.9.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (CuratedAtlasQueryR)

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.

> if(requireNamespace('spelling', quietly = TRUE))
+   spelling::spell_check_test(
+     # We hit https://github.com/ropensci/spelling/issues/62 if the 
+     # vignettes are checked
+     vignettes = FALSE,
+     error = FALSE,
+     skip_on_cran = TRUE
+  )
All Done!
> 
> proc.time()
   user  system elapsed 
  0.143   0.036   0.167 

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(CuratedAtlasQueryR)
> 
> test_check("CuratedAtlasQueryR")
[ FAIL 3 | WARN 2 | SKIP 0 | PASS 19 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-query.R:33:5'): sync_assay_files() syncs appropriate files ─────
<purrr_error_indexed/rlang_error/error/condition>
Error in `map_dbl(urls, function(url) {
    as.integer(HEAD(url)$headers$`content-length`)/10^9
})`: ℹ In index: 1.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [object-store.rc.nectar.org.au]:
SSL connection timeout
Backtrace:
     ▆
  1. ├─CuratedAtlasQueryR:::sync_assay_files(...) at test-query.R:33:5
  2. │ └─CuratedAtlasQueryR:::report_file_sizes(files$full_url)
  3. │   └─CuratedAtlasQueryR:::url_file_size(urls)
  4. │     └─purrr::map_dbl(...)
  5. │       └─purrr:::map_("double", .x, .f, ..., .progress = .progress)
  6. │         ├─purrr:::with_indexed_errors(...)
  7. │         │ └─base::withCallingHandlers(...)
  8. │         ├─purrr:::call_with_cleanup(...)
  9. │         └─CuratedAtlasQueryR (local) .f(.x[[i]], ...)
 10. │           └─httr::HEAD(url)
 11. │             └─httr:::request_perform(req, hu$handle$handle)
 12. │               ├─httr:::request_fetch(req$output, req$url, handle)
 13. │               └─httr:::request_fetch.write_memory(req$output, req$url, handle)
 14. │                 └─curl::curl_fetch_memory(url, handle = handle)
 15. ├─curl:::raise_libcurl_error(...)
 16. │ └─base::stop(e)
 17. └─purrr (local) `<fn>`(`<crl_rr__>`)
 18.   └─cli::cli_abort(...)
 19.     └─rlang::abort(...)
── Error ('test-query.R:57:5'): get_SingleCellExperiment() syncs appropriate files ──
<purrr_error_indexed/rlang_error/error/condition>
Error in `map_dbl(urls, function(url) {
    as.integer(HEAD(url)$headers$`content-length`)/10^9
})`: ℹ In index: 1.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [object-store.rc.nectar.org.au]:
SSL connection timeout
Backtrace:
     ▆
  1. ├─CuratedAtlasQueryR::get_SingleCellExperiment(meta, cache_directory = temp) at test-query.R:57:5
  2. │ └─CuratedAtlasQueryR::get_single_cell_experiment(...)
  3. │   └─CuratedAtlasQueryR:::sync_assay_files(...)
  4. │     └─CuratedAtlasQueryR:::report_file_sizes(files$full_url)
  5. │       └─CuratedAtlasQueryR:::url_file_size(urls)
  6. │         └─purrr::map_dbl(...)
  7. │           └─purrr:::map_("double", .x, .f, ..., .progress = .progress)
  8. │             ├─purrr:::with_indexed_errors(...)
  9. │             │ └─base::withCallingHandlers(...)
 10. │             ├─purrr:::call_with_cleanup(...)
 11. │             └─CuratedAtlasQueryR (local) .f(.x[[i]], ...)
 12. │               └─httr::HEAD(url)
 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(...)
 18. │ └─base::stop(e)
 19. └─purrr (local) `<fn>`(`<crl_rr__>`)
 20.   └─cli::cli_abort(...)
 21.     └─rlang::abort(...)
── Error ('test-utils.R:2:5'): url_file_size() returns the correct sizes ───────
<purrr_error_indexed/rlang_error/error/condition>
Error in `map_dbl(urls, function(url) {
    as.integer(HEAD(url)$headers$`content-length`)/10^9
})`: ℹ In index: 1.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [ftp.ncbi.nlm.nih.gov]:
SSL connection timeout
Backtrace:
     ▆
  1. ├─testthat::expect_equal(...) at test-utils.R:2:5
  2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
  3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
  4. ├─CuratedAtlasQueryR:::url_file_size(...)
  5. │ └─purrr::map_dbl(...)
  6. │   └─purrr:::map_("double", .x, .f, ..., .progress = .progress)
  7. │     ├─purrr:::with_indexed_errors(...)
  8. │     │ └─base::withCallingHandlers(...)
  9. │     ├─purrr:::call_with_cleanup(...)
 10. │     └─CuratedAtlasQueryR (local) .f(.x[[i]], ...)
 11. │       └─httr::HEAD(url)
 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(...)
 17. │ └─base::stop(e)
 18. └─purrr (local) `<fn>`(`<crl_rr__>`)
 19.   └─cli::cli_abort(...)
 20.     └─rlang::abort(...)

[ FAIL 3 | WARN 2 | SKIP 0 | PASS 19 ]
Error: Test failures
Execution halted