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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:hca.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings hca_1.14.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/hca.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘hca/DESCRIPTION’ ... OK
* this is package ‘hca’ version ‘1.14.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ‘hca’ 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 whether startup messages can be suppressed ... 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 ... ERROR
Running examples in ‘hca-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: project_information
> ### Title: Project Summaries from Project IDs
> ### Aliases: project_information project_title print.project_information
> 
> ### ** Examples
> 
> project_id <- "3c9d586e-bd26-4b46-8690-3faaa18ccf38"
> project_information(project_id)
Error in project_information(project_id) : 
  did not find project_id '3c9d586e-bd26-4b46-8690-3faaa18ccf38'
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:
    'test_manifest.R:2:5'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_projects.R:13:5'): 'projects()' works for projectTitles with special characters ──
  <subscriptOutOfBoundsError/error/condition>
  Error in `test_proj$projectId[[1]]`: subscript out of bounds
  Backtrace:
      ▆
   1. └─testthat::expect_equal(test_proj$projectId[[1]], "90bd6933-40c0-48d4-8d76-778c103bf545") at test_projects.R:13:5
   2.   └─testthat::quasi_label(enquo(object), label, arg = "object")
   3.     └─rlang::eval_bare(expr, quo_get_env(quo))
  
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 159 ]
  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
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/hca.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL hca
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘hca’ ...
** using staged installation
** R
** 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 (hca)

R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 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(hca)

Attaching package: 'hca'

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

    summary

> 
> test_check("hca")
requesting manifest
waiting 1 more seconds (1 seconds total)...
waiting 1 more seconds (2 seconds total)...
waiting 1 more seconds (3 seconds total)...
waiting 4 more seconds (7 seconds total)...
[ FAIL 1 | WARN 0 | SKIP 1 | PASS 159 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• manifest() generates an internal server 500 error, 7 February, 2022 (1):
  'test_manifest.R:2:5'

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_projects.R:13:5'): 'projects()' works for projectTitles with special characters ──
<subscriptOutOfBoundsError/error/condition>
Error in `test_proj$projectId[[1]]`: subscript out of bounds
Backtrace:
    ▆
 1. └─testthat::expect_equal(test_proj$projectId[[1]], "90bd6933-40c0-48d4-8d76-778c103bf545") at test_projects.R:13:5
 2.   └─testthat::quasi_label(enquo(object), label, arg = "object")
 3.     └─rlang::eval_bare(expr, quo_get_env(quo))

[ FAIL 1 | WARN 0 | SKIP 1 | PASS 159 ]
Error: Test failures
Execution halted