##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:hca.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings hca_1.17.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/hca.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* 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 ‘hca/DESCRIPTION’ ... OK
* this is package ‘hca’ version ‘1.17.0’
* 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 ‘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 loading without being on the library search path ... 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: projects
> ### Title: HCA Project Querying
> ### Aliases: projects projects_facets projects_default_columns
> ###   projects_detail
> 
> ### ** Examples
> 
> projects(filters(), size = 100)
Error in .hca_GET(index_path) : Bad Gateway (HTTP 502).
Calls: projects -> .index_GET -> .hca_GET -> stop_for_status
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
         user system elapsed
files   9.090  0.256  36.770
bundles 1.588  0.093  14.331
hca     0.348  0.004  21.907
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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 ‘hca_manifest_vignette.Rmd’ using rmarkdown
--- finished re-building ‘hca_manifest_vignette.Rmd’

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

Quitting from hca_vignette.Rmd:67-69 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.hca_GET()`:
! Bad Gateway (HTTP 502).
---
Backtrace:
    ▆
 1. └─hca::projects(size = 200)
 2.   └─hca:::.index_GET(...)
 3.     └─hca:::.hca_GET(index_path)
 4.       └─httr::stop_for_status(response)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'hca_vignette.Rmd' failed with diagnostics:
Bad Gateway (HTTP 502).
--- failed re-building ‘hca_vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted

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

Status: 2 ERRORs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/hca.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL hca
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘hca’ ...
** this is package ‘hca’ version ‘1.17.0’
** 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 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
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(hca)

Attaching package: 'hca'

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

    summary

> 
> test_check("hca")
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 160 ]

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

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 160 ]
> 
> proc.time()
   user  system elapsed 
  4.323   0.663  21.597