Build/check report for BioC 3.22 - BUILD results for hca on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4637
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

BUILD results for hca on kjohnson3

To the developers/maintainers of the hca package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/hca.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: hca

Version: 1.17.0

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data hca

StartedAt: 2025-10-26 16:47:56 -0400 (Sun, 26 Oct 2025)

EndedAt: 2025-10-26 16:53:58 -0400 (Sun, 26 Oct 2025)

EllapsedTime: 361.7 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data hca
###
##############################################################################
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* checking for file ‘hca/DESCRIPTION’ ... OK
* preparing ‘hca’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘hca_manifest_vignette.Rmd’ using rmarkdown

Quitting from hca_manifest_vignette.Rmd:70-76 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `open.connection()`:
! cannot open the connection to 'https://service.azul.data.humancellatlas.org/openapi.json'
---
Backtrace:
     ▆
  1. └─hca::filters(...)
  2.   └─hca:::.filters_validate(filters_list)
  3.     └─hca::facet_options()
  4.       └─hca:::.hca_openapi()
  5.         └─jsonlite::read_json(api)
  6.           └─jsonlite::parse_json(...)
  7.             └─jsonlite:::parse_and_simplify(...)
  8.               └─jsonlite:::parseJSON(txt, bigint_as_char)
  9.                 └─jsonlite:::parse_con(txt, bigint_as_char)
 10.                   ├─base::open(con, "rb")
 11.                   └─base::open.connection(con, "rb")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'hca_manifest_vignette.Rmd' failed with diagnostics:
cannot open the connection to 'https://service.azul.data.humancellatlas.org/openapi.json'
--- failed 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 `open.connection()`:
! cannot open the connection to 'https://service.azul.data.humancellatlas.org/openapi.json'
---
Backtrace:
     ▆
  1. └─hca::projects(size = 200)
  2.   └─hca::filters()
  3.     └─hca:::.filters_validate(filters_list)
  4.       └─hca::facet_options()
  5.         └─hca:::.hca_openapi()
  6.           └─jsonlite::read_json(api)
  7.             └─jsonlite::parse_json(...)
  8.               └─jsonlite:::parse_and_simplify(...)
  9.                 └─jsonlite:::parseJSON(txt, bigint_as_char)
 10.                   └─jsonlite:::parse_con(txt, bigint_as_char)
 11.                     ├─base::open(con, "rb")
 12.                     └─base::open.connection(con, "rb")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'hca_vignette.Rmd' failed with diagnostics:
cannot open the connection to 'https://service.azul.data.humancellatlas.org/openapi.json'
--- failed re-building ‘hca_vignette.Rmd’

SUMMARY: processing the following files failed:
  ‘hca_manifest_vignette.Rmd’ ‘hca_vignette.Rmd’

Error: Vignette re-building failed.
Execution halted