Multiple platform build/check report for BioC 3.21 - BUILD results for CATALYST on kunpeng2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4827
merida1	macOS 12.7.5 Monterey	x86_64	4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"	4608
kjohnson1	macOS 13.6.6 Ventura	arm64	4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"	4549
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4580
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 CATALYST on kunpeng2

To the developers/maintainers of the CATALYST package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CATALYST.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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results

Summary

Package: CATALYST

Version: 1.32.0

Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data CATALYST

StartedAt: 2025-09-25 23:27:13 -0000 (Thu, 25 Sep 2025)

EndedAt: 2025-09-25 23:31:23 -0000 (Thu, 25 Sep 2025)

EllapsedTime: 250.1 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data CATALYST
###
##############################################################################
##############################################################################


* checking for file ‘CATALYST/DESCRIPTION’ ... OK
* preparing ‘CATALYST’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘differential.Rmd’ using rmarkdown
--- finished re-building ‘differential.Rmd’

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

Quitting from preprocessing.Rmd:515-545 [sce2fcs-gating]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `NextMethod()`:
! wrong value for .Method
---
Backtrace:
     ▆
  1. └─tools::buildVignettes(dir = ".", tangle = TRUE)
  2.   ├─base::tryCatch(...)
  3.   │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  4.   │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
  5.   │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
  6.   └─engine$weave(file, quiet = quiet, encoding = enc)
  7.     └─knitr:::vweave_rmarkdown(...)
  8.       └─rmarkdown::render(...)
  9.         └─knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
 10.           └─knitr:::process_file(text, output)
 11.             ├─xfun:::handle_error(...)
 12.             ├─base::withCallingHandlers(...)
 13.             └─knitr:::process_group(group)
 14.               └─knitr:::call_block(x)
 15.                 └─knitr:::block_exec(params)
 16.                   └─knitr:::eng_r(options)
 17.                     ├─knitr:::in_input_dir(...)
 18.                     │ └─knitr:::in_dir(input_dir(), expr)
 19.                     └─knitr (local) evaluate(...)
 20.                       └─evaluate::evaluate(...)
 21.                         ├─base::withRestarts(...)
 22.                         │ └─base (local) withRestartList(expr, restarts)
 23.                         │   ├─base (local) withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
 24.                         │   │ └─base (local) doWithOneRestart(return(expr), restart)
 25.                         │   └─base (local) withRestartList(expr, restarts[-nr])
 26.                         │     └─base (local) withOneRestart(expr, restarts[[1L]])
 27.                         │       └─base (local) doWithOneRestart(return(expr), restart)
 28.                         ├─evaluate:::with_handlers(...)
 29.                         │ ├─base::eval(call)
 30.                         │ │ └─base::eval(call)
 31.                         │ └─base::withCallingHandlers(...)
 32.                         └─watcher$print_value(ev$value, ev$visible, envir)
 33.                           ├─base::withVisible(handle_value(handler, value, visible, envir))
 34.                           └─evaluate:::handle_value(handler, value, visible, envir)
 35.                             └─handler$value(value, visible)
 36.                               └─knitr (local) fun(x, options = options)
 37.                                 ├─base::withVisible(knit_print(x, ...))
 38.                                 ├─knitr::knit_print(x, ...)
 39.                                 └─knitr:::knit_print.default(x, ...)
 40.                                   └─knitr::normal_print(x)
 41.                                     ├─methods::show(x)
 42.                                     └─methods::show(x)
 43.                                       ├─base::print(object)
 44.                                       └─ggcyto::print(object)
 45.                                         └─base::NextMethod()
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'preprocessing.Rmd' failed with diagnostics:
wrong value for .Method
--- failed re-building ‘preprocessing.Rmd’

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

Error: Vignette re-building failed.
Execution halted