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This page was generated on 2025-10-13 11:41 -0400 (Mon, 13 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4833
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4614
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4555
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4586
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

Package 58/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AlphaMissenseR 1.4.2  (landing page)
Martin Morgan
Snapshot Date: 2025-10-09 13:40 -0400 (Thu, 09 Oct 2025)
git_url: https://git.bioconductor.org/packages/AlphaMissenseR
git_branch: RELEASE_3_21
git_last_commit: 8b54367
git_last_commit_date: 2025-07-19 16:34:52 -0400 (Sat, 19 Jul 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    ERROR  skipped
merida1macOS 12.7.5 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson1macOS 13.6.6 Ventura / arm64  OK    ERROR  skippedskipped
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    ERROR  skipped

BUILD results for AlphaMissenseR on kunpeng2

To the developers/maintainers of the AlphaMissenseR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/AlphaMissenseR.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: AlphaMissenseR
Version: 1.4.2
Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data AlphaMissenseR
StartedAt: 2025-10-09 22:32:07 -0000 (Thu, 09 Oct 2025)
EndedAt: 2025-10-09 23:07:50 -0000 (Thu, 09 Oct 2025)
EllapsedTime: 2143.5 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 AlphaMissenseR
###
##############################################################################
##############################################################################


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

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

Quitting from benchmarking.Rmd:297-330 [raincloud]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `use_defaults()`:
! unused argument (theme = list(<object>, <object>, <object>, <object>, <object>, <object>, <object>, 5.5, c(5.5, 5.5, 5.5, 5.5), NULL, NULL, <object>, <object>, NULL, <object>, NULL, <object>, <object>, <object>, <object>, NULL, <object>, NULL, <object>, NULL, <object>, <object>, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0.5, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0.75, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, <object>, NULL, NULL, NULL, NULL, NULL, 
    NULL, NULL, NULL, <object>, NULL, 2, NULL, NULL, NULL, 1.2, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0.2, NULL, <object>, NULL, <object>, NULL, "right", NULL, NULL, NULL, "center", NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, c(0, 0, 0, 0), <object>, 2, <object>, <object>, NULL, NULL, NULL, <object>, NULL, <object>, NULL, NULL, NULL, NULL, FALSE, NULL, NULL, <object>, <object>, "panel", <object>, <object>, "panel", <object>, "topleft", NULL, NULL, <object>, NULL, NULL, "on", "inside", 
    <object>, NULL, NULL, NULL, <object>, <object>, NULL, 2.75, 2.75))
---
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$value(value, visible)
 36.                               └─knitr (local) fun(x, options = options)
 37.                                 ├─base::withVisible(knit_print(x, ...))
 38.                                 ├─knitr::knit_print(x, ...)
 39.                                 └─knitr:::knit_print.default(x, ...)
 40.                                   └─knitr::normal_print(x)
 41.                                     ├─base::print(x)
 42.                                     └─ggplot2 (local) `print.ggplot2::ggplot`(x)
 43.                                       ├─ggplot2::ggplot_build(x)
 44.                                       └─ggplot2 (local) `ggplot_build.ggplot2::ggplot`(x)
 45.                                         └─plot@guides$build(npscales, plot@layers, plot@labels, data, plot@theme)
 46.                                           └─ggplot2 (local) build(..., self = self)
 47.                                             └─guides$process_layers(layers, layer_data, theme)
 48.                                               └─ggplot2 (local) process_layers(..., self = self)
 49.                                                 └─base::Map(...)
 50.                                                   └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE)
 51.                                                     └─ggplot2 (local) `<fn>`(guide = dots[[1L]][[2L]], param = dots[[2L]][[2L]])
 52.                                                       └─guide$process_layers(param, layers, data, theme)
 53.                                                         └─ggplot2 (local) process_layers(..., self = self)
 54.                                                           └─self$get_layer_key(params, layers[include], data[include], theme)
 55.                                                             └─ggplot2 (local) get_layer_key(...)
 56.                                                               └─base::Map(...)
 57.                                                                 └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE)
 58.                                                                   └─ggplot2 (local) `<fn>`(layer = dots[[1L]][[1L]], df = dots[[2L]][[1L]])
 59.                                                                     └─layer$compute_geom_2(key, single_params, theme)
 60.                                                                       └─ggplot2 (local) compute_geom_2(..., self = self)
 61.                                                                         └─self$geom$use_defaults(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'benchmarking.Rmd' failed with diagnostics:
unused argument (theme = list(<object>, <object>, <object>, <object>, <object>, <object>, <object>, 5.5, c(5.5, 5.5, 5.5, 5.5), NULL, NULL, <object>, <object>, NULL, <object>, NULL, <object>, <object>, <object>, <object>, NULL, <object>, NULL, <object>, NULL, <object>, <object>, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0.5, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0.75, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, <object>, NULL, NULL, NULL, NULL, NULL, 
    NULL, NULL, NULL, <object>, NULL, 2, NULL, NULL, NULL, 1.2, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0.2, NULL, <object>, NULL, <object>, NULL, "right", NULL, NULL, NULL, "center", NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, c(0, 0, 0, 0), <object>, 2, <object>, <object>, NULL, NULL, NULL, <object>, NULL, <object>, NULL, NULL, NULL, NULL, FALSE, NULL, NULL, <object>, <object>, "panel", <object>, <object>, "panel", <object>, "topleft", NULL, NULL, <object>, NULL, NULL, "on", "inside", 
    <object>, NULL, NULL, NULL, <object>, <object>, NULL, 2.75, 2.75))
--- failed re-building ‘benchmarking.Rmd’

--- re-building ‘clinvar.Rmd’ using rmarkdown
--- finished re-building ‘clinvar.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
--- finished re-building ‘introduction.Rmd’

--- re-building ‘issues.Rmd’ using rmarkdown
--- finished re-building ‘issues.Rmd’

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

Error: Vignette re-building failed.
Execution halted