Build/check report for BioC 3.24 - BUILD results for lemur on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.4 LTS)	x86_64	4.6.0 RC (2026-04-17 r89917) -- "Because it was There"	4900
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BUILD results for lemur on nebbiolo2

To the developers/maintainers of the lemur package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/lemur.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: lemur

Version: 1.11.1

Command: /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 lemur

StartedAt: 2026-05-19 18:32:00 -0400 (Tue, 19 May 2026)

EndedAt: 2026-05-19 18:32:56 -0400 (Tue, 19 May 2026)

EllapsedTime: 56.0 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 lemur
###
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* checking for file ‘lemur/DESCRIPTION’ ... OK
* preparing ‘lemur’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘Introduction.qmd’ using html
[31m

processing file: Introduction.qmd
[39m1/53                                         
2/53 [setup_alt_IS_THIS_REALLY_NEEDED]       
3/53 [initialize]                            
4/53                                         
5/53 [install1]                              
6/53                                         
7/53 [install2]                              
8/53                                         
9/53 [preparation]                           
10/53                                         
11/53 [quick_start]                           
[31mError in `check_legacy_args()`:
! Argument max.iter is unhandled. Please refer to the documentation for the valid harmony options!
Backtrace:
    ▆
 1. └─lemur::align_harmony(fit)
 2.   └─lemur:::harmony_init(...)
 3.     ├─harmony::RunHarmony(...)
 4.     └─harmony:::RunHarmony.default(...)
 5.       └─harmony:::check_legacy_args(...)
[39m[31m
Quitting from Introduction.qmd:107-116 [quick_start]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `check_legacy_args()`:
! Argument max.iter is unhandled. Please refer to the documentation for the valid harmony options!
---
Backtrace:
    ▆
 1. └─lemur::align_harmony(fit)
 2.   └─lemur:::harmony_init(...)
 3.     ├─harmony::RunHarmony(...)
 4.     └─harmony:::RunHarmony.default(...)
 5.       └─harmony:::check_legacy_args(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Execution halted
[39mError: processing vignette 'Introduction.qmd' failed with diagnostics:
! Error running quarto CLI from R.
Caused by error in `quarto_render()`:
✖ Error returned by quarto CLI.
  -----------------------------
  
  
  processing file: Introduction.qmd
  1/53
  2/53 [setup_alt_IS_THIS_REALLY_NEEDED]
  3/53 [initialize]
  4/53
  5/53 [install1]
  6/53
  7/53 [install2]
  8/53
  9/53 [preparation]
  10/53
  11/53 [quick_start]
  [31mError in `check_legacy_args()`:[39m
  ! Argument max.iter is unhandled. Please refer to the documentation for the
  valid harmony options!
  Backtrace:
  ▆
  1. └─lemur::align_harmony(fit)
  2.  └─lemur:::harmony_init(...)
  3.  ├─harmony::RunHarmony(...)
  4.  └─harmony:::RunHarmony.default(...)
  5.  └─harmony:::check_legacy_args(...)
  
  Quitting from Introduction.qmd:107-116 [quick_start]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  <error/rlang_error>
  Error in `check_legacy_args()`:
  ! Argument max.iter is unhandled. Please refer to the documentation for the
  valid harmony options!
  ---
  Backtrace:
  ▆
  1. └─lemur::align_harmony(fit)
  2.  └─lemur:::harmony_init(...)
  3.  ├─harmony::RunHarmony(...)
  4.  └─harmony:::RunHarmony.default(...)
  5.  └─harmony:::check_legacy_args(...)
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Execution halted
  
Caused by error in `processx::run()`:
! System command 'quarto' failed
--- failed re-building ‘Introduction.qmd’

SUMMARY: processing the following file failed:
  ‘Introduction.qmd’

Error: Vignette re-building failed.
Execution halted