Multiple platform build/check report for BioC 3.23 - BUILD results for lemur on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.4 LTS)	x86_64	4.6.0 RC (2026-04-17 r89917) -- "Because it was There"	4988
kjohnson3	macOS 13.7.7 Ventura	arm64	4.6.0 Patched (2026-04-24 r89963) -- "Because it was There"	4694
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 lemur on nebbiolo1

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: 1.10.0

Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data lemur

StartedAt: 2026-04-28 18:53:57 -0400 (Tue, 28 Apr 2026)

EndedAt: 2026-04-28 18:54:54 -0400 (Tue, 28 Apr 2026)

EllapsedTime: 57.0 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data lemur
###
##############################################################################
##############################################################################


* 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
[39m1/51                                        
2/51 [setup_alt_IS_THIS_REALLY_NEEDED]      
3/51 [init]                                 
4/51                                        
5/51 [install1]                             
6/51                                        
7/51 [install2]                             
8/51                                        
9/51 [preparation]                          
10/51                                        
11/51 [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[31mWarning message:
Duplicated chunk option(s) 'label' in both chunk header and pipe comments of the chunk 'init'. 

Quitting from Introduction.qmd:113-122 [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
[39m[33mWARN: Error encountered when rendering files[39m
Error: 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
  1/51
  2/51 [setup_alt_IS_THIS_REALLY_NEEDED]
  3/51 [init]
  4/51
  5/51 [install1]
  6/51
  7/51 [install2]
  8/51
  9/51 [preparation]
  10/51
  11/51 [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(...)
  [31mWarning message:[39m
  Duplicated chunk option(s) 'label' in both chunk header and pipe comments of
  the chunk 'init'.
  
  Quitting from Introduction.qmd:113-122 [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
  [33mWARN: Error encountered when rendering files[39m
  
Caused by error in `processx::run()`:
! System command 'quarto' failed
Warning: Duplicated chunk option(s) 'label' in both chunk header and pipe comments of the chunk 'init'.
--- failed re-building ‘Introduction.qmd’

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

Error: Vignette re-building failed.
Execution halted