Build/check report for BioC 3.23 - BUILD results for blase on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
kjohnson3	macOS 13.7.7 Ventura	arm64	R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"	4013
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 blase on kjohnson3

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

Version: 1.1.0

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

StartedAt: 2025-11-12 15:53:50 -0500 (Wed, 12 Nov 2025)

EndedAt: 2025-11-12 15:54:30 -0500 (Wed, 12 Nov 2025)

EllapsedTime: 39.5 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data blase
###
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* checking for file ‘blase/DESCRIPTION’ ... OK
* preparing ‘blase’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘BLASE-for-annotating-scRNA-seq.Rmd’ using rmarkdown
2025-11-12 15:54:12.910 R[94790:1779995] XType: Using static font registry.

Quitting from BLASE-for-annotating-scRNA-seq.Rmd:102-118 [calculate_gene_peakedness]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `reducer$value.cache[[as.character(idx)]] <- values`:
! wrong args for environment subassignment
---
Backtrace:
     ▆
  1. └─blase::calculate_gene_peakedness(...)
  2.   ├─BiocParallel::bplapply(...)
  3.   └─BiocParallel::bplapply(...)
  4.     └─BiocParallel:::.bpinit(...)
  5.       ├─BiocParallel::bploop(...)
  6.       └─BiocParallel:::bploop.lapply(...)
  7.         └─BiocParallel:::.bploop_impl(...)
  8.           └─BiocParallel:::.collect_result(manager, reducer, progress, BPPARAM)
  9.             ├─BiocParallel:::.reducer_add(reducer, njob, value)
 10.             └─BiocParallel:::.reducer_add(reducer, njob, value)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'BLASE-for-annotating-scRNA-seq.Rmd' failed with diagnostics:
wrong args for environment subassignment
--- failed re-building ‘BLASE-for-annotating-scRNA-seq.Rmd’

--- re-building ‘BLASE-for-excluding-developmental-genes-from-bulk-RNA-seq.Rmd’ using rmarkdown
Warning in dir.create(biocDir) :
  cannot create dir '/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpb6QqiE/BiocStyle', reason 'No such file or directory'
Warning in file(con, "w") :
  cannot open file '/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpb6QqiE/BiocStyle/template.html': No such file or directory
Error: processing vignette 'BLASE-for-excluding-developmental-genes-from-bulk-RNA-seq.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘BLASE-for-excluding-developmental-genes-from-bulk-RNA-seq.Rmd’

--- re-building ‘assign-bulk-to-pseudotime.Rmd’ using rmarkdown
Warning in dir.create(biocDir) :
  cannot create dir '/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpb6QqiE/BiocStyle', reason 'No such file or directory'
Warning in file(con, "w") :
  cannot open file '/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpb6QqiE/BiocStyle/template.html': No such file or directory
Error: processing vignette 'assign-bulk-to-pseudotime.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘assign-bulk-to-pseudotime.Rmd’

SUMMARY: processing the following files failed:
  ‘BLASE-for-annotating-scRNA-seq.Rmd’
  ‘BLASE-for-excluding-developmental-genes-from-bulk-RNA-seq.Rmd’
  ‘assign-bulk-to-pseudotime.Rmd’

Error: Vignette re-building failed.
Execution halted