| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-11-13 11:32 -0500 (Thu, 13 Nov 2025).
| 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 | ||||
| Package 2121/2325 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SuperCellCyto 1.1.0 (landing page) Givanna Putri
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | ERROR | skipped | skipped | ||||||||
|
To the developers/maintainers of the SuperCellCyto package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SuperCellCyto.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. |
| Package: SuperCellCyto |
| Version: 1.1.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data SuperCellCyto |
| StartedAt: 2025-11-12 17:19:56 -0500 (Wed, 12 Nov 2025) |
| EndedAt: 2025-11-12 17:20:11 -0500 (Wed, 12 Nov 2025) |
| EllapsedTime: 15.2 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data SuperCellCyto
###
##############################################################################
##############################################################################
* checking for file ‘SuperCellCyto/DESCRIPTION’ ... OK
* preparing ‘SuperCellCyto’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘SuperCellCyto.Rmd’ using rmarkdown
Quitting from SuperCellCyto.Rmd:283-292 [run_supercellcyto_parallel]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `reducer$value.cache[[as.character(idx)]] <- values`:
! wrong args for environment subassignment
---
Backtrace:
▆
1. └─SuperCellCyto::runSuperCellCyto(...)
2. └─SuperCellCyto:::.run_supercells_bplapply(...)
3. ├─BiocParallel::bplapply(...)
4. └─BiocParallel::bplapply(...)
5. └─BiocParallel:::.bpinit(...)
6. ├─BiocParallel::bploop(...)
7. └─BiocParallel:::bploop.lapply(...)
8. └─BiocParallel:::.bploop_impl(...)
9. └─BiocParallel:::.collect_result(manager, reducer, progress, BPPARAM)
10. ├─BiocParallel:::.reducer_add(reducer, njob, value)
11. └─BiocParallel:::.reducer_add(reducer, njob, value)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'SuperCellCyto.Rmd' failed with diagnostics:
wrong args for environment subassignment
--- failed re-building ‘SuperCellCyto.Rmd’
--- re-building ‘how_to_prepare_data.Rmd’ using rmarkdown
Warning in dir.create(biocDir) :
cannot create dir '/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpY46Tin/BiocStyle', reason 'No such file or directory'
Warning in file(con, "w") :
cannot open file '/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpY46Tin/BiocStyle/template.html': No such file or directory
Error: processing vignette 'how_to_prepare_data.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘how_to_prepare_data.Rmd’
--- re-building ‘interoperability_with_sce.Rmd’ using rmarkdown
Warning in dir.create(biocDir) :
cannot create dir '/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpY46Tin/BiocStyle', reason 'No such file or directory'
Warning in file(con, "w") :
cannot open file '/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpY46Tin/BiocStyle/template.html': No such file or directory
Error: processing vignette 'interoperability_with_sce.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘interoperability_with_sce.Rmd’
--- re-building ‘interoperability_with_seurat.Rmd’ using rmarkdown
Warning in dir.create(biocDir) :
cannot create dir '/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpY46Tin/BiocStyle', reason 'No such file or directory'
Warning in file(con, "w") :
cannot open file '/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpY46Tin/BiocStyle/template.html': No such file or directory
Error: processing vignette 'interoperability_with_seurat.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘interoperability_with_seurat.Rmd’
--- re-building ‘using_supercellcyto_for_stratified_summarising.Rmd’ using rmarkdown
Warning in dir.create(biocDir) :
cannot create dir '/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpY46Tin/BiocStyle', reason 'No such file or directory'
Warning in file(con, "w") :
cannot open file '/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpY46Tin/BiocStyle/template.html': No such file or directory
Error: processing vignette 'using_supercellcyto_for_stratified_summarising.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘using_supercellcyto_for_stratified_summarising.Rmd’
SUMMARY: processing the following files failed:
‘SuperCellCyto.Rmd’ ‘how_to_prepare_data.Rmd’
‘interoperability_with_sce.Rmd’ ‘interoperability_with_seurat.Rmd’
‘using_supercellcyto_for_stratified_summarising.Rmd’
Error: Vignette re-building failed.
Execution halted