| Back to Multiple platform build/check report for BioC 3.23: simplified long |
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This page was generated on 2026-04-14 11:35 -0400 (Tue, 14 Apr 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 alpha (2026-04-05 r89794) | 4924 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 alpha (2026-04-08 r89818) | 4655 |
| 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 904/2394 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Glimma 2.21.0 (landing page) Shian Su
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
| See other builds for Glimma in R Universe. | ||||||||||||||
|
To the developers/maintainers of the Glimma package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Glimma.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: Glimma |
| Version: 2.21.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data Glimma |
| StartedAt: 2026-04-13 16:35:58 -0400 (Mon, 13 Apr 2026) |
| EndedAt: 2026-04-13 16:36:35 -0400 (Mon, 13 Apr 2026) |
| EllapsedTime: 37.4 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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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 Glimma
###
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* checking for file ‘Glimma/DESCRIPTION’ ... OK
* preparing ‘Glimma’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘DESeq2.Rmd’ using rmarkdown
--- finished re-building ‘DESeq2.Rmd’
--- re-building ‘limma_edger.Rmd’ using rmarkdown
--- finished re-building ‘limma_edger.Rmd’
--- re-building ‘single_cell_edger.Rmd’ using rmarkdown
Quitting from single_cell_edger.Rmd:56-64 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.local()`:
! size factors should be positive
---
Backtrace:
▆
1. ├─scuttle::logNormCounts(sce)
2. └─scuttle::logNormCounts(sce)
3. └─scuttle (local) .local(x, ...)
4. └─scuttle (local) FUN(x, size.factors = size.factors, center.size.factors = FALSE)
5. ├─base::do.call(normalizeCounts, c(list(x, ...), args))
6. ├─scuttle (local) `<stndrdGn>`(...)
7. └─scuttle (local) `<stndrdGn>`(...)
8. └─scuttle (local) .local(x, ...)
9. ├─methods::callNextMethod(x = x, size.factors = size.factors, ...)
10. │ └─base::eval(call, callEnv)
11. │ └─base::eval(call, callEnv)
12. └─scuttle (local) .nextMethod(x = x, size.factors = size.factors, ...)
13. └─scuttle (local) .local(x, ...)
14. ├─scuttle::normalizeCounts(assay(x, assay.type), ...)
15. └─scuttle::normalizeCounts(assay(x, assay.type), ...)
16. └─scuttle (local) .local(x, ...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'single_cell_edger.Rmd' failed with diagnostics:
size factors should be positive
--- failed re-building ‘single_cell_edger.Rmd’
SUMMARY: processing the following file failed:
‘single_cell_edger.Rmd’
Error: Vignette re-building failed.
Execution halted