| Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-03-19 11:45 -0400 (Wed, 19 Mar 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences" | 4742 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" | 4545 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4576 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4528 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4459 |
| 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 1867/2313 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SCArray 1.15.1 (landing page) Xiuwen Zheng
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | ERROR | skipped | skipped | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
|
To the developers/maintainers of the SCArray package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SCArray.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: SCArray |
| Version: 1.15.1 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data SCArray |
| StartedAt: 2025-03-18 18:23:41 -0400 (Tue, 18 Mar 2025) |
| EndedAt: 2025-03-18 18:25:04 -0400 (Tue, 18 Mar 2025) |
| EllapsedTime: 83.4 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
##############################################################################
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### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data SCArray
###
##############################################################################
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* checking for file ‘SCArray/DESCRIPTION’ ... OK
* preparing ‘SCArray’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘Overview.Rmd’ using rmarkdown
--- finished re-building ‘Overview.Rmd’
--- re-building ‘SCArray.Rmd’ using rmarkdown
Quitting from SCArray.Rmd:173-178 [unnamed-chunk-9]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! non-numeric argument to binary operator
---
Backtrace:
▆
1. ├─BiocSingular::runPCA(sce)
2. └─scater::runPCA(sce)
3. └─scater (local) .local(x, ...)
4. ├─scater::calculatePCA(y, ...)
5. └─scater::calculatePCA(y, ...)
6. └─scater (local) .local(x, ...)
7. └─scater:::.calculate_pca(mat, transposed = !is.null(dimred), ...)
8. └─scater:::.get_mat_for_reddim(...)
9. ├─MatrixGenerics::rowVars(DelayedArray(x), useNames = TRUE)
10. └─MatrixGenerics::rowVars(DelayedArray(x), useNames = TRUE)
11. └─SCArray:::.x_row_vars(x, na.rm, center, ...)
12. └─SCArray:::.parallel_col_reduce(...)
13. └─DelayedArray::blockReduce(...)
14. └─DelayedArray::gridReduce(...)
15. └─DelayedArray (local) FUN(viewport, init, ...)
16. └─S4Arrays::read_block(x, viewport, as.sparse = as.sparse)
17. └─S4Arrays:::.read_block(x, viewport, as.sparse = as.sparse)
18. ├─SparseArray::read_block_as_sparse(x, viewport)
19. └─SparseArray::read_block_as_sparse(x, viewport)
20. ├─SparseArray::extract_sparse_array(x, Nindex)
21. └─DelayedArray::extract_sparse_array(x, Nindex)
22. ├─SparseArray::extract_sparse_array(x@seed, index)
23. └─DelayedArray::extract_sparse_array(x@seed, index)
24. ├─SparseArray::extract_sparse_array(x@seed, index)
25. └─DelayedArray::extract_sparse_array(x@seed, index)
26. ├─SparseArray::extract_sparse_array(x@seed, seed_index)
27. └─DelayedArray::extract_sparse_array(x@seed, seed_index)
28. ├─BiocGenerics::do.call(x@OP, c(Largs, list(svt), Rargs))
29. └─base::do.call(x@OP, c(Largs, list(svt), Rargs))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'SCArray.Rmd' failed with diagnostics:
non-numeric argument to binary operator
--- failed re-building ‘SCArray.Rmd’
SUMMARY: processing the following file failed:
‘SCArray.Rmd’
Error: Vignette re-building failed.
Execution halted