Steve Lianoglou
| Snapshot Date: 2026-01-21 13:40 -0500 (Wed, 21 Jan 2026) |
| git_url: https://git.bioconductor.org/packages/sparrow |
| git_branch: devel |
| git_last_commit: 03b668b |
| git_last_commit_date: 2025-10-29 11:12:41 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-01-22 11:35 -0500 (Thu, 22 Jan 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences" | 4808 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences" | 4542 |
| 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 2056/2345 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| sparrow 1.17.0 (landing page) Steve Lianoglou
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
|
To the developers/maintainers of the sparrow package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/sparrow.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: sparrow |
| Version: 1.17.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data sparrow |
| StartedAt: 2026-01-21 17:42:40 -0500 (Wed, 21 Jan 2026) |
| EndedAt: 2026-01-21 17:43:32 -0500 (Wed, 21 Jan 2026) |
| EllapsedTime: 51.5 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 sparrow
###
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* checking for file ‘sparrow/DESCRIPTION’ ... OK
* preparing ‘sparrow’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘sparrow.Rmd’ using rmarkdown
Quitting from sparrow.Rmd:312-314 [mg-res]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 25/25 in VECTOR_ELT
---
Backtrace:
▆
1. ├─base::withVisible(knit_print(x, ...))
2. ├─knitr::knit_print(x, ...)
3. └─knitr:::knit_print.default(x, ...)
4. └─knitr::normal_print(x)
5. ├─methods::show(x)
6. └─methods::show(x)
7. ├─base::as.data.frame(tabulateResults(object, max.p = def.fdr))
8. └─sparrow::tabulateResults(object, max.p = def.fdr)
9. └─base::lapply(...)
10. └─sparrow (local) FUN(X[[i]], ...)
11. ├─sparrow::result(x, wut, as.dt = TRUE)
12. └─sparrow:::result.SparrowResult(x, wut, as.dt = TRUE)
13. ├─out[, `:=`(padj.by.collection, p.adjust(pval, "BH")), by = "collection"]
14. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'sparrow.Rmd' failed with diagnostics:
attempt access index 25/25 in VECTOR_ELT
--- failed re-building ‘sparrow.Rmd’
SUMMARY: processing the following file failed:
‘sparrow.Rmd’
Error: Vignette re-building failed.
Execution halted