Russell Bainer
| Snapshot Date: 2026-01-21 13:40 -0500 (Wed, 21 Jan 2026) |
| git_url: https://git.bioconductor.org/packages/gCrisprTools |
| git_branch: devel |
| git_last_commit: d372d36 |
| git_last_commit_date: 2025-10-29 10:34:14 -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 798/2345 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| gCrisprTools 2.17.0 (landing page) Russell Bainer
| 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 gCrisprTools package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/gCrisprTools.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: gCrisprTools |
| Version: 2.17.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data gCrisprTools |
| StartedAt: 2026-01-21 16:23:38 -0500 (Wed, 21 Jan 2026) |
| EndedAt: 2026-01-21 16:25:29 -0500 (Wed, 21 Jan 2026) |
| EllapsedTime: 111.2 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 gCrisprTools
###
##############################################################################
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* checking for file ‘gCrisprTools/DESCRIPTION’ ... OK
* preparing ‘gCrisprTools’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘Contrast_Comparisons.Rmd’ using knitr
2026-01-21 16:23:57.840 R[14948:797562398] XType: Using static font registry.
Quitting from Contrast_Comparisons.Rmd:211-228 [unnamed-chunk-11]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 29/29 in VECTOR_ELT
---
Backtrace:
▆
1. ├─methods::show(sparrowList)
2. └─methods::show(sparrowList)
3. └─methods::showDefault(object)
4. ├─base::print(object, useS4 = FALSE)
5. └─base::print.default(object, useS4 = FALSE)
6. ├─methods (local) `<stndrdGn>`(`<SprrwRsl>`)
7. └─sparrow (local) `<stndrdGn>`(`<SprrwRsl>`)
8. ├─base::as.data.frame(tabulateResults(object, max.p = def.fdr))
9. └─sparrow::tabulateResults(object, max.p = def.fdr)
10. └─base::lapply(...)
11. └─sparrow (local) FUN(X[[i]], ...)
12. ├─sparrow::result(x, wut, as.dt = TRUE)
13. └─sparrow:::result.SparrowResult(x, wut, as.dt = TRUE)
14. ├─out[, `:=`(padj.by.collection, p.adjust(pval, "BH")), by = "collection"]
15. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Contrast_Comparisons.Rmd' failed with diagnostics:
attempt access index 29/29 in VECTOR_ELT
--- failed re-building ‘Contrast_Comparisons.Rmd’
--- re-building ‘Crispr_example_workflow.Rmd’ using knitr
Quitting from Crispr_example_workflow.Rmd:224-238 [unnamed-chunk-22]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 29/29 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. ├─base::print(x)
6. └─base::print.default(x)
7. ├─methods (local) `<stndrdGn>`(`<SprrwRsl>`)
8. └─sparrow (local) `<stndrdGn>`(`<SprrwRsl>`)
9. ├─base::as.data.frame(tabulateResults(object, max.p = def.fdr))
10. └─sparrow::tabulateResults(object, max.p = def.fdr)
11. └─base::lapply(...)
12. └─sparrow (local) FUN(X[[i]], ...)
13. ├─sparrow::result(x, wut, as.dt = TRUE)
14. └─sparrow:::result.SparrowResult(x, wut, as.dt = TRUE)
15. ├─out[, `:=`(padj.by.collection, p.adjust(pval, "BH")), by = "collection"]
16. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Crispr_example_workflow.Rmd' failed with diagnostics:
attempt access index 29/29 in VECTOR_ELT
--- failed re-building ‘Crispr_example_workflow.Rmd’
--- re-building ‘gCrisprTools_Vignette.Rmd’ using knitr
--- finished re-building ‘gCrisprTools_Vignette.Rmd’
SUMMARY: processing the following files failed:
‘Contrast_Comparisons.Rmd’ ‘Crispr_example_workflow.Rmd’
Error: Vignette re-building failed.
Execution halted