Back to Multiple platform build/check report for BioC 3.21:   simplified   long
ABCDEF[G]HIJKLMNOPQRSTUVWXYZ

This page was generated on 2025-03-19 11:44 -0400 (Wed, 19 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences" 4742
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" 4545
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4576
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4528
kunpeng2Linux (openEuler 24.03 LTS)aarch64R 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 780/2313HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gCrisprTools 2.13.0  (landing page)
Russell Bainer
Snapshot Date: 2025-03-18 13:40 -0400 (Tue, 18 Mar 2025)
git_url: https://git.bioconductor.org/packages/gCrisprTools
git_branch: devel
git_last_commit: 1bb7f87
git_last_commit_date: 2024-10-29 10:13:45 -0400 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    ERROR  skipped
palomino7Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
lconwaymacOS 12.7.1 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson3macOS 13.7.1 Ventura / arm64  OK    ERROR  skippedskipped
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    ERROR  skipped


BUILD results for gCrisprTools on lconway

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.

raw results


Summary

Package: gCrisprTools
Version: 2.13.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data gCrisprTools
StartedAt: 2025-03-18 16:53:22 -0400 (Tue, 18 Mar 2025)
EndedAt: 2025-03-18 16:56:57 -0400 (Tue, 18 Mar 2025)
EllapsedTime: 215.3 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data gCrisprTools
###
##############################################################################
##############################################################################


* checking for file ‘gCrisprTools/DESCRIPTION’ ... OK
* preparing ‘gCrisprTools’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘Contrast_Comparisons.Rmd’ using knitr
2025-03-18 16:54:09.261 R[1079:435139383] XType: com.apple.fonts is not accessible.
2025-03-18 16:54:09.261 R[1079:435139383] XType: XTFontStaticRegistry is enabled.

Quitting from Contrast_Comparisons.Rmd:211-228 [unnamed-chunk-11]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `GeneSetDb.data.frame()`:
! is.data.frame(x) && nrow(x) > 0 is not TRUE
---
Backtrace:
    ▆
 1. └─sparrow::getMSigGeneSetDb(...)
 2.   ├─sparrow::GeneSetDb(ret)
 3.   └─sparrow:::GeneSetDb.data.frame(ret)
 4.     └─base::stopifnot(is.data.frame(x) && nrow(x) > 0)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'Contrast_Comparisons.Rmd' failed with diagnostics:
is.data.frame(x) && nrow(x) > 0 is not TRUE
--- 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 `GeneSetDb.data.frame()`:
! is.data.frame(x) && nrow(x) > 0 is not TRUE
---
Backtrace:
    ▆
 1. └─sparrow::getMSigGeneSetDb(...)
 2.   ├─sparrow::GeneSetDb(ret)
 3.   └─sparrow:::GeneSetDb.data.frame(ret)
 4.     └─base::stopifnot(is.data.frame(x) && nrow(x) > 0)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'Crispr_example_workflow.Rmd' failed with diagnostics:
is.data.frame(x) && nrow(x) > 0 is not TRUE
--- 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