Multiple platform build/check report for BioC 3.21 - BUILD results for sparrow on palomino7

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*

BUILD results for sparrow on palomino7

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.

raw results

Summary

Package: sparrow

Version: 1.13.9

Command: chmod a+r sparrow -R && E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data sparrow

StartedAt: 2025-03-18 22:02:42 -0400 (Tue, 18 Mar 2025)

EndedAt: 2025-03-18 22:04:01 -0400 (Tue, 18 Mar 2025)

EllapsedTime: 79.4 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

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###
### Running command:
###
###   chmod a+r sparrow -R && E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe 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 to build vignettes
* creating vignettes ... ERROR
--- re-building 'sparrow.Rmd' using rmarkdown

Quitting from sparrow.Rmd:215-217 [build-gdb]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `GeneSetDb.data.frame()`:
! is.data.frame(x) && nrow(x) > 0 is not TRUE
---
Backtrace:
    ▆
 1. └─sparrow::getMSigGeneSetDb(c("h", "c2"), "human", id.type = "entrez")
 2.   ├─sparrow::GeneSetDb(ret)
 3.   └─sparrow:::GeneSetDb.data.frame(ret)
 4.     └─base::stopifnot(is.data.frame(x) && nrow(x) > 0)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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

SUMMARY: processing the following file failed:
  'sparrow.Rmd'

Error: Vignette re-building failed.
Execution halted