Multiple platform build/check report for BioC 3.22 - BUILD results for dmGsea on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.2 LTS)	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4818
palomino8	Windows Server 2022 Datacenter	x64	4.5.1 (2025-06-13 ucrt) -- "Great Square Root"	4553
lconway	macOS 12.7.1 Monterey	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4595
kjohnson3	macOS 13.7.1 Ventura	arm64	4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"	4537
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 dmGsea on kjohnson3

To the developers/maintainers of the dmGsea package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/dmGsea.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: dmGsea

Version: 0.99.11

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data dmGsea

StartedAt: 2025-08-08 16:10:57 -0400 (Fri, 08 Aug 2025)

EndedAt: 2025-08-08 16:11:27 -0400 (Fri, 08 Aug 2025)

EllapsedTime: 30.3 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data dmGsea
###
##############################################################################
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* checking for file ‘dmGsea/DESCRIPTION’ ... OK
* preparing ‘dmGsea’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘dmGsea.Rmd’ using rmarkdown

Quitting from dmGsea.Rmd:58-76 [example1]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! Diagonal values in 'R' must all be equal to 1.
---
Backtrace:
     ▆
  1. └─dmGsea::gsGene(...)
  2.   └─dmGsea:::calcGeneP(...)
  3.     └─parallel::mclapply(...)
  4.       └─base::lapply(X = X, FUN = FUN, ...)
  5.         └─dmGsea (local) FUN(X[[i]], ...)
  6.           ├─base::eval(parse(text = paste0("poolr::", combpMethod, "(p=allp,adjust=combpAdjust,\n            R=Rmatrix)")))
  7.           │ └─base::eval(parse(text = paste0("poolr::", combpMethod, "(p=allp,adjust=combpAdjust,\n            R=Rmatrix)")))
  8.           └─poolr::fisher(p = allp, adjust = combpAdjust, R = Rmatrix)
  9.             └─poolr:::.check.m(R = R, adjust = adjust, m = m, k = k, ...)
 10.               └─poolr::meff(R = R, method = adjust, ...)
 11.                 └─poolr:::.check.R(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'dmGsea.Rmd' failed with diagnostics:
Diagonal values in 'R' must all be equal to 1.
--- failed re-building ‘dmGsea.Rmd’

SUMMARY: processing the following file failed:
  ‘dmGsea.Rmd’

Error: Vignette re-building failed.
Execution halted