Multiple platform build/check report for BioC 3.20 - BUILD results for psygenet2r on palomino8

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.3 (2025-02-28) -- "Trophy Case"	4764
palomino8	Windows Server 2022 Datacenter	x64	4.4.3 (2025-02-28 ucrt) -- "Trophy Case"	4495
merida1	macOS 12.7.5 Monterey	x86_64	4.4.3 (2025-02-28) -- "Trophy Case"	4522
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.3 (2025-02-28) -- "Trophy Case"	4449
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.4.3 (2025-02-28) -- "Trophy Case"	4426
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 psygenet2r on palomino8

To the developers/maintainers of the psygenet2r package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/psygenet2r.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: psygenet2r

Version: 1.38.0

Command: chmod a+r psygenet2r -R && F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data psygenet2r

StartedAt: 2025-03-31 21:10:31 -0400 (Mon, 31 Mar 2025)

EndedAt: 2025-03-31 21:11:17 -0400 (Mon, 31 Mar 2025)

EllapsedTime: 45.2 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

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###
### Running command:
###
###   chmod a+r psygenet2r -R && F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data psygenet2r
###
##############################################################################
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* checking for file 'psygenet2r/DESCRIPTION' ... OK
* preparing 'psygenet2r':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'case_study.Rmd' using rmarkdown

Quitting from case_study.Rmd:116-124 [search_multiple]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `genes[, c(1, 2)]`:
! incorrect number of dimensions
---
Backtrace:
    ▆
 1. └─psygenet2r::psygenetGene(...)
 2.   └─psygenet2r:::ListPsyGeNETIds(database, "Gene")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'case_study.Rmd' failed with diagnostics:
incorrect number of dimensions
--- failed re-building 'case_study.Rmd'

--- re-building 'general_overview.Rmd' using rmarkdown

Quitting from general_overview.Rmd:91-94 [dataGenet1]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `genes[, c(1, 2)]`:
! incorrect number of dimensions
---
Backtrace:
    ▆
 1. └─psygenet2r::psygenetGene(gene = 4852, database = "ALL")
 2.   └─psygenet2r:::ListPsyGeNETIds(database, "Gene")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'general_overview.Rmd' failed with diagnostics:
incorrect number of dimensions
--- failed re-building 'general_overview.Rmd'

SUMMARY: processing the following files failed:
  'case_study.Rmd' 'general_overview.Rmd'

Error: Vignette re-building failed.
Execution halted