Multiple platform build/check report for BioC 3.23 - BUILD results for PharmacoGx on kjohnson3

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*

BUILD results for PharmacoGx on kjohnson3

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

Version: 3.15.0

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

StartedAt: 2026-01-21 17:15:38 -0500 (Wed, 21 Jan 2026)

EndedAt: 2026-01-21 17:16:09 -0500 (Wed, 21 Jan 2026)

EllapsedTime: 31.3 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 PharmacoGx
###
##############################################################################
##############################################################################


* checking for file ‘PharmacoGx/DESCRIPTION’ ... OK
* preparing ‘PharmacoGx’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘CreatingPharmacoSet.Rmd’ using rmarkdown
--- finished re-building ‘CreatingPharmacoSet.Rmd’

--- re-building ‘DetectingDrugSynergyAndAntagonism.Rmd’ using rmarkdown

Quitting from DetectingDrugSynergyAndAntagonism.Rmd:224-226 [metaconstruct_the_tre]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 7/7 in VECTOR_ELT
---
Backtrace:
    ▆
 1. ├─CoreGx::metaConstruct(treMapper)
 2. └─CoreGx::metaConstruct(treMapper)
 3.   └─CoreGx (local) .local(mapper, ...)
 4.     └─CoreGx:::.metaConstruct(mapper, constructor = CoreGx::TreatmentResponseExperiment)
 5.       └─CoreGx (local) constructor(...)
 6.         └─CoreGx::LongTable(...)
 7.           ├─rowData[, `:=`(c("rowKey"), .GRP), keyby = c(rowIDs)]
 8.           └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'DetectingDrugSynergyAndAntagonism.Rmd' failed with diagnostics:
attempt access index 7/7 in VECTOR_ELT
--- failed re-building ‘DetectingDrugSynergyAndAntagonism.Rmd’

--- re-building ‘PharmacoGx.Rmd’ using rmarkdown
2026-01-21 17:16:04.942 R[13367:798393469] XType: Using static font registry.
--- finished re-building ‘PharmacoGx.Rmd’

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

Error: Vignette re-building failed.
Execution halted