Benjamin Haibe-Kains
| Snapshot Date: 2026-01-21 13:40 -0500 (Wed, 21 Jan 2026) |
| git_url: https://git.bioconductor.org/packages/CoreGx |
| git_branch: devel |
| git_last_commit: e18fa83 |
| git_last_commit_date: 2025-10-29 10:59:21 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-01-22 11:35 -0500 (Thu, 22 Jan 2026).
| 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 | ||||
| Package 447/2345 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CoreGx 2.15.0 (landing page) Benjamin Haibe-Kains
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
|
To the developers/maintainers of the CoreGx package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CoreGx.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. |
| Package: CoreGx |
| Version: 2.15.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data CoreGx |
| StartedAt: 2026-01-21 15:59:06 -0500 (Wed, 21 Jan 2026) |
| EndedAt: 2026-01-21 15:59:26 -0500 (Wed, 21 Jan 2026) |
| EllapsedTime: 20.2 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data CoreGx
###
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* checking for file ‘CoreGx/DESCRIPTION’ ... OK
* preparing ‘CoreGx’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘TreatmentResponseExperiment.Rmd’ using rmarkdown
Quitting from TreatmentResponseExperiment.Rmd:269-271 [unnamed-chunk-1]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 5/5 in VECTOR_ELT
---
Backtrace:
▆
1. ├─CoreGx::metaConstruct(TREdataMapper)
2. └─CoreGx::metaConstruct(TREdataMapper)
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 'TreatmentResponseExperiment.Rmd' failed with diagnostics:
attempt access index 5/5 in VECTOR_ELT
--- failed re-building ‘TreatmentResponseExperiment.Rmd’
--- re-building ‘coreGx.Rmd’ using knitr
Quitting from coreGx.Rmd:140-143 [cSet_accessor_demo2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 10/10 in VECTOR_ELT
---
Backtrace:
▆
1. ├─CoreGx::sensitivityProfiles(clevelandSmall_cSet)
2. └─CoreGx::sensitivityProfiles(clevelandSmall_cSet)
3. └─CoreGx (local) .local(object, ...)
4. └─CoreGx:::.rebuildProfiles(treatmentResponse(object))
5. ├─profDT[, `:=`(treatment_uid, eval(trt)), by = .I]
6. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'coreGx.Rmd' failed with diagnostics:
attempt access index 10/10 in VECTOR_ELT
--- failed re-building ‘coreGx.Rmd’
SUMMARY: processing the following files failed:
‘TreatmentResponseExperiment.Rmd’ ‘coreGx.Rmd’
Error: Vignette re-building failed.
Execution halted