Gabriel Odom
| Snapshot Date: 2026-03-09 13:40 -0400 (Mon, 09 Mar 2026) |
| git_url: https://git.bioconductor.org/packages/pathwayPCA |
| git_branch: devel |
| git_last_commit: 9b31249 |
| git_last_commit_date: 2025-10-29 10:50:50 -0400 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-03-10 11:33 -0400 (Tue, 10 Mar 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-03-05 r89546) -- "Unsuffered Consequences" | 4522 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2026-03-01 r89506) -- "Unsuffered Consequences" | 2847 |
| 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 1564/2360 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| pathwayPCA 1.27.0 (landing page) Gabriel Odom
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
| See other builds for pathwayPCA in R Universe. | ||||||||||||||
|
To the developers/maintainers of the pathwayPCA package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/pathwayPCA.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: pathwayPCA |
| Version: 1.27.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data pathwayPCA |
| StartedAt: 2026-03-09 15:39:18 -0400 (Mon, 09 Mar 2026) |
| EndedAt: 2026-03-09 15:40:10 -0400 (Mon, 09 Mar 2026) |
| EllapsedTime: 51.7 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 pathwayPCA
###
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* checking for file ‘pathwayPCA/DESCRIPTION’ ... OK
* preparing ‘pathwayPCA’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘Introduction_to_pathwayPCA.Rmd’ using rmarkdown
2026-03-09 15:39:28.818 R[30187:122265431] XType: Using static font registry.
--- finished re-building ‘Introduction_to_pathwayPCA.Rmd’
--- re-building ‘Supplement1-Quickstart_Guide.Rmd’ using rmarkdown
Warning: The vignette title specified in \VignetteIndexEntry{} is different from the title in the YAML metadata. The former is "Suppl. 1. Quickstart Guide", and the latter is "Suppl. Ch. 1 - Quickstart Guide for New R Users". If that is intentional, you may set options(rmarkdown.html_vignette.check_title = FALSE) to suppress this check.
--- finished re-building ‘Supplement1-Quickstart_Guide.Rmd’
--- re-building ‘Supplement2-Importing_Data.Rmd’ using rmarkdown
Quitting from Supplement2-Importing_Data.Rmd:189-194 [stdExpr_Example]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `library()`:
! there is no package called 'SummarizedExperiment'
---
Backtrace:
▆
1. └─base::library(SummarizedExperiment)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Supplement2-Importing_Data.Rmd' failed with diagnostics:
there is no package called 'SummarizedExperiment'
--- failed re-building ‘Supplement2-Importing_Data.Rmd’
--- re-building ‘Supplement3-Create_Omics_Objects.Rmd’ using rmarkdown
Warning: The vignette title specified in \VignetteIndexEntry{} is different from the title in the YAML metadata. The former is "Suppl. 3. Create Data Objects", and the latter is "Suppl. Ch. 3 - Creating Data Objects". If that is intentional, you may set options(rmarkdown.html_vignette.check_title = FALSE) to suppress this check.
--- finished re-building ‘Supplement3-Create_Omics_Objects.Rmd’
--- re-building ‘Supplement4-Methods_Walkthrough.Rmd’ using rmarkdown
Warning: The vignette title specified in \VignetteIndexEntry{} is different from the title in the YAML metadata. The former is "Suppl. 4. Test Pathway Significance", and the latter is "Suppl. Ch. 4 - Test Pathway Significance". If that is intentional, you may set options(rmarkdown.html_vignette.check_title = FALSE) to suppress this check.
--- finished re-building ‘Supplement4-Methods_Walkthrough.Rmd’
--- re-building ‘Supplement5-Analyse_Results.Rmd’ using rmarkdown
Warning: The vignette title specified in \VignetteIndexEntry{} is different from the title in the YAML metadata. The former is "Suppl. 5. Visualizing the Results", and the latter is "Suppl. Ch. 5 - Visualizing the Results". If that is intentional, you may set options(rmarkdown.html_vignette.check_title = FALSE) to suppress this check.
--- finished re-building ‘Supplement5-Analyse_Results.Rmd’
SUMMARY: processing the following file failed:
‘Supplement2-Importing_Data.Rmd’
Error: Vignette re-building failed.
Execution halted