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This page was generated on 2025-10-27 12:45 -0400 (Mon, 27 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4637
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 1562/2361HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pathwayPCA 1.25.0  (landing page)
Gabriel Odom
Snapshot Date: 2025-10-26 13:45 -0400 (Sun, 26 Oct 2025)
git_url: https://git.bioconductor.org/packages/pathwayPCA
git_branch: devel
git_last_commit: 9941354
git_last_commit_date: 2025-04-15 11:42:25 -0400 (Tue, 15 Apr 2025)
kjohnson3macOS 13.7.7 Ventura / arm64  OK    ERROR  skippedskipped

BUILD results for pathwayPCA on kjohnson3

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.

raw results


Summary

Package: pathwayPCA
Version: 1.25.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data pathwayPCA
StartedAt: 2025-10-26 17:31:03 -0400 (Sun, 26 Oct 2025)
EndedAt: 2025-10-26 17:31:30 -0400 (Sun, 26 Oct 2025)
EllapsedTime: 27.3 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

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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 to build vignettes
* creating vignettes ... ERROR
--- re-building ‘Introduction_to_pathwayPCA.Rmd’ using rmarkdown

Quitting from Introduction_to_pathwayPCA.Rmd:83-88 [loadAssay]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `readRDS()`:
! cannot open the connection to 'https://raw.githubusercontent.com/lizhongliu1996/pathwayPCAdata/master/ovarian_PNNL_survival.RDS'
---
Backtrace:
    ▆
 1. └─base::readRDS(url(paste0(gitHubPath_char, "ovarian_PNNL_survival.RDS")))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'Introduction_to_pathwayPCA.Rmd' failed with diagnostics:
cannot open the connection to 'https://raw.githubusercontent.com/lizhongliu1996/pathwayPCAdata/master/ovarian_PNNL_survival.RDS'
--- failed re-building ‘Introduction_to_pathwayPCA.Rmd’

--- re-building ‘Supplement1-Quickstart_Guide.Rmd’ using rmarkdown
2025-10-26 17:31:15.917 R[90584:550832701] XType: Using static font registry.
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
Warning: The vignette title specified in \VignetteIndexEntry{} is different from the title in the YAML metadata. The former is "Suppl. 2. Importing Data", and the latter is "Suppl. Ch. 2 - Import and Tidy Data". If that is intentional, you may set options(rmarkdown.html_vignette.check_title = FALSE) to suppress this check.
--- finished 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:
  ‘Introduction_to_pathwayPCA.Rmd’

Error: Vignette re-building failed.
Execution halted