Johannes Griss
| Snapshot Date: 2025-09-19 13:45 -0400 (Fri, 19 Sep 2025) |
| git_url: https://git.bioconductor.org/packages/ReactomeGSA |
| git_branch: devel |
| git_last_commit: d9a274e |
| git_last_commit_date: 2025-04-15 11:49:59 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-09-20 12:05 -0400 (Sat, 20 Sep 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4814 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4603 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4547 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4553 |
| 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 1721/2333 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReactomeGSA 1.23.0 (landing page) Johannes Griss
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the ReactomeGSA package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ReactomeGSA.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: ReactomeGSA |
| Version: 1.23.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data ReactomeGSA |
| StartedAt: 2025-09-19 18:14:16 -0400 (Fri, 19 Sep 2025) |
| EndedAt: 2025-09-19 18:19:43 -0400 (Fri, 19 Sep 2025) |
| EllapsedTime: 327.2 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data ReactomeGSA
###
##############################################################################
##############################################################################
* checking for file ‘ReactomeGSA/DESCRIPTION’ ... OK
* preparing ‘ReactomeGSA’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘analysing-scRNAseq.Rmd’ using rmarkdown
|
| | 0%
|
|= | 2%
|
|=== | 4%
|
|==== | 6%
|
|===== | 8%
|
|======= | 10%
|
|======== | 12%
|
|========= | 13%
|
|=========== | 15%
|
|============ | 17%
|
|============= | 19%
|
|=============== | 21%
|
|================ | 23%
|
|================== | 25%
|
|=================== | 27%
|
|==================== | 29%
|
|====================== | 31%
|
|======================= | 33%
|
|======================== | 35%
|
|========================== | 37%
|
|=========================== | 38%
|
|============================ | 40%
|
|============================== | 42%
|
|=============================== | 44%
|
|================================ | 46%
|
|================================== | 48%
|
|=================================== | 50%
|
|==================================== | 52%
|
|====================================== | 54%
|
|======================================= | 56%
|
|======================================== | 58%
|
|========================================== | 60%
|
|=========================================== | 62%
|
|============================================ | 63%
|
|============================================== | 65%
|
|=============================================== | 67%
|
|================================================ | 69%
|
|================================================== | 71%
|
|=================================================== | 73%
|
|==================================================== | 75%
|
|====================================================== | 77%
|
|======================================================= | 79%
|
|========================================================= | 81%
|
|========================================================== | 83%
|
|=========================================================== | 85%
|
|============================================================= | 87%
|
|============================================================== | 88%
|
|=============================================================== | 90%
|
|================================================================= | 92%
|
|================================================================== | 94%
|
|=================================================================== | 96%
|
|===================================================================== | 98%
|
|======================================================================| 100%
|
| | 0%
|
|=== | 4%
|
|====== | 8%
|
|========= | 12%
|
|============ | 17%
|
|=============== | 21%
|
|================== | 25%
|
|==================== | 29%
|
|======================= | 33%
|
|========================== | 38%
|
|============================= | 42%
|
|================================ | 46%
|
|=================================== | 50%
|
|====================================== | 54%
|
|========================================= | 58%
|
|============================================ | 62%
|
|=============================================== | 67%
|
|================================================== | 71%
|
|==================================================== | 75%
|
|======================================================= | 79%
|
|========================================================== | 83%
|
|============================================================= | 88%
|
|================================================================ | 92%
|
|=================================================================== | 96%
|
|======================================================================| 100%
2025-09-19 18:15:50.472 R[93001:329689583] XType: com.apple.fonts is not accessible.
2025-09-19 18:15:50.472 R[93001:329689583] XType: XTFontStaticRegistry is enabled.
Warning: The vignette title specified in \VignetteIndexEntry{} is different from the title in the YAML metadata. The former is "Analysing single-cell RNAseq data", and the latter is "Analysing single-cell RNA-sequencing Data". If that is intentional, you may set options(rmarkdown.html_vignette.check_title = FALSE) to suppress this check.
--- finished re-building ‘analysing-scRNAseq.Rmd’
--- re-building ‘reanalysing-public-data.Rmd’ using rmarkdown
Quitting from reanalysing-public-data.Rmd:153-164 [unnamed-chunk-10]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! unable to find an inherited method for function 'pathways' for signature 'x = "NULL"'
---
Backtrace:
▆
1. └─ReactomeGSA::pathways(res)
2. └─methods (local) `<fn>`(`<list>`, `<stndrdGn>`, `<env>`)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'reanalysing-public-data.Rmd' failed with diagnostics:
unable to find an inherited method for function 'pathways' for signature 'x = "NULL"'
--- failed re-building ‘reanalysing-public-data.Rmd’
--- re-building ‘using-reactomegsa.Rmd’ using rmarkdown
--- finished re-building ‘using-reactomegsa.Rmd’
SUMMARY: processing the following file failed:
‘reanalysing-public-data.Rmd’
Error: Vignette re-building failed.
Execution halted