Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-03-18 11:44 -0400 (Tue, 18 Mar 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences" | 4537 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" | 4543 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4576 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4528 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4459 |
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 513/2313 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Kim Philipp Jablonski
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | ERROR | skipped | skipped | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
To the developers/maintainers of the dce package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/dce.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: dce |
Version: 1.15.1 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data dce |
StartedAt: 2025-03-17 16:31:28 -0400 (Mon, 17 Mar 2025) |
EndedAt: 2025-03-17 16:34:13 -0400 (Mon, 17 Mar 2025) |
EllapsedTime: 164.9 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 dce ### ############################################################################## ############################################################################## * checking for file ‘dce/DESCRIPTION’ ... OK * preparing ‘dce’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘dce.Rmd’ using rmarkdown 2025-03-17 16:32:29.387 R[15661:425120710] XType: com.apple.fonts is not accessible. 2025-03-17 16:32:29.388 R[15661:425120710] XType: XTFontStaticRegistry is enabled. INFO [2025-03-17 16:33:43] Processing kegg Quitting from dce.Rmd:241-243 [unnamed-chunk-16] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `dce()`: ! Not all nodes have expression vector in WT data --- Backtrace: ▆ 1. ├─dce::dce(brca_pathway, t(brca_wt), t(brca_mt)) 2. └─dce::dce(brca_pathway, t(brca_wt), t(brca_mt)) 3. ├─dce::dce(...) 4. └─dce::dce(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'dce.Rmd' failed with diagnostics: Not all nodes have expression vector in WT data --- failed re-building ‘dce.Rmd’ --- re-building ‘pathway_databases.Rmd’ using rmarkdown INFO [2025-03-17 16:33:52] Processing pathbank INFO [2025-03-17 16:34:10] Processing kegg Quitting from pathway_databases.Rmd:63-80 [unnamed-chunk-5] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `buildEdgeList()`: ! attempt to set index 12/12 in SET_STRING_ELT --- Backtrace: ▆ 1. ├─BiocGenerics::lapply(...) 2. └─base::lapply(...) 3. └─global FUN(X[[i]], ...) 4. └─dce::plot_network(...) 5. ├─purrr::map_dfr(...) 6. │ └─purrr::map(.x, .f, ...) 7. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress) 8. │ └─purrr:::vctrs_vec_compat(.x, .purrr_user_env) 9. └─Rgraphviz::agopen(as(tmp, "graphNEL"), name = "foo", layoutType = "dot") 10. └─Rgraphviz::buildEdgeList(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'pathway_databases.Rmd' failed with diagnostics: attempt to set index 12/12 in SET_STRING_ELT --- failed re-building ‘pathway_databases.Rmd’ SUMMARY: processing the following files failed: ‘dce.Rmd’ ‘pathway_databases.Rmd’ Error: Vignette re-building failed. Execution halted