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This page was generated on 2025-03-18 11:44 -0400 (Tue, 18 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences" 4537
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" 4543
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4576
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4528
kunpeng2Linux (openEuler 24.03 LTS)aarch64R 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 513/2313HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
dce 1.15.1  (landing page)
Kim Philipp Jablonski
Snapshot Date: 2025-03-17 13:40 -0400 (Mon, 17 Mar 2025)
git_url: https://git.bioconductor.org/packages/dce
git_branch: devel
git_last_commit: 0c098ac
git_last_commit_date: 2024-12-17 10:47:08 -0400 (Tue, 17 Dec 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    ERROR  skipped
palomino7Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
lconwaymacOS 12.7.1 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson3macOS 13.7.1 Ventura / arm64  OK    ERROR  skippedskipped
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    ERROR  skipped


BUILD results for dce on lconway

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.

raw results


Summary

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

Command output

##############################################################################
##############################################################################
###
### 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