Multiple platform build/check report for BioC 3.21 - BUILD results for dce on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
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*

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