Multiple platform build/check report for BioC 3.23 - BUILD results for pathlinkR on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"	4878
kjohnson3	macOS 13.7.7 Ventura	arm64	R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"	4593
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BUILD results for pathlinkR on nebbiolo1

To the developers/maintainers of the pathlinkR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/pathlinkR.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: pathlinkR

Version: 1.7.7

Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data pathlinkR

StartedAt: 2025-12-21 19:06:37 -0500 (Sun, 21 Dec 2025)

EndedAt: 2025-12-21 19:07:19 -0500 (Sun, 21 Dec 2025)

EllapsedTime: 42.0 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
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### Running command:
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###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data pathlinkR
###
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* checking for file ‘pathlinkR/DESCRIPTION’ ... OK
* preparing ‘pathlinkR’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘pathlinkR.Rmd’ using rmarkdown
Warning: ggrepel: 45 unlabeled data points (too many overlaps). Consider increasing max.overlaps

Quitting from pathlinkR.Rmd:158-165 [ppiEnrichNetwork]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/purrr_error_indexed>
Error in `map2()`:
ℹ In index: 1.
ℹ With name: network.
Caused by error in `map2()`:
ℹ In index: 1.
ℹ With name: All.
Caused by error:
! object 'load_OrgDb' is not exported by 'namespace:GOSemSim'
---
Backtrace:
     ▆
  1. ├─pathlinkR::ppiEnrichNetwork(...)
  2. │ ├─... %>% select(-c(comparison, direction))
  3. │ └─pathlinkR::pathwayEnrichment(...)
  4. │   └─purrr::imap(...)
  5. │     └─purrr::map2(.x, vec_index(.x), .f, ...)
  6. │       └─purrr:::map2_("list", .x, .y, .f, ..., .progress = .progress)
  7. │         ├─purrr:::with_indexed_errors(...)
  8. │         │ └─base::withCallingHandlers(...)
  9. │         ├─purrr:::call_with_cleanup(...)
 10. │         └─pathlinkR (local) .f(.x[[i]], .y[[i]], ...)
 11. │           ├─... %>% distinct()
 12. │           └─purrr::imap_dfr(...)
 13. │             └─purrr::map2(.x, vec_index(.x), .f, ...)
 14. │               └─purrr:::map2_("list", .x, .y, .f, ..., .progress = .progress)
 15. │                 ├─purrr:::with_indexed_errors(...)
 16. │                 │ └─base::withCallingHandlers(...)
 17. │                 ├─purrr:::call_with_cleanup(...)
 18. │                 └─pathlinkR (local) .f(.x[[i]], .y[[i]], ...)
 19. │                   └─tibble::as_tibble(...)
 20. ├─dplyr::select(., -c(comparison, direction))
 21. ├─dplyr::distinct(.)
 22. ├─dplyr::select(., -hgncSymbol)
 23. ├─dplyr::ungroup(.)
 24. ├─dplyr::mutate(., genes = paste(hgncSymbol, collapse = ";"))
 25. ├─dplyr::group_by(., ID)
 26. ├─dplyr::select(., -any_of(c("geneID", "entrezGeneId", "ensemblGeneId")))
 27. ├─dplyr::left_join(...)
 28. ├─tidyr::separate_longer_delim(., geneID, delim = "/")
 29. │ └─tidyr:::check_data_frame(data)
 30. │   └─base::is.data.frame(x)
 31. └─base::loadNamespace(x)
 32.   ├─base::namespaceImportFrom(...)
 33.   │ └─base::asNamespace(ns)
 34.   └─base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
 35.     └─base::namespaceImportFrom(...)
 36.       └─base::importIntoEnv(impenv, impnames, ns, impvars)
 37.         └─base::stop(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'pathlinkR.Rmd' failed with diagnostics:
ℹ In index: 1.
ℹ With name: network.
Caused by error in `map2()`:
ℹ In index: 1.
ℹ With name: All.
Caused by error:
! object 'load_OrgDb' is not exported by 'namespace:GOSemSim'
--- failed re-building ‘pathlinkR.Rmd’

SUMMARY: processing the following file failed:
  ‘pathlinkR.Rmd’

Error: Vignette re-building failed.
Execution halted