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This page was generated on 2026-02-05 11:32 -0500 (Thu, 05 Feb 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences" | 4852 |
| 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 903/2347 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GNET2 1.27.0 (landing page) Chen Chen
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| See other builds for GNET2 in R Universe. | ||||||||||||||
|
To the developers/maintainers of the GNET2 package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GNET2.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: GNET2 |
| Version: 1.27.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data GNET2 |
| StartedAt: 2026-02-04 17:55:41 -0500 (Wed, 04 Feb 2026) |
| EndedAt: 2026-02-04 17:56:29 -0500 (Wed, 04 Feb 2026) |
| EllapsedTime: 48.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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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 GNET2
###
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* checking for file ‘GNET2/DESCRIPTION’ ... OK
* preparing ‘GNET2’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘run_gnet2.Rmd’ using rmarkdown
Quitting from run_gnet2.Rmd:130-133 [unnamed-chunk-10]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/lifecycle_error_deprecated>
Error:
! `group_by_()` was deprecated in dplyr 0.7.0 and is now defunct.
ℹ Please use `group_by()` instead.
ℹ See vignette('programming') for more help
---
Backtrace:
▆
1. ├─GNET2::extract_edges(gnet_result)
2. │ └─el %>% group_by_(.dots = c("regulator", "target")) %>% ...
3. ├─dplyr::summarise_all(., list(score = sum))
4. │ └─dplyr:::manip_all(...)
5. │ ├─rlang::syms(tbl_nongroup_vars(.tbl))
6. │ │ └─rlang:::map(x, sym)
7. │ │ └─base::lapply(.x, .f, ...)
8. │ └─dplyr::tbl_nongroup_vars(.tbl)
9. │ ├─generics::setdiff(tbl_vars(x), group_vars(x))
10. │ └─dplyr::tbl_vars(x)
11. │ ├─dplyr:::new_sel_vars(tbl_vars_dispatch(x), group_vars(x))
12. │ │ └─base::structure(...)
13. │ └─dplyr:::tbl_vars_dispatch(x)
14. └─dplyr::group_by_(., .dots = c("regulator", "target"))
15. └─dplyr:::lazy_defunct("group_by")
16. └─lifecycle::deprecate_stop(...)
17. └─lifecycle:::deprecate_stop0(msg)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'run_gnet2.Rmd' failed with diagnostics:
`group_by_()` was deprecated in dplyr 0.7.0 and is now defunct.
ℹ Please use `group_by()` instead.
ℹ See vignette('programming') for more help
--- failed re-building ‘run_gnet2.Rmd’
SUMMARY: processing the following file failed:
‘run_gnet2.Rmd’
Error: Vignette re-building failed.
Execution halted