| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-11-13 11:32 -0500 (Thu, 13 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4013 |
| 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 883/2325 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| glmSparseNet 1.29.0 (landing page) André Veríssimo
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | ERROR | skipped | skipped | ||||||||
|
To the developers/maintainers of the glmSparseNet package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/glmSparseNet.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: glmSparseNet |
| Version: 1.29.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data glmSparseNet |
| StartedAt: 2025-11-12 16:22:50 -0500 (Wed, 12 Nov 2025) |
| EndedAt: 2025-11-12 16:22:56 -0500 (Wed, 12 Nov 2025) |
| EllapsedTime: 6.1 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 glmSparseNet
###
##############################################################################
##############################################################################
* checking for file ‘glmSparseNet/DESCRIPTION’ ... OK
* preparing ‘glmSparseNet’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘example_brca_logistic.Rmd’ using rmarkdown
Quitting from example_brca_logistic.Rmd:28-47 [packages]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `library()`:
! there is no package called 'curatedTCGAData'
---
Backtrace:
▆
1. └─base::library(curatedTCGAData)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'example_brca_logistic.Rmd' failed with diagnostics:
there is no package called 'curatedTCGAData'
--- failed re-building ‘example_brca_logistic.Rmd’
--- re-building ‘example_brca_protein-protein-interactions_survival.Rmd’ using rmarkdown
Quitting from example_brca_protein-protein-interactions_survival.Rmd:28-53 [packages]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `library()`:
! there is no package called 'curatedTCGAData'
---
Backtrace:
▆
1. └─base::library(curatedTCGAData)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'example_brca_protein-protein-interactions_survival.Rmd' failed with diagnostics:
there is no package called 'curatedTCGAData'
--- failed re-building ‘example_brca_protein-protein-interactions_survival.Rmd’
--- re-building ‘example_brca_survival.Rmd’ using rmarkdown
Quitting from example_brca_survival.Rmd:28-47 [packages]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `library()`:
! there is no package called 'curatedTCGAData'
---
Backtrace:
▆
1. └─base::library(curatedTCGAData)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'example_brca_survival.Rmd' failed with diagnostics:
there is no package called 'curatedTCGAData'
--- failed re-building ‘example_brca_survival.Rmd’
--- re-building ‘example_prad_survival.Rmd’ using rmarkdown
Quitting from example_prad_survival.Rmd:28-47 [packages]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `library()`:
! there is no package called 'curatedTCGAData'
---
Backtrace:
▆
1. └─base::library(curatedTCGAData)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'example_prad_survival.Rmd' failed with diagnostics:
there is no package called 'curatedTCGAData'
--- failed re-building ‘example_prad_survival.Rmd’
--- re-building ‘example_skcm_survival.Rmd’ using rmarkdown
Quitting from example_skcm_survival.Rmd:28-47 [packages]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `library()`:
! there is no package called 'curatedTCGAData'
---
Backtrace:
▆
1. └─base::library(curatedTCGAData)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'example_skcm_survival.Rmd' failed with diagnostics:
there is no package called 'curatedTCGAData'
--- failed re-building ‘example_skcm_survival.Rmd’
--- re-building ‘separate2GroupsCox.Rmd’ using rmarkdown
2025-11-12 16:22:53.877 R[9598:2247003] XType: Using static font registry.
--- finished re-building ‘separate2GroupsCox.Rmd’
SUMMARY: processing the following files failed:
‘example_brca_logistic.Rmd’
‘example_brca_protein-protein-interactions_survival.Rmd’
‘example_brca_survival.Rmd’ ‘example_prad_survival.Rmd’
‘example_skcm_survival.Rmd’
Error: Vignette re-building failed.
Execution halted