| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-11-17 11:39 -0500 (Mon, 17 Nov 2025).
| 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" | 4826 |
| lconway | macOS 12.7.6 Monterey | x86_64 | R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences" | 4491 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4562 |
| 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 1407/2325 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MungeSumstats 1.19.1 (landing page) Alan Murphy
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
|
To the developers/maintainers of the MungeSumstats package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MungeSumstats.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: MungeSumstats |
| Version: 1.19.1 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data MungeSumstats |
| StartedAt: 2025-11-16 22:55:12 -0500 (Sun, 16 Nov 2025) |
| EndedAt: 2025-11-16 22:56:21 -0500 (Sun, 16 Nov 2025) |
| EllapsedTime: 69.5 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 MungeSumstats
###
##############################################################################
##############################################################################
* checking for file ‘MungeSumstats/DESCRIPTION’ ... OK
* preparing ‘MungeSumstats’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘MungeSumstats.Rmd’ using rmarkdown
Quitting from MungeSumstats.Rmd:261-272 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! To use dbSNP=155 on GRCh37, please install the Bioconductor package 'SNPlocs.Hsapiens.dbSNP155.GRCh37'.
---
Backtrace:
▆
1. └─MungeSumstats::format_sumstats(...)
2. └─MungeSumstats:::validate_parameters(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'MungeSumstats.Rmd' failed with diagnostics:
To use dbSNP=155 on GRCh37, please install the Bioconductor package 'SNPlocs.Hsapiens.dbSNP155.GRCh37'.
--- failed re-building ‘MungeSumstats.Rmd’
--- re-building ‘OpenGWAS.Rmd’ using rmarkdown
--- finished re-building ‘OpenGWAS.Rmd’
--- re-building ‘docker.Rmd’ using rmarkdown
--- finished re-building ‘docker.Rmd’
SUMMARY: processing the following file failed:
‘MungeSumstats.Rmd’
Error: Vignette re-building failed.
Execution halted