| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-12-31 11:34 -0500 (Wed, 31 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-12-22 r89219) -- "Unsuffered Consequences" | 4808 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4593 |
| 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 838/2332 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GenomicDistributions 1.19.0 (landing page) Kristyna Kupkova
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK |  | ||||||||
|
To the developers/maintainers of the GenomicDistributions package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GenomicDistributions.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: GenomicDistributions |
| Version: 1.19.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data GenomicDistributions |
| StartedAt: 2025-12-30 17:42:01 -0500 (Tue, 30 Dec 2025) |
| EndedAt: 2025-12-30 17:42:44 -0500 (Tue, 30 Dec 2025) |
| EllapsedTime: 43.0 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data GenomicDistributions
###
##############################################################################
##############################################################################
* checking for file ‘GenomicDistributions/DESCRIPTION’ ... OK
* preparing ‘GenomicDistributions’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘full-power.Rmd’ using rmarkdown
--- finished re-building ‘full-power.Rmd’
--- re-building ‘intro.Rmd’ using rmarkdown
Warning: stack imbalance in '::', 65 then 67
Warning: stack imbalance in '=', 63 then 65
Warning: stack imbalance in 'withVisible', 57 then 59
Quitting from intro.Rmd:174-177 [multiple-proportional-partition-plot]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `foverlaps()`:
! attempt access index -1/2673 in VECTOR_ELT
---
Backtrace:
▆
1. └─GenomicDistributions::calcPartitionsRef(queryList, "hg19", bpProportion = TRUE)
2. └─GenomicDistributions::calcPartitions(query, partitionList, bpProportion = bpProportion)
3. └─base::lapply(...)
4. └─GenomicDistributions (local) FUN(X[[i]], ...)
5. └─base::lapply(partitionList, overlapWidths, query)
6. └─GenomicDistributions (local) FUN(X[[i]], ...)
7. └─data.table::foverlaps(partitionDT, queryDT, nomatch = NULL)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'intro.Rmd' failed with diagnostics:
attempt access index -1/2673 in VECTOR_ELT
--- failed re-building ‘intro.Rmd’
SUMMARY: processing the following file failed:
‘intro.Rmd’
Error: Vignette re-building failed.
Execution halted