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This page was generated on 2025-09-18 12:02 -0400 (Thu, 18 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4808
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4597
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4541
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4554
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 126/2330HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
bambu 3.11.2  (landing page)
Ying Chen
Snapshot Date: 2025-09-17 13:45 -0400 (Wed, 17 Sep 2025)
git_url: https://git.bioconductor.org/packages/bambu
git_branch: devel
git_last_commit: 062d127
git_last_commit_date: 2025-06-21 19:21:39 -0400 (Sat, 21 Jun 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    ERROR  skipped
lconwaymacOS 12.7.1 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson3macOS 13.7.7 Ventura / arm64  OK    ERROR  skippedskipped
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    ERROR  skipped

BUILD results for bambu on nebbiolo2

To the developers/maintainers of the bambu package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/bambu.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: bambu
Version: 3.11.2
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 bambu
StartedAt: 2025-09-17 16:25:48 -0400 (Wed, 17 Sep 2025)
EndedAt: 2025-09-17 16:33:07 -0400 (Wed, 17 Sep 2025)
EllapsedTime: 438.4 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 bambu
###
##############################################################################
##############################################################################


* checking for file ‘bambu/DESCRIPTION’ ... OK
* preparing ‘bambu’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘bambu.Rmd’ using rmarkdown
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/3f63d56ba9abac_3845'
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/3f63d56ba9abac_3845'
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/3f63d56ba9abac_3845'
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/3f63d56ba9abac_3845'
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/3f63d567f72dad_3847'
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/3f63d5761b13cf_3849'
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/3f63d57f1aae4f_3851'
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/3f63d52c6944dd_3853'
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/3f63d56453b2cb_3855'
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/3f63d56ba9abac_3845'
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/3f63d567f72dad_3847'
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/3f63d5761b13cf_3849'
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/3f63d57f1aae4f_3851'
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/3f63d52c6944dd_3853'
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/3f63d56453b2cb_3855'
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/3f63d56ba9abac_3845'
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/3f63d567f72dad_3847'
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/3f63d5761b13cf_3849'
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/3f63d57f1aae4f_3851'
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/3f63d52c6944dd_3853'
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/3f63d56453b2cb_3855'
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/3f63d56ba9abac_3845'
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/3f63d567f72dad_3847'
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/3f63d5761b13cf_3849'
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/3f63d57f1aae4f_3851'
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/3f63d52c6944dd_3853'
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/3f63d56453b2cb_3855'

Quitting from bambu.Rmd:237-239 [unnamed-chunk-20]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `validObject()`:
! invalid class "GGbio" object: invalid object for slot "ggplot" in class "GGbio": got class "ggplot2::ggplot", should be or extend class "gg_OR_NULL"
---
Backtrace:
     ▆
  1. └─bambu::plotBambu(se.multiSample, type = "annotation", gene_id = "ENSG00000099968")
  2.   └─bambu:::plotAnnotation(se, gene_id, transcript_id)
  3.     └─bambu:::plotAnnotation_withExpression(se, gene_id, transcript_id)
  4.       ├─BiocGenerics::lapply(...)
  5.       └─base::lapply(...)
  6.         └─bambu (local) FUN(X[[i]], ...)
  7.           └─bambu:::plotAnnotation_plotFunction(...)
  8.             ├─ggbio::autoplot(geneRange, group.selfish = TRUE)
  9.             └─ggbio::autoplot(geneRange, group.selfish = TRUE)
 10.               └─ggbio (local) .local(object, ...)
 11.                 ├─BiocGenerics::do.call(autoplot, args.res)
 12.                 ├─base::do.call(autoplot, args.res)
 13.                 ├─ggplot2 (local) `<stndrdGn>`(...)
 14.                 └─ggbio (local) `<stndrdGn>`(...)
 15.                   └─ggbio (local) .local(object, ...)
 16.                     ├─BiocGenerics::do.call(ggplot, c(list(data = object), list(aes.res)))
 17.                     ├─base::do.call(ggplot, c(list(data = object), list(aes.res)))
 18.                     ├─ggplot2 (local) `<fn>`(data = `<GRanges>`, `<ggplt2::>`)
 19.                     └─ggbio:::ggplot.Vector(data = `<GRanges>`, `<ggplt2::>`)
 20.                       └─ggbio::GGbio(gg, data = data)
 21.                         ├─BiocGenerics::do.call(...)
 22.                         ├─base::do.call(...)
 23.                         └─methods (local) `<fn>`(...)
 24.                           ├─methods::initialize(value, ...)
 25.                           └─methods::initialize(value, ...)
 26.                             └─methods::validObject(.Object)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'bambu.Rmd' failed with diagnostics:
invalid class "GGbio" object: invalid object for slot "ggplot" in class "GGbio": got class "ggplot2::ggplot", should be or extend class "gg_OR_NULL"
--- failed re-building ‘bambu.Rmd’

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

Error: Vignette re-building failed.
Execution halted