| Back to Multiple platform build/check report for BioC 3.24: simplified long |
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This page was generated on 2026-05-06 11:34 -0400 (Wed, 06 May 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4878 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4663 |
| 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 2222/2366 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Timothy Keyes
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
| See other builds for tidytof in R Universe. | ||||||||||||||
|
To the developers/maintainers of the tidytof package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/tidytof.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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: tidytof |
| Version: 1.7.0 |
| Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data tidytof |
| StartedAt: 2026-05-05 06:29:37 -0000 (Tue, 05 May 2026) |
| EndedAt: 2026-05-05 06:32:23 -0000 (Tue, 05 May 2026) |
| EllapsedTime: 166.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
##############################################################################
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### Running command:
###
### /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data tidytof
###
##############################################################################
##############################################################################
* checking for file ‘tidytof/DESCRIPTION’ ... OK
* preparing ‘tidytof’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘quality-control.Rmd’ using rmarkdown
Quitting from quality-control.Rmd:61-76 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `loadNamespace()`:
! there is no package called 'ExperimentHub'
---
Backtrace:
▆
1. ├─tidytof::tof_preprocess(...)
2. │ └─dplyr::mutate(...)
3. ├─dplyr::mutate(...)
4. ├─dplyr::rename_with(...)
5. ├─dplyr::mutate(...)
6. ├─tidytof::as_tof_tbl(HDCytoData::Levine_32dim_flowSet())
7. └─base::loadNamespace(x)
8. ├─base::namespaceImportFrom(...)
9. │ └─base::asNamespace(ns)
10. └─base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
11. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
12. └─base (local) withOneRestart(expr, restarts[[1L]])
13. └─base (local) doWithOneRestart(return(expr), restart)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'quality-control.Rmd' failed with diagnostics:
there is no package called 'ExperimentHub'
--- failed re-building ‘quality-control.Rmd’
--- re-building ‘clustering.Rmd’ using knitr
--- finished re-building ‘clustering.Rmd’
--- re-building ‘contributing-to-tidytof.Rmd’ using knitr
--- finished re-building ‘contributing-to-tidytof.Rmd’
--- re-building ‘differential-discovery-analysis.Rmd’ using knitr
Quitting from differential-discovery-analysis.Rmd:54-60 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `loadNamespace()`:
! there is no package called 'ExperimentHub'
---
Backtrace:
▆
1. └─base::loadNamespace(x)
2. ├─base::namespaceImportFrom(...)
3. │ └─base::asNamespace(ns)
4. └─base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
5. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
6. └─base (local) withOneRestart(expr, restarts[[1L]])
7. └─base (local) doWithOneRestart(return(expr), restart)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'differential-discovery-analysis.Rmd' failed with diagnostics:
there is no package called 'ExperimentHub'
--- failed re-building ‘differential-discovery-analysis.Rmd’
--- re-building ‘dimensionality-reduction.Rmd’ using knitr
--- finished re-building ‘dimensionality-reduction.Rmd’
--- re-building ‘downsampling.Rmd’ using knitr
--- finished re-building ‘downsampling.Rmd’
--- re-building ‘feature-extraction.Rmd’ using knitr
Quitting from feature-extraction.Rmd:51-57 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `loadNamespace()`:
! there is no package called 'ExperimentHub'
---
Backtrace:
▆
1. └─base::loadNamespace(x)
2. ├─base::namespaceImportFrom(...)
3. │ └─base::asNamespace(ns)
4. └─base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
5. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
6. └─base (local) withOneRestart(expr, restarts[[1L]])
7. └─base (local) doWithOneRestart(return(expr), restart)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'feature-extraction.Rmd' failed with diagnostics:
there is no package called 'ExperimentHub'
--- failed re-building ‘feature-extraction.Rmd’
--- re-building ‘modeling.Rmd’ using knitr
Quitting from modeling.Rmd:39-57 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `open.connection()`:
! cannot open the connection
---
Backtrace:
▆
1. ├─dplyr::filter(...)
2. ├─dplyr::left_join(...)
3. ├─dplyr::rename(...)
4. ├─readr::read_csv(data_link, skip = 2L, n_max = 78L, show_col_types = FALSE)
5. │ └─vroom::vroom(...)
6. │ └─vroom:::vroom_(...)
7. ├─base (local) `<fn>`(`<curl>`, "rb")
8. └─base::open.connection(`<curl>`, "rb")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'modeling.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘modeling.Rmd’
--- re-building ‘preprocessing.Rmd’ using knitr
--- finished re-building ‘preprocessing.Rmd’
--- re-building ‘reading-and-writing-data.Rmd’ using knitr
--- finished re-building ‘reading-and-writing-data.Rmd’
--- re-building ‘tidytof.Rmd’ using knitr
--- finished re-building ‘tidytof.Rmd’
SUMMARY: processing the following files failed:
‘quality-control.Rmd’ ‘differential-discovery-analysis.Rmd’
‘feature-extraction.Rmd’ ‘modeling.Rmd’
Error: Vignette re-building failed.
Execution halted