| Back to Build/check report for BioC 3.22 experimental data |
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This page was generated on 2025-11-18 15:41 -0500 (Tue, 18 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4786 |
| 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 246/435 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | ||||||||
| MicrobiomeBenchmarkData 1.12.0 (landing page) Samuel Gamboa
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | ||||||||
|
To the developers/maintainers of the MicrobiomeBenchmarkData package: - 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: MicrobiomeBenchmarkData |
| Version: 1.12.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data MicrobiomeBenchmarkData |
| StartedAt: 2025-11-18 11:48:17 -0500 (Tue, 18 Nov 2025) |
| EndedAt: 2025-11-18 12:00:09 -0500 (Tue, 18 Nov 2025) |
| EllapsedTime: 711.9 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data MicrobiomeBenchmarkData
###
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* checking for file ‘MicrobiomeBenchmarkData/DESCRIPTION’ ... OK
* preparing ‘MicrobiomeBenchmarkData’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘MicrobiomeBenchmarkData.Rmd’ using rmarkdown
1 HMP_2012_16S_gingival_V13
2 HMP_2012_16S_gingival_V35
3 HMP_2012_16S_gingival_V35_subset
4 HMP_2012_WMS_gingival
5 Stammler_2016_16S_spikein
6 Ravel_2011_16S_BV
Use vignette('datasets', package = 'MicrobiomeBenchmarkData') for a detailed description of the datasets.
Use getBenchmarkData(dryrun = FALSE) to import all of the datasets.
Quitting from MicrobiomeBenchmarkData.Rmd:98-101 [unnamed-chunk-7]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `BiocFileCache::bfcrpath()`:
! not all 'rnames' found or unique.
---
Backtrace:
▆
1. └─MicrobiomeBenchmarkData::getBenchmarkData(...)
2. └─base::lapply(dataset_names, .assembleTreeSummarizedExperiment)
3. └─MicrobiomeBenchmarkData (local) FUN(X[[i]], ...)
4. └─MicrobiomeBenchmarkData:::.getResourcePath(x, "_taxonomy_tree")
5. ├─BiocFileCache::bfcrpath(...)
6. └─BiocFileCache::bfcrpath(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'MicrobiomeBenchmarkData.Rmd' failed with diagnostics:
not all 'rnames' found or unique.
--- failed re-building ‘MicrobiomeBenchmarkData.Rmd’
--- re-building ‘datasets.Rmd’ using rmarkdown
--- finished re-building ‘datasets.Rmd’
--- re-building ‘recalibrare_spikein_data.Rmd’ using rmarkdown
Quitting from recalibrare_spikein_data.Rmd:40-43 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `BiocFileCache::bfcrpath()`:
! not all 'rnames' found or unique.
---
Backtrace:
▆
1. └─MicrobiomeBenchmarkData::getBenchmarkData(...)
2. └─base::lapply(dataset_names, .assembleTreeSummarizedExperiment)
3. └─MicrobiomeBenchmarkData (local) FUN(X[[i]], ...)
4. ├─S4Vectors::DataFrame(...)
5. ├─utils::read.table(...)
6. └─MicrobiomeBenchmarkData:::.getResourcePath(x, "_taxonomy_table")
7. ├─BiocFileCache::bfcrpath(...)
8. └─BiocFileCache::bfcrpath(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'recalibrare_spikein_data.Rmd' failed with diagnostics:
not all 'rnames' found or unique.
--- failed re-building ‘recalibrare_spikein_data.Rmd’
SUMMARY: processing the following files failed:
‘MicrobiomeBenchmarkData.Rmd’ ‘recalibrare_spikein_data.Rmd’
Error: Vignette re-building failed.
Execution halted