Tiago Chedraoui Silva
| Snapshot Date: 2025-08-28 13:40 -0400 (Thu, 28 Aug 2025) |
| git_url: https://git.bioconductor.org/packages/ELMER |
| git_branch: RELEASE_3_21 |
| git_last_commit: b1c7e3b |
| git_last_commit_date: 2025-04-15 10:51:24 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-09-01 11:39 -0400 (Mon, 01 Sep 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4824 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4606 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4547 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4579 |
| 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 652/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ELMER 2.32.0 (landing page) Tiago Chedraoui Silva
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | TIMEOUT | ||||||||||
|
To the developers/maintainers of the ELMER package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ELMER.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: ELMER |
| Version: 2.32.0 |
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data ELMER |
| StartedAt: 2025-08-31 17:10:10 -0400 (Sun, 31 Aug 2025) |
| EndedAt: 2025-08-31 17:15:23 -0400 (Sun, 31 Aug 2025) |
| EllapsedTime: 313.4 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data ELMER
###
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* checking for file ‘ELMER/DESCRIPTION’ ... OK
* preparing ‘ELMER’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘analysis_data_input.Rmd’ using rmarkdown
--- finished re-building ‘analysis_data_input.Rmd’
--- re-building ‘analysis_diff_meth.Rmd’ using rmarkdown
--- finished re-building ‘analysis_diff_meth.Rmd’
--- re-building ‘analysis_get_pair.Rmd’ using rmarkdown
--- finished re-building ‘analysis_get_pair.Rmd’
--- re-building ‘analysis_gui.Rmd’ using rmarkdown
--- finished re-building ‘analysis_gui.Rmd’
--- re-building ‘analysis_motif_enrichment.Rmd’ using rmarkdown
--- finished re-building ‘analysis_motif_enrichment.Rmd’
--- re-building ‘analysis_regulatory_tf.Rmd’ using rmarkdown
--- finished re-building ‘analysis_regulatory_tf.Rmd’
--- re-building ‘index.Rmd’ using rmarkdown
--- finished re-building ‘index.Rmd’
--- re-building ‘input.Rmd’ using rmarkdown
Quitting from input.Rmd:132-190 [unnamed-chunk-4]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `h()`:
! error in evaluating the argument 'i' in selecting a method for function '[': invalid argument type
---
Backtrace:
▆
1. ├─ELMER::createMAE(...)
2. │ └─ELMER:::makeSummarizedExperimentFromDNAMethylation(...)
3. │ └─rowRanges[!rowRanges$MASK_general]
4. └─base::.handleSimpleError(`<fn>`, "invalid argument type", base::quote(!rowRanges$MASK_general))
5. └─base (local) h(simpleError(msg, call))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'input.Rmd' failed with diagnostics:
error in evaluating the argument 'i' in selecting a method for function '[': invalid argument type
--- failed re-building ‘input.Rmd’
--- re-building ‘pipe.Rmd’ using rmarkdown
--- finished re-building ‘pipe.Rmd’
--- re-building ‘plots_TF.Rmd’ using rmarkdown
Warning: ggrepel: 66 unlabeled data points (too many overlaps). Consider increasing max.overlaps
--- finished re-building ‘plots_TF.Rmd’
--- re-building ‘plots_heatmap.Rmd’ using rmarkdown
--- finished re-building ‘plots_heatmap.Rmd’
--- re-building ‘plots_motif_enrichment.Rmd’ using rmarkdown
--- finished re-building ‘plots_motif_enrichment.Rmd’
--- re-building ‘plots_scatter.Rmd’ using rmarkdown
--- finished re-building ‘plots_scatter.Rmd’
--- re-building ‘plots_schematic.Rmd’ using rmarkdown
--- finished re-building ‘plots_schematic.Rmd’
--- re-building ‘usecase.Rmd’ using rmarkdown
--- finished re-building ‘usecase.Rmd’
SUMMARY: processing the following file failed:
‘input.Rmd’
Error: Vignette re-building failed.
Execution halted