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This page was generated on 2025-10-22 12:06 -0400 (Wed, 22 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4890
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4680
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4625
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4642
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 658/2355HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ELMER 2.33.1  (landing page)
Tiago Chedraoui Silva
Snapshot Date: 2025-10-21 13:45 -0400 (Tue, 21 Oct 2025)
git_url: https://git.bioconductor.org/packages/ELMER
git_branch: devel
git_last_commit: fa33cdb
git_last_commit_date: 2025-07-22 19:32:00 -0400 (Tue, 22 Jul 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    ERROR  skipped
lconwaymacOS 12.7.6 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson3macOS 13.7.7 Ventura / arm64  OK    ERROR  skippedskipped
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    NA  

BUILD results for ELMER on kjohnson3

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.

raw results


Summary

Package: ELMER
Version: 2.33.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data ELMER
StartedAt: 2025-10-21 16:18:47 -0400 (Tue, 21 Oct 2025)
EndedAt: 2025-10-21 16:21:37 -0400 (Tue, 21 Oct 2025)
EllapsedTime: 169.8 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data ELMER
###
##############################################################################
##############################################################################


* 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
2025-10-21 16:19:52.136 R[60669:512372915] XType: Using static font registry.
--- 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

Quitting from analysis_motif_enrichment.Rmd:67-85 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `fix.by()`:
! 'by' must specify a uniquely valid column
---
Backtrace:
    ▆
 1. └─ELMER::get.enriched.motif(...)
 2.   └─ELMER:::getHocomocoTable()
 3.     ├─base::merge(hocomoco, x, by = "Model")
 4.     ├─base::merge(hocomoco, x, by = "Model")
 5.     └─base::merge.data.frame(hocomoco, x, by = "Model")
 6.       └─base (local) fix.by(by.x, x)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'analysis_motif_enrichment.Rmd' failed with diagnostics:
'by' must specify a uniquely valid column
--- failed re-building ‘analysis_motif_enrichment.Rmd’

--- re-building ‘analysis_regulatory_tf.Rmd’ using rmarkdown

Quitting from analysis_regulatory_tf.Rmd:86-90 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `readChar()`:
! cannot open the connection
---
Backtrace:
    ▆
 1. └─base::load("result/getMotif.hypo.enriched.motifs.rda")
 2.   └─base::readChar(con, 5L, useBytes = TRUE)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'analysis_regulatory_tf.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘analysis_regulatory_tf.Rmd’

--- re-building ‘index.Rmd’ using rmarkdown
--- finished re-building ‘index.Rmd’

--- re-building ‘input.Rmd’ using rmarkdown
--- finished re-building ‘input.Rmd’

--- re-building ‘pipe.Rmd’ using rmarkdown
--- finished re-building ‘pipe.Rmd’

--- re-building ‘plots_TF.Rmd’ using rmarkdown

Quitting from plots_TF.Rmd:40-48 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `readChar()`:
! cannot open the connection
---
Backtrace:
    ▆
 1. └─base::load("result/getTF.hypo.TFs.with.motif.pvalue.rda")
 2.   └─base::readChar(con, 5L, useBytes = TRUE)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'plots_TF.Rmd' failed with diagnostics:
cannot open the connection
--- failed 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

Quitting from plots_motif_enrichment.Rmd:35-40 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `file()`:
! cannot open the connection
---
Backtrace:
    ▆
 1. └─ELMER::motif.enrichment.plot(...)
 2.   └─utils::read.csv(motif.enrichment, stringsAsFactors = FALSE)
 3.     └─utils::read.table(...)
 4.       └─base::file(file, "rt")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'plots_motif_enrichment.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘plots_motif_enrichment.Rmd’

--- re-building ‘plots_scatter.Rmd’ using rmarkdown

Quitting from plots_scatter.Rmd:68-77 [unnamed-chunk-5]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `readChar()`:
! cannot open the connection
---
Backtrace:
    ▆
 1. └─base::load("result/getMotif.hypo.enriched.motifs.rda")
 2.   └─base::readChar(con, 5L, useBytes = TRUE)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'plots_scatter.Rmd' failed with diagnostics:
cannot open the connection
--- failed 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 files failed:
  ‘analysis_motif_enrichment.Rmd’ ‘analysis_regulatory_tf.Rmd’
  ‘plots_TF.Rmd’ ‘plots_motif_enrichment.Rmd’ ‘plots_scatter.Rmd’

Error: Vignette re-building failed.
Execution halted