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This page was generated on 2026-05-06 11:34 -0400 (Wed, 06 May 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.4 LTS)x86_644.6.0 RC (2026-04-17 r89917) -- "Because it was There" 4878
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (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 656/2366HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ELMER 2.37.0  (landing page)
Tiago Chedraoui Silva
Snapshot Date: 2026-05-05 13:45 -0400 (Tue, 05 May 2026)
git_url: https://git.bioconductor.org/packages/ELMER
git_branch: devel
git_last_commit: b7f87ea
git_last_commit_date: 2026-04-28 08:41:23 -0400 (Tue, 28 Apr 2026)
nebbiolo2Linux (Ubuntu 24.04.4 LTS) / x86_64  OK    ERROR  skipped
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    ERROR  skipped
See other builds for ELMER in R Universe.

BUILD results for ELMER on taishan

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: ELMER
Version: 2.37.0
Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data ELMER
StartedAt: 2026-05-05 02:55:27 -0000 (Tue, 05 May 2026)
EndedAt: 2026-05-05 02:57:18 -0000 (Tue, 05 May 2026)
EllapsedTime: 111.0 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/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

Quitting from analysis_data_input.Rmd:53-60 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! sesameData package is needed for this function to work. Please install it.
---
Backtrace:
    ▆
 1. └─ELMER::get.feature.probe(...)
 2.   └─ELMER:::getInfiniumAnnotation(plat = toupper(met.platform), genome = genome)
 3.     └─ELMER:::check_package("sesameData")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'analysis_data_input.Rmd' failed with diagnostics:
sesameData package is needed for this function to work. Please install it.
--- failed re-building ‘analysis_data_input.Rmd’

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

Quitting from analysis_diff_meth.Rmd:68-83 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `readChar()`:
! cannot open the connection
---
Backtrace:
    ▆
 1. ├─base::get(load("mae.rda"))
 2. └─base::load("mae.rda")
 3.   └─base::readChar(con, 5L, useBytes = TRUE)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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

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

Quitting from analysis_get_pair.Rmd:108-138 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `readChar()`:
! cannot open the connection
---
Backtrace:
    ▆
 1. ├─base::get(load("mae.rda"))
 2. └─base::load("mae.rda")
 3.   └─base::readChar(con, 5L, useBytes = TRUE)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'analysis_get_pair.Rmd' failed with diagnostics:
cannot open the connection
--- failed 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 `readChar()`:
! cannot open the connection
---
Backtrace:
    ▆
 1. ├─base::get(load("mae.rda"))
 2. └─base::load("mae.rda")
 3.   └─base::readChar(con, 5L, useBytes = TRUE)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'analysis_motif_enrichment.Rmd' failed with diagnostics:
cannot open the connection
--- 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::get(load("mae.rda"))
 2. └─base::load("mae.rda")
 3.   └─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

Quitting from input.Rmd:132-190 [unnamed-chunk-4]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! sesameData package is needed for this function to work. Please install it.
---
Backtrace:
    ▆
 1. └─ELMER::createMAE(...)
 2.   └─ELMER:::makeSummarizedExperimentFromDNAMethylation(...)
 3.     └─ELMER:::getInfiniumAnnotation(plat = met.platform, genome = genome)
 4.       └─ELMER:::check_package("sesameData")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'input.Rmd' failed with diagnostics:
sesameData package is needed for this function to work. Please install it.
--- failed 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

Quitting from plots_heatmap.Rmd:32-35 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `h()`:
! error in evaluating the argument 'x' in selecting a method for function 'get': cannot open the connection
---
Backtrace:
    ▆
 1. ├─BiocGenerics::get(load("mae.rda"))
 2. ├─base::load("mae.rda")
 3. │ └─base::readChar(con, 5L, useBytes = TRUE)
 4. └─base::.handleSimpleError(...)
 5.   └─base (local) h(simpleError(msg, call))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'plots_heatmap.Rmd' failed with diagnostics:
error in evaluating the argument 'x' in selecting a method for function 'get': cannot open the connection
--- failed 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:32-35 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `h()`:
! error in evaluating the argument 'x' in selecting a method for function 'get': cannot open the connection
---
Backtrace:
    ▆
 1. ├─BiocGenerics::get(load("mae.rda"))
 2. ├─base::load("mae.rda")
 3. │ └─base::readChar(con, 5L, useBytes = TRUE)
 4. └─base::.handleSimpleError(...)
 5.   └─base (local) h(simpleError(msg, call))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'plots_scatter.Rmd' failed with diagnostics:
error in evaluating the argument 'x' in selecting a method for function 'get': cannot open the connection
--- failed re-building ‘plots_scatter.Rmd’

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

Quitting from plots_schematic.Rmd:31-35 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `h()`:
! error in evaluating the argument 'x' in selecting a method for function 'get': cannot open the connection
---
Backtrace:
    ▆
 1. ├─BiocGenerics::get(load("mae.rda"))
 2. ├─base::load("mae.rda")
 3. │ └─base::readChar(con, 5L, useBytes = TRUE)
 4. └─base::.handleSimpleError(...)
 5.   └─base (local) h(simpleError(msg, call))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'plots_schematic.Rmd' failed with diagnostics:
error in evaluating the argument 'x' in selecting a method for function 'get': cannot open the connection
--- failed re-building ‘plots_schematic.Rmd’

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

SUMMARY: processing the following files failed:
  ‘analysis_data_input.Rmd’ ‘analysis_diff_meth.Rmd’
  ‘analysis_get_pair.Rmd’ ‘analysis_motif_enrichment.Rmd’
  ‘analysis_regulatory_tf.Rmd’ ‘input.Rmd’ ‘plots_TF.Rmd’
  ‘plots_heatmap.Rmd’ ‘plots_motif_enrichment.Rmd’ ‘plots_scatter.Rmd’
  ‘plots_schematic.Rmd’

Error: Vignette re-building failed.
Execution halted