Multiple platform build/check report for BioC 3.23 - BUILD results for EpiMix on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.4 LTS)	x86_64	4.6.0 RC (2026-04-17 r89917) -- "Because it was There"	4990
kjohnson3	macOS 13.7.7 Ventura	arm64	4.6.0 Patched (2026-04-24 r89963) -- "Because it was There"	4723
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*

BUILD results for EpiMix on kjohnson3

To the developers/maintainers of the EpiMix package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/EpiMix.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: EpiMix

Version: 1.14.0

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data EpiMix

StartedAt: 2026-05-06 16:56:13 -0400 (Wed, 06 May 2026)

EndedAt: 2026-05-06 17:01:11 -0400 (Wed, 06 May 2026)

EllapsedTime: 298.3 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 EpiMix
###
##############################################################################
##############################################################################


* checking for file ‘EpiMix/DESCRIPTION’ ... OK
* preparing ‘EpiMix’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘Methylation_Modeling.Rmd’ using rmarkdown
trying URL 'https://egg2.wustl.edu/roadmap/data/byFileType/chromhmmSegmentations/ChmmModels/core_K27ac/jointModel/final/E096_18_core_K27ac_hg38lift_mnemonics.bed.gz'
Content type 'application/x-gzip' length 3835377 bytes (3.7 MB)
==================================================
downloaded 3.7 MB

trying URL 'https://gdac.broadinstitute.org/runs/stddata__latest/data/OV/20160128/gdac.broadinstitute.org_OV.Merge_methylation__humanmethylation27__jhu_usc_edu__Level_3__within_bioassay_data_set_function__data.Level_3.2016012800.0.0.tar.gz'
Content type 'application/x-gzip' length 152968396 bytes (145.9 MB)
==================================================
downloaded 145.9 MB

trying URL 'https://gdac.broadinstitute.org/runs/stddata__latest/data/OV/20160128/gdac.broadinstitute.org_OV.Merge_methylation__humanmethylation450__jhu_usc_edu__Level_3__within_bioassay_data_set_function__data.Level_3.2016012800.0.0.tar.gz'
Content type 'application/x-gzip' length 51525820 bytes (49.1 MB)
==================================================
downloaded 49.1 MB

trying URL 'https://gdac.broadinstitute.org/runs/stddata__latest/data/OV/20160128/gdac.broadinstitute.org_OV.Merge_transcriptome__agilentg4502a_07_3__unc_edu__Level_3__unc_lowess_normalization_gene_level__data.Level_3.2016012800.0.0.tar.gz'
Content type 'application/x-gzip' length 36996192 bytes (35.3 MB)
==================================================
downloaded 35.3 MB

trying URL 'https://gdac.broadinstitute.org/runs/stddata__latest/data/OV/20160128/gdac.broadinstitute.org_OV.miRseq_Preprocess.Level_3.2016012800.0.0.tar.gz'
Content type 'application/x-gzip' length 2663096 bytes (2.5 MB)
==================================================
downloaded 2.5 MB

trying URL 'https://gdac.broadinstitute.org/runs/stddata__latest/data/LUAD/20160128/gdac.broadinstitute.org_LUAD.Merge_Clinical.Level_1.2016012800.0.0.tar.gz'
Content type 'application/x-gzip' length 1777018 bytes (1.7 MB)
==================================================
downloaded 1.7 MB

trying URL 'https://gdac.broadinstitute.org/runs/stddata__latest/data/LUAD/20160128/gdac.broadinstitute.org_LUAD.Merge_Clinical.Level_1.2016012800.0.0.tar.gz'
Content type 'application/x-gzip' length 1777018 bytes (1.7 MB)
==================================================
downloaded 1.7 MB


Quitting from Methylation_Modeling.Rmd:584-592 [unnamed-chunk-40]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/purrr_error_indexed>
Error in `map()`:
ℹ In index: 1.
ℹ With name: mirtarbase.
Caused by error:
! Gateway Timeout
---
Backtrace:
     ▆
  1. └─EpiMix::find_miRNA_targets(...)
  2.   └─multiMiR::get_multimir(...)
  3.     └─purrr::map(queries, query_multimir, org = org, add.link = add.link, use.tibble = use.tibble)
  4.       └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
  5.         ├─purrr:::with_indexed_errors(...)
  6.         │ └─base::withCallingHandlers(...)
  7.         ├─purrr:::call_with_cleanup(...)
  8.         └─multiMiR (local) .f(.x[[i]], ...)
  9.           └─multiMiR::search_multimir(x$query)
 10.             └─multiMiR:::submit_request(...)
 11.               └─RCurl::postForm(url, query = query, ..., .opts = myOpts)
 12.                 └─RCurl:::stop.if.HTTP.error(http.header)
 13.                   └─base::stop(err)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'Methylation_Modeling.Rmd' failed with diagnostics:
ℹ In index: 1.
ℹ With name: mirtarbase.
Caused by error:
! Gateway Timeout
--- failed re-building ‘Methylation_Modeling.Rmd’

SUMMARY: processing the following file failed:
  ‘Methylation_Modeling.Rmd’

Error: Vignette re-building failed.
Execution halted