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This page was generated on 2026-03-18 11:57 -0400 (Wed, 18 Mar 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4892
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Package 1257/2361HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
metaseqR2 1.22.1  (landing page)
Panagiotis Moulos
Snapshot Date: 2026-03-17 13:45 -0400 (Tue, 17 Mar 2026)
git_url: https://git.bioconductor.org/packages/metaseqR2
git_branch: RELEASE_3_22
git_last_commit: de81e3a
git_last_commit_date: 2026-03-04 09:58:25 -0400 (Wed, 04 Mar 2026)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    ERROR  skipped
See other builds for metaseqR2 in R Universe.

BUILD results for metaseqR2 on nebbiolo2

To the developers/maintainers of the metaseqR2 package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/metaseqR2.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: metaseqR2
Version: 1.22.1
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 metaseqR2
StartedAt: 2026-03-17 18:31:35 -0400 (Tue, 17 Mar 2026)
EndedAt: 2026-03-17 18:37:43 -0400 (Tue, 17 Mar 2026)
EllapsedTime: 368.3 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 metaseqR2
###
##############################################################################
##############################################################################


* checking for file ‘metaseqR2/DESCRIPTION’ ... OK
* preparing ‘metaseqR2’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘metaseqr2-annotation.Rmd’ using rmarkdown

Quitting from metaseqr2-annotation.Rmd:107-122 [example-1]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/httr2_http_500>
Error in `req_perform()`:
! HTTP 500 Internal Server Error.
---
Backtrace:
    ▆
 1. └─metaseqR2::buildAnnotationDatabase(...)
 2.   └─metaseqR2::getAnnotation(o, "gene", refdb = s, ver = v, rc = rc)
 3.     └─metaseqR2:::getEnsemblAnnotation(org, type, ver)
 4.       └─biomaRt::useMart(biomart = dat, host = host, dataset = getDataset(org))
 5.         └─biomaRt:::.useMart(...)
 6.           └─biomaRt:::.listMarts(...)
 7.             └─biomaRt:::bmRequest(...)
 8.               └─httr2::req_perform(request)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'metaseqr2-annotation.Rmd' failed with diagnostics:
HTTP 500 Internal Server Error.
--- failed re-building ‘metaseqr2-annotation.Rmd’

--- re-building ‘metaseqr2-statistics.Rmd’ using rmarkdown
Warning: call dbDisconnect() when finished working with a connection
  adding: tmp/RtmpMXoQIQ/test1/plots/qc/correlation_correlogram.png (deflated 1%)
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  adding: tmp/RtmpMXoQIQ/test1/plots/qc/filtered_genes.png (deflated 5%)
  adding: tmp/RtmpMXoQIQ/test1/plots/qc/mds.png (deflated 44%)
  adding: tmp/RtmpMXoQIQ/test1/plots/normalization/boxplot_normalized.png (deflated 17%)
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statEdger              package:metaseqR2               R Documentation

_S_t_a_t_i_s_t_i_c_a_l _t_e_s_t_i_n_g _w_i_t_h _e_d_g_e_R

_D_e_s_c_r_i_p_t_i_o_n:

     This function is a wrapper over edgeR statistical testing. It
     accepts a matrix of normalized gene counts or an S4 object
     specific to each normalization algorithm supported by metaseqR2.

_U_s_a_g_e:

         statEdger(object, sampleList, contrastList = NULL,
             statArgs = NULL)
     
_A_r_g_u_m_e_n_t_s:

  object: a matrix or an object specific to each normalization
          algorithm supported by metaseqR2, containing normalized
          counts. See also Details.

sampleList: the list containing condition names and the samples under
          each condition.

contrastList: vector of contrasts as defined in the main help page of
          'metaseqr2'. See also Details.

statArgs: a list of edgeR statistical algorithm parameters. See the
          result of 'getDefaults("statistics",' '"edger")' for an
          example and how you can modify it.

_D_e_t_a_i_l_s:

     Regarding 'object', apart from 'matrix' (also for NOISeq), the
     object can be a 'SeqExpressionSet' (EDASeq), 'CountDataSet'
     (DESeq), 'DGEList' (edgeR), 'DESeqDataSet' (DESeq2), 'SeqCountSet'
     (DSS) or 'ABSDataSet' (ABSSeq).

     Regarding 'contrastList' it can also be a named structured list of
     contrasts as returned by the internal function
     'metaseqR2:::makeContrastList'.

_V_a_l_u_e:

     A named list of p-values, whose names are the names of the
     contrasts.

_A_u_t_h_o_r(_s):

     Panagiotis Moulos

_E_x_a_m_p_l_e_s:

     require(edgeR)
     dataMatrix <- metaseqR2:::exampleCountData(2000)
     sampleList <- list(A=c("A1","A2"),B=c("B1","B2","B3"))
     contrast <- "A_vs_B"
     normDataMatrix <- normalizeEdger(dataMatrix,sampleList)
     p <- statEdger(normDataMatrix,sampleList,contrast)
     

--- finished re-building ‘metaseqr2-statistics.Rmd’

SUMMARY: processing the following file failed:
  ‘metaseqr2-annotation.Rmd’

Error: Vignette re-building failed.
Execution halted