Multiple platform build/check report for BioC 3.22 - BUILD results for metaseqR2 on taishan

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4823
lconway	macOS 12.7.1 Monterey	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4618
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"	4565
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4544
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 metaseqR2 on taishan

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

Package: metaseqR2
Version: 1.21.1
Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data metaseqR2
StartedAt: 2025-09-05 01:04:10 -0000 (Fri, 05 Sep 2025)
EndedAt: 2025-09-05 01:22:44 -0000 (Fri, 05 Sep 2025)
EllapsedTime: 1114.5 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 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
trying URL 'https://bioconductor.org/packages/3.22/data/annotation/src/contrib/BSgenome.Mmusculus.UCSC.mm10_1.4.3.tar.gz'
Content type 'application/x-gzip' length 649827309 bytes (619.7 MB)
==================================================
downloaded 619.7 MB

* installing *source* package ‘BSgenome.Mmusculus.UCSC.mm10’ ...
** this is package ‘BSgenome.Mmusculus.UCSC.mm10’ version ‘1.4.3’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BSgenome.Mmusculus.UCSC.mm10)

The downloaded source packages are in
	'/home/biocbuild/tmp/Rtmp8CXOym/downloaded_packages'
trying URL 'http://hgdownload.cse.ucsc.edu/goldenPath/eboVir3/database/ncbiGene.txt.gz'
Content type 'application/x-gzip' length 238 bytes
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trying URL 'http://hgdownload.cse.ucsc.edu/goldenPath/eboVir3/database/chromInfo.txt.gz'
Content type 'application/x-gzip' length 71 bytes
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/home/biocbuild/bin/genePredToGtf: error while loading shared libraries: libssl.so.1.1: cannot open shared object file: No such file or directory

Quitting from metaseqr2-annotation.Rmd:190-254 [example-4]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `open.connection()`:
! cannot open the connection
---
Backtrace:
     ▆
  1. └─metaseqR2::buildCustomAnnotation(...)
  2.   └─metaseqR2:::parseCustomGtf(gtfFile)
  3.     ├─BiocIO::import(gtfFile, colnames = desiredColumns, feature.type = .GFF_FEATURE_TYPES)
  4.     └─BiocIO::import(gtfFile, colnames = desiredColumns, feature.type = .GFF_FEATURE_TYPES)
  5.       ├─BiocIO::import(FileForFormat(con), ...)
  6.       └─rtracklayer::import(FileForFormat(con), ...)
  7.         └─rtracklayer (local) .local(con, format, text, ...)
  8.           └─BiocIO:::connection(m, con, "r")
  9.             └─BiocIO:::connectionForResource(manager, resource(x), open = open)
 10.               ├─base::open(con, open)
 11.               └─base::open.connection(con, open)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'metaseqr2-annotation.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘metaseqr2-annotation.Rmd’

--- re-building ‘metaseqr2-statistics.Rmd’ using rmarkdown
Warning: call dbDisconnect() when finished working with a connection
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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)
     

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