Back to Multiple platform build/check report for BioC 3.21:   simplified   long
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This page was generated on 2025-01-11 11:46 -0500 (Sat, 11 Jan 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4760
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4479
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4443
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4398
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4391
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 1211/2277HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
metaseqR2 1.19.0  (landing page)
Panagiotis Moulos
Snapshot Date: 2025-01-10 13:40 -0500 (Fri, 10 Jan 2025)
git_url: https://git.bioconductor.org/packages/metaseqR2
git_branch: devel
git_last_commit: 22e1b29
git_last_commit_date: 2024-10-29 10:46:48 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'DESeq2' which is only available as a source package that needs compilation
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  NO, package depends on 'DESeq2' which is only available as a source package that needs compilation
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  NO, package depends on 'DESeq2' which is only available as a source package that needs compilation
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    ERROR  skipped

BUILD results for metaseqR2 on kunpeng2

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: 1.19.0
Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data metaseqR2
StartedAt: 2025-01-11 00:19:51 -0000 (Sat, 11 Jan 2025)
EndedAt: 2025-01-11 00:29:19 -0000 (Sat, 11 Jan 2025)
EllapsedTime: 568.2 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
Warning: program compiled against libxml 212 using older 211
Warning: call dbDisconnect() when finished working with a connection
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 lines 191-254 [example-4] (metaseqr2-annotation.Rmd)
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
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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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