Back to Build/check report for BioC 3.17:   simplified   long
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This page was generated on 2023-03-01 07:38:44 -0000 (Wed, 01 Mar 2023).

HostnameOSArch (*)R versionInstalled pkgs
kunpeng1Linux (Ubuntu 22.04.1 LTS)aarch64R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" 4266
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 kunpeng1


To the developers/maintainers of the metaseqR2 package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1146/2171HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
metaseqR2 1.11.0  (landing page)
Panagiotis Moulos
Snapshot Date: 2023-02-27 07:53:22 -0000 (Mon, 27 Feb 2023)
git_url: https://git.bioconductor.org/packages/metaseqR2
git_branch: master
git_last_commit: 36efa5b
git_last_commit_date: 2022-11-01 15:22:03 -0000 (Tue, 01 Nov 2022)
kunpeng1Linux (Ubuntu 22.04.1 LTS) / aarch64  OK    ERROR  skipped

Summary

Package: metaseqR2
Version: 1.11.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data metaseqR2
StartedAt: 2023-02-27 15:11:01 -0000 (Mon, 27 Feb 2023)
EndedAt: 2023-02-27 15:23:26 -0000 (Mon, 27 Feb 2023)
EllapsedTime: 746.0 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/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 '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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downloaded 71 bytes

trying URL 'http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/genePredToGtf'
Content type 'unknown' length 35788952 bytes (34.1 MB)
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sh: 1: /tmp/Rtmp5jSbBD/test_custom/genePredToGtf: Exec format error
Quitting from lines 190-248 (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
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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