Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-01-26 11:07:35 -0500 (Wed, 26 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4164
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4059
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 4001
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4118
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

CHECK results for epigenomix on riesling1


To the developers/maintainers of the epigenomix package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/epigenomix.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here 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 588/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
epigenomix 1.35.1  (landing page)
Hans-Ulrich Klein
Snapshot Date: 2022-01-25 13:55:17 -0500 (Tue, 25 Jan 2022)
git_url: https://git.bioconductor.org/packages/epigenomix
git_branch: master
git_last_commit: bf5904f
git_last_commit_date: 2021-11-18 19:30:22 -0500 (Thu, 18 Nov 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'Biobase' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: epigenomix
Version: 1.35.1
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:epigenomix.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings epigenomix_1.35.1.tar.gz
StartedAt: 2022-01-25 18:54:23 -0500 (Tue, 25 Jan 2022)
EndedAt: 2022-01-25 18:58:47 -0500 (Tue, 25 Jan 2022)
EllapsedTime: 263.6 seconds
RetCode: 0
Status:   OK  
CheckDir: epigenomix.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:epigenomix.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings epigenomix_1.35.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/epigenomix.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'epigenomix/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'epigenomix' version '1.35.1'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'epigenomix' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
plotChains    24.65   0.05   24.70
bayesMixModel 22.82   0.09   22.91
mlMixModel    11.03   0.06   11.09
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

epigenomix.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL epigenomix
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'epigenomix' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'epigenomix'
    finding HTML links ... done
    ChIPseqSet-class                        html  
    finding level-2 HTML links ... done

    MixModel-class                          html  
    MixModelBayes-class                     html  
    MixModelML-class                        html  
    MixtureComponent-class                  html  
    bayesMixModel                           html  
    calculateCrossCorrelation               html  
    eSet                                    html  
    fpkm                                    html  
    getAlignmentQuality                     html  
    integrateData                           html  
    mappedReads                             html  
    matchProbeToPromoter                    html  
    mlMixModel                              html  
    normalize                               html  
    normalizeChIP                           html  
    plotChains                              html  
    plotClassification                      html  
    plotComponents                          html  
    summarizeReads                          html  
    transToTSS                              html  
** building package indices
** installing vignettes
** 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 (epigenomix)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'plotGrouper' is missing or broken
 done

Tests output


Example timings

epigenomix.Rcheck/epigenomix-Ex.timings

nameusersystemelapsed
ChIPseqSet-class000
MixModel-class000
MixModelBayes-class000
MixModelML-class0.010.000.02
MixtureComponent-class000
bayesMixModel22.82 0.0922.91
calculateCrossCorrelation0.840.020.85
eSet0.000.010.02
fpkm0.030.000.03
getAlignmentQuality000
integrateData0.170.020.18
mappedReads0.050.000.05
matchProbeToPromoter0.330.000.33
mlMixModel11.03 0.0611.09
normalize0.190.000.19
normalizeChIP0.110.000.11
plotChains24.65 0.0524.70
plotClassification0.030.000.03
plotComponents0.070.000.06
summarizeReads0.340.000.35
transToTSS000