Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-09-24 15:06:09 -0400 (Fri, 24 Sep 2021).

CHECK results for epigenomix on tokay2

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 582/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
epigenomix 1.32.0  (landing page)
Hans-Ulrich Klein
Snapshot Date: 2021-09-23 04:50:12 -0400 (Thu, 23 Sep 2021)
git_url: https://git.bioconductor.org/packages/epigenomix
git_branch: RELEASE_3_13
git_last_commit: dc1b2d5
git_last_commit_date: 2021-05-19 11:57:59 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: epigenomix
Version: 1.32.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:epigenomix.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings epigenomix_1.32.0.tar.gz
StartedAt: 2021-09-23 22:01:10 -0400 (Thu, 23 Sep 2021)
EndedAt: 2021-09-23 22:08:20 -0400 (Thu, 23 Sep 2021)
EllapsedTime: 430.3 seconds
RetCode: 0
Status:   OK  
CheckDir: epigenomix.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:epigenomix.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings epigenomix_1.32.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/epigenomix.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.32.0'
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
plotChains    28.01   0.02   28.03
bayesMixModel 20.15   0.27   20.42
mlMixModel    10.29   0.13   10.41
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
plotChains    25.78   0.11   26.11
bayesMixModel 20.96   0.02   20.97
mlMixModel    11.00   0.02   11.02
* 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

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/epigenomix_1.32.0.tar.gz && rm -rf epigenomix.buildbin-libdir && mkdir epigenomix.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=epigenomix.buildbin-libdir epigenomix_1.32.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL epigenomix_1.32.0.zip && rm epigenomix_1.32.0.tar.gz epigenomix_1.32.0.zip
###
##############################################################################
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  213k  100  213k    0     0   934k      0 --:--:-- --:--:-- --:--:--  937k

install for i386

* 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

install for x64

* installing *source* package 'epigenomix' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'epigenomix' as epigenomix_1.32.0.zip
* DONE (epigenomix)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'epigenomix' successfully unpacked and MD5 sums checked

Tests output


Example timings

epigenomix.Rcheck/examples_i386/epigenomix-Ex.timings

nameusersystemelapsed
ChIPseqSet-class000
MixModel-class000
MixModelBayes-class000
MixModelML-class000
MixtureComponent-class000
bayesMixModel20.15 0.2720.42
calculateCrossCorrelation0.830.000.83
eSet0.000.010.02
fpkm0.030.000.04
getAlignmentQuality000
integrateData0.220.000.22
mappedReads0.060.030.09
matchProbeToPromoter0.50.00.5
mlMixModel10.29 0.1310.41
normalize0.210.000.22
normalizeChIP0.150.000.14
plotChains28.01 0.0228.03
plotClassification0.020.000.02
plotComponents0.030.000.03
summarizeReads0.390.000.39
transToTSS000

epigenomix.Rcheck/examples_x64/epigenomix-Ex.timings

nameusersystemelapsed
ChIPseqSet-class000
MixModel-class000
MixModelBayes-class000
MixModelML-class000
MixtureComponent-class000
bayesMixModel20.96 0.0220.97
calculateCrossCorrelation0.790.000.80
eSet0.020.000.01
fpkm0.050.020.07
getAlignmentQuality000
integrateData0.330.000.33
mappedReads0.050.010.06
matchProbeToPromoter0.460.000.47
mlMixModel11.00 0.0211.02
normalize0.300.000.29
normalizeChIP0.250.000.25
plotChains25.78 0.1126.11
plotClassification0.030.000.03
plotComponents0.030.000.03
summarizeReads0.370.000.37
transToTSS0.020.000.02