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BioC 3.2: CHECK report for epigenomix on moscato1

This page was generated on 2015-08-20 13:21:28 -0700 (Thu, 20 Aug 2015).

Package 313/1069HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
epigenomix 1.9.2
Hans-Ulrich Klein
Snapshot Date: 2015-08-19 16:24:33 -0700 (Wed, 19 Aug 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/epigenomix
Last Changed Rev: 105144 / Revision: 107602
Last Changed Date: 2015-06-18 19:12:23 -0700 (Thu, 18 Jun 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: epigenomix
Version: 1.9.2
Command: rm -rf epigenomix.buildbin-libdir epigenomix.Rcheck && mkdir epigenomix.buildbin-libdir epigenomix.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=epigenomix.buildbin-libdir epigenomix_1.9.2.tar.gz >epigenomix.Rcheck\00install.out 2>&1 && cp epigenomix.Rcheck\00install.out epigenomix-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=epigenomix.buildbin-libdir --install="check:epigenomix-install.out" --force-multiarch --no-vignettes --timings epigenomix_1.9.2.tar.gz
StartedAt: 2015-08-20 04:08:38 -0700 (Thu, 20 Aug 2015)
EndedAt: 2015-08-20 04:22:58 -0700 (Thu, 20 Aug 2015)
EllapsedTime: 859.2 seconds
RetCode: 0
Status:  OK  
CheckDir: epigenomix.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf epigenomix.buildbin-libdir epigenomix.Rcheck && mkdir epigenomix.buildbin-libdir epigenomix.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=epigenomix.buildbin-libdir epigenomix_1.9.2.tar.gz >epigenomix.Rcheck\00install.out 2>&1 && cp epigenomix.Rcheck\00install.out epigenomix-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=epigenomix.buildbin-libdir --install="check:epigenomix-install.out" --force-multiarch --no-vignettes --timings epigenomix_1.9.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/epigenomix.Rcheck'
* using R version 3.2.2 (2015-08-14)
* 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 '1.9.2'
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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 ... NOTE
.calculateCrossCorrelation: no visible global function definition for
  'mclapply'
.calculateCrossCorrelation : <anonymous>: no visible global function
  definition for 'keepSeqlevels'
.getAlignmentQuality: no visible global function definition for
  'mclapply'
calculateCrossCorrelation,GRanges: no visible global function
  definition for 'mclapply'
calculateCrossCorrelation,GRanges : <anonymous>: no visible global
  function definition for 'keepSeqlevels'
getAlignmentQuality,character: no visible global function definition
  for 'mclapply'
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [273s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
bayesMixModel 188.06  11.98  200.24
plotChains     46.28   0.02   46.31
mlMixModel     15.27   0.02   15.28
** running examples for arch 'x64' ... [281s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
bayesMixModel 194.61  12.23  206.88
plotChains     46.67   0.00   46.68
mlMixModel     15.79   0.04   15.83
* 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: 1 NOTE
See
  'D:/biocbld/bbs-3.2-bioc/meat/epigenomix.Rcheck/00check.log'
for details.


epigenomix.Rcheck/00install.out:


install for i386

* installing *source* package 'epigenomix' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'epigenomix' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'epigenomix' as epigenomix_1.9.2.zip
* DONE (epigenomix)

epigenomix.Rcheck/examples_i386/epigenomix-Ex.timings:

nameusersystemelapsed
ChIPseqSet-class0.020.000.01
MixModel-class000
MixModelBayes-class000
MixModelML-class000
MixtureComponent-class000
bayesMixModel188.06 11.98200.24
calculateCrossCorrelation0.820.000.83
eSet0.020.000.02
fpkm0.060.000.06
getAlignmentQuality000
integrateData0.190.000.19
mappedReads0.060.000.06
matchProbeToPromoter0.360.000.36
mlMixModel15.27 0.0215.28
normalizeChIP0.070.000.07
plotChains46.28 0.0246.31
plotClassification0.030.000.04
plotComponents0.110.000.10
summarizeReads0.470.000.47
transToTSS0.010.000.02

epigenomix.Rcheck/examples_x64/epigenomix-Ex.timings:

nameusersystemelapsed
ChIPseqSet-class000
MixModel-class000
MixModelBayes-class000
MixModelML-class000
MixtureComponent-class000
bayesMixModel194.61 12.23206.88
calculateCrossCorrelation1.040.001.04
eSet0.040.000.03
fpkm0.040.000.05
getAlignmentQuality000
integrateData0.20.00.2
mappedReads0.050.000.05
matchProbeToPromoter0.330.000.33
mlMixModel15.79 0.0415.83
normalizeChIP0.040.000.05
plotChains46.67 0.0046.68
plotClassification0.050.000.05
plotComponents0.080.000.08
summarizeReads0.370.000.37
transToTSS0.000.010.02