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BioC 3.2: CHECK report for epigenomix on windows1.bioconductor.org

This page was generated on 2015-10-27 17:30:23 -0400 (Tue, 27 Oct 2015).

Package 322/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
epigenomix 1.10.0
Hans-Ulrich Klein
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/epigenomix
Last Changed Rev: 109589 / Revision: 109947
Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 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: 1.10.0
Command: rm -rf epigenomix.buildbin-libdir epigenomix.Rcheck && mkdir epigenomix.buildbin-libdir epigenomix.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=epigenomix.buildbin-libdir epigenomix_1.10.0.tar.gz >epigenomix.Rcheck\00install.out 2>&1 && cp epigenomix.Rcheck\00install.out epigenomix-install.out && C:\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_1.10.0.tar.gz
StartedAt: 2015-10-27 01:33:07 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 01:42:23 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 556.4 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 && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=epigenomix.buildbin-libdir epigenomix_1.10.0.tar.gz >epigenomix.Rcheck\00install.out 2>&1 && cp epigenomix.Rcheck\00install.out epigenomix-install.out  && C:\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_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/biocbld/bbs-3.2-bioc/meat/epigenomix.Rcheck'
* using R version 3.2.2 Patched (2015-08-16 r69094)
* 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 '1.10.0'
* 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
** 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' ... [181s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
bayesMixModel 125.89  11.89  137.81
plotChains     28.25   0.00   28.25
mlMixModel      8.78   0.08    8.86
** running examples for arch 'x64' ... [199s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
bayesMixModel 138.64  12.75  151.41
plotChains     30.56   0.04   30.62
mlMixModel      9.89   0.05    9.93
* 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
  'C:/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_1.10.0.zip
* DONE (epigenomix)

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

nameusersystemelapsed
ChIPseqSet-class000
MixModel-class000
MixModelBayes-class000
MixModelML-class000
MixtureComponent-class000
bayesMixModel125.89 11.89137.81
calculateCrossCorrelation0.510.010.53
eSet000
fpkm0.050.000.05
getAlignmentQuality000
integrateData0.090.000.09
mappedReads0.050.000.05
matchProbeToPromoter0.170.000.17
mlMixModel8.780.088.86
normalizeChIP0.030.000.03
plotChains28.25 0.0028.25
plotClassification0.040.000.03
plotComponents0.040.000.05
summarizeReads0.190.000.19
transToTSS0.000.010.01

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

nameusersystemelapsed
ChIPseqSet-class000
MixModel-class000
MixModelBayes-class000
MixModelML-class0.010.000.01
MixtureComponent-class000
bayesMixModel138.64 12.75151.41
calculateCrossCorrelation0.690.000.69
eSet0.020.000.01
fpkm0.030.000.03
getAlignmentQuality000
integrateData0.120.000.13
mappedReads0.050.000.05
matchProbeToPromoter0.250.000.25
mlMixModel9.890.059.93
normalizeChIP0.050.000.05
plotChains30.56 0.0430.62
plotClassification0.050.000.05
plotComponents0.080.000.08
summarizeReads0.210.000.22
transToTSS000