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BioC 2.14: CHECK report for epigenomix on moscato2

This page was generated on 2014-10-08 08:55:24 -0700 (Wed, 08 Oct 2014).

Package 258/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
epigenomix 1.4.1
Hans-Ulrich Klein
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/epigenomix
Last Changed Rev: 89478 / Revision: 95116
Last Changed Date: 2014-04-25 06:27:30 -0700 (Fri, 25 Apr 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: epigenomix
Version: 1.4.1
Command: rm -rf epigenomix.buildbin-libdir && mkdir epigenomix.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=epigenomix.buildbin-libdir epigenomix_1.4.1.tar.gz >epigenomix-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=epigenomix.buildbin-libdir --install="check:epigenomix-install.out" --force-multiarch --no-vignettes --timings epigenomix_1.4.1.tar.gz
StartedAt: 2014-10-08 00:51:20 -0700 (Wed, 08 Oct 2014)
EndedAt: 2014-10-08 01:01:58 -0700 (Wed, 08 Oct 2014)
EllapsedTime: 637.7 seconds
RetCode: 0
Status:  OK  
CheckDir: epigenomix.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf epigenomix.buildbin-libdir && mkdir epigenomix.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=epigenomix.buildbin-libdir epigenomix_1.4.1.tar.gz >epigenomix-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=epigenomix.buildbin-libdir --install="check:epigenomix-install.out" --force-multiarch --no-vignettes --timings epigenomix_1.4.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-2.14-bioc/meat/epigenomix.Rcheck'
* using R version 3.1.1 (2014-07-10)
* using platform: i386-w64-mingw32 (32-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 '1.4.1'
* 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
* 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 ... 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [214s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
bayesMixModel 138.87  11.45  150.35
plotChains     42.93   0.00   42.94
mlMixModel     13.35   0.03   13.43
** running examples for arch 'x64' ... [236s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
bayesMixModel 158.22  10.12  168.37
plotChains     43.04   0.01   43.05
mlMixModel     16.49   0.03   16.54
* 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

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_1.4.1.zip
* DONE (epigenomix)

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

nameusersystemelapsed
ChIPseqSet-class000
MixModel-class000
MixModelBayes-class000
MixModelML-class000
MixtureComponent-class000
bayesMixModel138.87 11.45150.35
eSet0.030.000.03
fpkm0.030.020.05
integrateData0.130.000.12
mappedReads0.090.000.10
matchProbeToPromoter0.440.020.45
mlMixModel13.35 0.0313.43
normalizeChIP0.050.000.05
plotChains42.93 0.0042.94
plotClassification0.030.000.04
plotComponents0.040.010.06
summarizeReads0.400.000.41
transToTSS000

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

nameusersystemelapsed
ChIPseqSet-class000
MixModel-class0.010.000.01
MixModelBayes-class000
MixModelML-class000
MixtureComponent-class000
bayesMixModel158.22 10.12168.37
eSet0.040.000.05
fpkm0.040.000.03
integrateData0.150.000.16
mappedReads0.10.00.1
matchProbeToPromoter0.540.000.54
mlMixModel16.49 0.0316.54
normalizeChIP0.050.000.05
plotChains43.04 0.0143.05
plotClassification0.060.000.07
plotComponents0.080.000.07
summarizeReads0.480.000.49
transToTSS000