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BioC 3.0: CHECK report for ARRmNormalization on moscato1

This page was generated on 2015-04-10 09:48:41 -0700 (Fri, 10 Apr 2015).

Package 56/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ARRmNormalization 1.6.0
Jean-Philippe Fortin
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/ARRmNormalization
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: ARRmNormalization
Version: 1.6.0
Command: rm -rf ARRmNormalization.buildbin-libdir ARRmNormalization.Rcheck && mkdir ARRmNormalization.buildbin-libdir ARRmNormalization.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ARRmNormalization.buildbin-libdir ARRmNormalization_1.6.0.tar.gz >ARRmNormalization.Rcheck\00install.out 2>&1 && cp ARRmNormalization.Rcheck\00install.out ARRmNormalization-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=ARRmNormalization.buildbin-libdir --install="check:ARRmNormalization-install.out" --force-multiarch --no-vignettes --timings ARRmNormalization_1.6.0.tar.gz
StartedAt: 2015-04-09 22:41:00 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 22:46:02 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 301.8 seconds
RetCode: 0
Status:  OK  
CheckDir: ARRmNormalization.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   rm -rf ARRmNormalization.buildbin-libdir ARRmNormalization.Rcheck && mkdir ARRmNormalization.buildbin-libdir ARRmNormalization.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ARRmNormalization.buildbin-libdir ARRmNormalization_1.6.0.tar.gz >ARRmNormalization.Rcheck\00install.out 2>&1 && cp ARRmNormalization.Rcheck\00install.out ARRmNormalization-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=ARRmNormalization.buildbin-libdir --install="check:ARRmNormalization-install.out" --force-multiarch --no-vignettes --timings ARRmNormalization_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/ARRmNormalization.Rcheck'
* using R version 3.1.3 (2015-03-09)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ARRmNormalization/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ARRmNormalization' version '1.6.0'
* 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 'ARRmNormalization' 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 ... NOTE
Package in Depends field not imported from: 'ARRmData'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
getQuantiles: no visible binding for global variable 'ProbesType'
normalizeARRm: no visible binding for global variable 'ProbesType'
* 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' ... [123s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
normalizeARRm   55.88   2.31   58.19
getCoefficients 18.46   0.90   22.61
positionPlots   13.12   0.56   13.76
getQuantiles    12.70   0.75   13.46
quantilePlots   12.56   0.58   13.13
** running examples for arch 'x64' ... [127s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
normalizeARRm   58.56   2.54   61.11
getCoefficients 18.63   1.03   19.66
positionPlots   15.17   0.63   16.59
getQuantiles    13.10   0.73   13.83
quantilePlots   12.88   0.59   13.50
* 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

NOTE: There were 2 notes.
See
  'D:/biocbld/bbs-3.0-bioc/meat/ARRmNormalization.Rcheck/00check.log'
for details.

ARRmNormalization.Rcheck/00install.out:


install for i386

* installing *source* package 'ARRmNormalization' ...
** 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 'ARRmNormalization' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ARRmNormalization' as ARRmNormalization_1.6.0.zip
* DONE (ARRmNormalization)

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

nameusersystemelapsed
ProbesType1.270.001.26
getBackground0.070.000.36
getCoefficients18.46 0.9022.61
getDesignInfo000
getQuantiles12.70 0.7513.46
normalizeARRm55.88 2.3158.19
positionPlots13.12 0.5613.76
quantilePlots12.56 0.5813.13

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

nameusersystemelapsed
ProbesType1.450.021.46
getBackground0.170.000.17
getCoefficients18.63 1.0319.66
getDesignInfo000
getQuantiles13.10 0.7313.83
normalizeARRm58.56 2.5461.11
positionPlots15.17 0.6316.59
quantilePlots12.88 0.5913.50