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BioC 2.14: CHECK report for CRImage on moscato2

This page was generated on 2014-10-08 08:53:36 -0700 (Wed, 08 Oct 2014).

Package 197/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CRImage 1.12.0
Henrik Failmezger , Yinyin Yuan
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/CRImage
Last Changed Rev: 88838 / Revision: 95116
Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 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: CRImage
Version: 1.12.0
Command: rm -rf CRImage.buildbin-libdir && mkdir CRImage.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CRImage.buildbin-libdir CRImage_1.12.0.tar.gz >CRImage-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=CRImage.buildbin-libdir --install="check:CRImage-install.out" --force-multiarch --no-vignettes --timings CRImage_1.12.0.tar.gz
StartedAt: 2014-10-08 00:16:56 -0700 (Wed, 08 Oct 2014)
EndedAt: 2014-10-08 00:19:30 -0700 (Wed, 08 Oct 2014)
EllapsedTime: 153.9 seconds
RetCode: 0
Status:  OK  
CheckDir: CRImage.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf CRImage.buildbin-libdir && mkdir CRImage.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CRImage.buildbin-libdir CRImage_1.12.0.tar.gz >CRImage-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=CRImage.buildbin-libdir --install="check:CRImage-install.out" --force-multiarch --no-vignettes --timings CRImage_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-2.14-bioc/meat/CRImage.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 'CRImage/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CRImage' version '1.12.0'
* 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 'CRImage' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc       1.4Mb
    extdata   5.4Mb
* 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
'library' or 'require' calls to packages already attached by Depends:
  'DNAcopy' 'aCGH'
  Please remove these calls from your code.
':::' call which should be '::': 'aCGH:::combine.func'
  See the note in ?`:::` about the use of this operator.
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [31s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
calculateCellularity 6.59   0.78    7.41
classifyCells        5.40   0.70    6.10
** running examples for arch 'x64' ... [36s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
calculateCellularity 6.85   0.97    8.16
classifyCells        5.57   0.62    6.19
convertRGBToHSV      5.02   0.11    5.13
* 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

NOTE: There were 2 notes.
See
  'E:/biocbld/bbs-2.14-bioc/meat/CRImage.Rcheck/00check.log'
for details.

CRImage.Rcheck/00install.out:


install for i386

* installing *source* package 'CRImage' ...
** R
** 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 'CRImage' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CRImage' as CRImage_1.12.0.zip
* DONE (CRImage)

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

nameusersystemelapsed
CRImage-package0.300.000.92
SauvolaThreshold0.860.090.98
calculateCellularity6.590.787.41
calculateMeanStdTarget1.460.752.20
calculateOtsu0.290.050.34
classifyCells5.40.76.1
colorCorrection1.670.612.28
convertHSVToRGB0.780.140.92
convertLABToRGB0.550.160.70
convertRGBToHSV3.700.153.85
convertRGBToLAB0.430.150.59
correctCopyNumber0.110.000.11
createBinaryImage1.840.412.24
createClassifier0.160.000.15
labelCells000
plotCorrectedCN0.120.000.13
processAperio0.010.000.02
segmentImage000

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

nameusersystemelapsed
CRImage-package0.360.000.36
SauvolaThreshold0.810.091.09
calculateCellularity6.850.978.16
calculateMeanStdTarget1.680.542.23
calculateOtsu0.240.100.33
classifyCells5.570.626.19
colorCorrection2.920.703.70
convertHSVToRGB0.940.141.07
convertLABToRGB0.810.251.07
convertRGBToHSV5.020.115.13
convertRGBToLAB0.590.080.67
correctCopyNumber0.160.000.15
createBinaryImage2.980.143.12
createClassifier0.150.000.16
labelCells000
plotCorrectedCN0.130.000.13
processAperio0.020.000.01
segmentImage000