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BioC 3.1: CHECK report for CRImage on moscato2

This page was generated on 2015-10-09 09:28:58 -0700 (Fri, 09 Oct 2015).

Package 225/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CRImage 1.16.0
Henrik Failmezger , Yinyin Yuan
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/CRImage
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: CRImage
Version: 1.16.0
Command: rm -rf CRImage.buildbin-libdir CRImage.Rcheck && mkdir CRImage.buildbin-libdir CRImage.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CRImage.buildbin-libdir CRImage_1.16.0.tar.gz >CRImage.Rcheck\00install.out 2>&1 && cp CRImage.Rcheck\00install.out CRImage-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=CRImage.buildbin-libdir --install="check:CRImage-install.out" --force-multiarch --no-vignettes --timings CRImage_1.16.0.tar.gz
StartedAt: 2015-10-09 00:51:21 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 00:53:47 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 145.4 seconds
RetCode: 0
Status:  OK  
CheckDir: CRImage.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf CRImage.buildbin-libdir CRImage.Rcheck && mkdir CRImage.buildbin-libdir CRImage.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CRImage.buildbin-libdir CRImage_1.16.0.tar.gz >CRImage.Rcheck\00install.out 2>&1 && cp CRImage.Rcheck\00install.out CRImage-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=CRImage.buildbin-libdir --install="check:CRImage-install.out" --force-multiarch --no-vignettes --timings CRImage_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/CRImage.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 'CRImage/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CRImage' version '1.16.0'
* 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.
* 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' ... [30s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
calculateCellularity 6.78   0.86    8.63
classifyCells        4.90   0.60    5.49
** running examples for arch 'x64' ... [33s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
calculateCellularity 6.57   0.77    7.70
classifyCells        4.81   0.93    5.74
* 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: 2 NOTEs
See
  'E:/biocbld/bbs-3.1-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
Warning in namespaceImportMethods(ns, loadNamespace(j <- imp[[1L]], c(lib.loc,  :
  No generic function found corresponding to requested imported methods for "as.list" from package "multtest" (malformed exports?)
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in namespaceImportMethods(ns, loadNamespace(j <- imp[[1L]], c(lib.loc,  :
  No generic function found corresponding to requested imported methods for "as.list" from package "multtest" (malformed exports?)

install for x64

* installing *source* package 'CRImage' ...
** testing if installed package can be loaded
Warning in namespaceImportMethods(ns, loadNamespace(j <- imp[[1L]], c(lib.loc,  :
  No generic function found corresponding to requested imported methods for "as.list" from package "multtest" (malformed exports?)
* MD5 sums
packaged installation of 'CRImage' as CRImage_1.16.0.zip
* DONE (CRImage)

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

nameusersystemelapsed
CRImage-package0.310.000.34
SauvolaThreshold0.690.120.84
calculateCellularity6.780.868.63
calculateMeanStdTarget1.390.622.01
calculateOtsu0.220.080.30
classifyCells4.900.605.49
colorCorrection1.570.842.42
convertHSVToRGB0.580.120.70
convertLABToRGB0.730.140.87
convertRGBToHSV2.980.073.04
convertRGBToLAB0.780.211.00
correctCopyNumber0.110.000.11
createBinaryImage2.110.472.58
createClassifier0.140.000.14
labelCells000
plotCorrectedCN0.130.000.13
processAperio0.010.000.01
segmentImage000

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

nameusersystemelapsed
CRImage-package0.280.010.30
SauvolaThreshold0.830.091.66
calculateCellularity6.570.777.70
calculateMeanStdTarget1.870.812.68
calculateOtsu0.220.050.26
classifyCells4.810.935.74
colorCorrection2.480.613.09
convertHSVToRGB0.920.241.15
convertLABToRGB0.940.231.17
convertRGBToHSV3.500.143.63
convertRGBToLAB0.540.220.77
correctCopyNumber0.110.000.11
createBinaryImage2.060.582.63
createClassifier0.140.000.14
labelCells000
plotCorrectedCN0.130.000.13
processAperio0.010.000.01
segmentImage000