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BioC 3.0: CHECK report for CRImage on perceval

This page was generated on 2015-04-10 09:55:21 -0700 (Fri, 10 Apr 2015).

Package 208/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CRImage 1.14.0
Henrik Failmezger , Yinyin Yuan
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/CRImage
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: CRImage
Version: 1.14.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch CRImage_1.14.0.tar.gz
StartedAt: 2015-04-10 00:27:14 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 00:29:38 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 144.3 seconds
RetCode: 0
Status:  OK 
CheckDir: CRImage.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch CRImage_1.14.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/CRImage.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CRImage/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CRImage’ version ‘1.14.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘CRImage’ can be installed ... [7s/9s] OK
* checking installed package size ... NOTE
  installed size is  7.0Mb
  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
* 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:
  ‘aCGH’ ‘DNAcopy’
  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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [60s/60s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
calculateCellularity 11.766  1.919  13.701
classifyCells         8.184  1.660   9.845
convertRGBToHSV       8.644  0.406   9.053
createBinaryImage     4.611  0.978   5.595
colorCorrection       3.935  1.190   5.130
* 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
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/CRImage.Rcheck/00check.log’
for details.

CRImage.Rcheck/00install.out:

* 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?)
* DONE (CRImage)

CRImage.Rcheck/CRImage-Ex.timings:

nameusersystemelapsed
CRImage-package0.3640.0370.578
SauvolaThreshold1.8640.1072.093
calculateCellularity11.766 1.91913.701
calculateMeanStdTarget3.2741.2614.544
calculateOtsu0.4470.2220.669
classifyCells8.1841.6609.845
colorCorrection3.9351.1905.130
convertHSVToRGB1.2460.3331.580
convertLABToRGB1.8560.3182.174
convertRGBToHSV8.6440.4069.053
convertRGBToLAB1.2050.3261.531
correctCopyNumber0.1170.0010.119
createBinaryImage4.6110.9785.595
createClassifier0.1330.0040.136
labelCells0.0010.0010.001
plotCorrectedCN0.1250.0020.127
processAperio0.0190.0020.021
segmentImage0.0010.0000.001