BioC 2.12: CHECK report for CRImage on petty

Package: CRImage

Version: 1.8.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch CRImage_1.8.0.tar.gz

StartedAt: 2013-10-08 22:05:53 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 22:08:39 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 165.6 seconds

RetCode: 0

Status:  OK

CheckDir: CRImage.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/CRImage.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'CRImage/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CRImage' version '1.8.0'
* 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 ... [9s/9s] OK
* checking installed package size ... NOTE
  installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc       2.1Mb
    extdata   5.4Mb
* checking package 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 for unstated 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [64s/65s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
calculateCellularity 11.515  2.064  13.701
convertRGBToHSV      10.825  0.372  11.499
classifyCells         9.042  1.897  11.091
createBinaryImage     4.602  1.141   5.763
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/CRImage.Rcheck/00check.log'
for details.

* 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
* DONE (CRImage)

name	user	system	elapsed
CRImage-package	0.528	0.021	0.692
SauvolaThreshold	1.998	0.163	2.176
calculateCellularity	11.515	2.064	13.701
calculateMeanStdTarget	3.497	1.181	4.721
calculateOtsu	0.573	0.313	0.893
classifyCells	9.042	1.897	11.091
colorCorrection	2.690	1.398	4.097
convertHSVToRGB	0.967	0.431	1.401
convertLABToRGB	1.198	0.365	1.613
convertRGBToHSV	10.825	0.372	11.499
convertRGBToLAB	1.113	0.356	1.502
correctCopyNumber	0.207	0.030	0.240
createBinaryImage	4.602	1.141	5.763
createClassifier	0.287	0.012	0.299
labelCells	0.009	0.009	0.019
plotCorrectedCN	0.238	0.013	0.254
processAperio	0.036	0.013	0.050
segmentImage	0.003	0.005	0.008