BioC 2.14: CHECK report for CRImage on petty

Package: CRImage

Version: 1.12.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch CRImage_1.12.0.tar.gz

StartedAt: 2014-10-07 21:31:52 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 21:34:58 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 186.7 seconds

RetCode: 0

Status:  OK

CheckDir: CRImage.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch CRImage_1.12.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/CRImage.Rcheck’
* using R version 3.1.1 (2014-07-10)
* 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 ‘1.12.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘CRImage’ can be installed ... [10s/10s] 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.
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [60s/68s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
calculateCellularity   11.707  1.704  14.546
classifyCells           8.728  1.722  11.897
convertRGBToHSV         9.891  0.334  12.039
createBinaryImage       4.280  0.850   5.181
colorCorrection         3.262  1.054   5.199
calculateMeanStdTarget  2.630  1.479   5.840
* 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
  ‘/Users/biocbuild/bbs-2.14-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	0.565	0.028	0.867
SauvolaThreshold	1.481	0.083	1.595
calculateCellularity	11.707	1.704	14.546
calculateMeanStdTarget	2.630	1.479	5.840
calculateOtsu	0.307	0.184	0.710
classifyCells	8.728	1.722	11.897
colorCorrection	3.262	1.054	5.199
convertHSVToRGB	1.599	0.341	1.953
convertLABToRGB	1.305	0.237	1.546
convertRGBToHSV	9.891	0.334	12.039
convertRGBToLAB	0.881	0.269	1.156
correctCopyNumber	0.211	0.001	0.219
createBinaryImage	4.280	0.850	5.181
createClassifier	0.218	0.008	0.226
labelCells	0.001	0.000	0.001
plotCorrectedCN	0.223	0.001	0.226
processAperio	0.029	0.001	0.030
segmentImage	0.001	0.000	0.001