BioC 3.1: CHECK report for CRImage on petty

Package: CRImage

Version: 1.16.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CRImage_1.16.0.tar.gz

StartedAt: 2015-10-08 22:23:56 -0700 (Thu, 08 Oct 2015)

EndedAt: 2015-10-08 22:25:52 -0700 (Thu, 08 Oct 2015)

EllapsedTime: 115.7 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 CRImage_1.16.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/CRImage.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* 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 ‘1.16.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘CRImage’ can be installed ... [6s/6s] 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 ... [41s/41s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
calculateCellularity 7.469  1.835   9.310
classifyCells        5.656  1.469   7.130
convertRGBToHSV      5.388  0.264   5.656
* 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
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/CRImage.Rcheck/00check.log’
for details.

* 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)

name	user	system	elapsed
CRImage-package	0.389	0.018	0.589
SauvolaThreshold	1.030	0.082	1.130
calculateCellularity	7.469	1.835	9.310
calculateMeanStdTarget	2.183	1.098	3.283
calculateOtsu	0.278	0.200	0.478
classifyCells	5.656	1.469	7.130
colorCorrection	2.257	0.962	3.221
convertHSVToRGB	0.767	0.311	1.077
convertLABToRGB	0.862	0.241	1.104
convertRGBToHSV	5.388	0.264	5.656
convertRGBToLAB	0.895	0.324	1.220
correctCopyNumber	0.160	0.001	0.162
createBinaryImage	2.690	0.788	3.480
createClassifier	0.149	0.030	0.179
labelCells	0.001	0.000	0.001
plotCorrectedCN	0.181	0.002	0.187
processAperio	0.026	0.001	0.027
segmentImage	0.001	0.001	0.001