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BioC 3.1: CHECK report for CRImage on petty

This page was generated on 2015-10-09 09:34:16 -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: /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

Command output

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


* 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.


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-package0.3890.0180.589
SauvolaThreshold1.0300.0821.130
calculateCellularity7.4691.8359.310
calculateMeanStdTarget2.1831.0983.283
calculateOtsu0.2780.2000.478
classifyCells5.6561.4697.130
colorCorrection2.2570.9623.221
convertHSVToRGB0.7670.3111.077
convertLABToRGB0.8620.2411.104
convertRGBToHSV5.3880.2645.656
convertRGBToLAB0.8950.3241.220
correctCopyNumber0.1600.0010.162
createBinaryImage2.6900.7883.480
createClassifier0.1490.0300.179
labelCells0.0010.0000.001
plotCorrectedCN0.1810.0020.187
processAperio0.0260.0010.027
segmentImage0.0010.0010.001