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BioC 2.12: CHECK report for CRImage on george2

This page was generated on 2013-10-09 09:37:40 -0700 (Wed, 09 Oct 2013).

Package 156/671HostnameOS / ArchBUILDCHECKBUILD BIN
CRImage 1.8.0
Henrik Failmezger
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/CRImage
Last Changed Rev: 75263 / Revision: 81334
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: CRImage
Version: 1.8.0
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings CRImage_1.8.0.tar.gz
StartedAt: 2013-10-09 01:10:46 -0700 (Wed, 09 Oct 2013)
EndedAt: 2013-10-09 01:13:40 -0700 (Wed, 09 Oct 2013)
EllapsedTime: 173.7 seconds
RetCode: 0
Status:  OK 
CheckDir: CRImage.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/CRImage.Rcheck’
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-unknown-linux-gnu (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 ‘1.8.0’
* 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  7.7Mb
  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 installed files from ‘inst/doc’ ... OK
* checking examples ... [78s/80s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
calculateCellularity   16.989  0.380  17.449
classifyCells          13.385  0.184  13.581
convertRGBToHSV        13.289  0.020  13.678
colorCorrection         5.877  0.116   6.200
createBinaryImage       5.464  0.296   5.763
calculateMeanStdTarget  5.408  0.016   5.579
* 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
  ‘/home/biocbuild/bbs-2.12-bioc/meat/CRImage.Rcheck/00check.log’
for details.

CRImage.Rcheck/00install.out:

* 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)

CRImage.Rcheck/CRImage-Ex.timings:

nameusersystemelapsed
CRImage-package0.4200.0280.531
SauvolaThreshold3.7920.1483.956
calculateCellularity16.989 0.38017.449
calculateMeanStdTarget5.4080.0165.579
calculateOtsu1.2400.0081.249
classifyCells13.385 0.18413.581
colorCorrection5.8770.1166.200
convertHSVToRGB1.9720.1522.486
convertLABToRGB3.1560.0563.317
convertRGBToHSV13.289 0.02013.678
convertRGBToLAB1.4720.0201.492
correctCopyNumber0.1720.0000.172
createBinaryImage5.4640.2965.763
createClassifier0.1600.0040.163
labelCells0.0040.0000.005
plotCorrectedCN0.1720.0000.171
processAperio0.0240.0080.032
segmentImage0.0000.0040.005