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BioC 3.0: CHECK report for imageHTS on zin1

This page was generated on 2015-04-10 09:39:06 -0700 (Fri, 10 Apr 2015).

Package 452/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
imageHTS 1.16.0
Joseph Barry
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/imageHTS
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

Package: imageHTS
Version: 1.16.0
Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings imageHTS_1.16.0.tar.gz
StartedAt: 2015-04-10 01:12:28 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 01:17:19 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 291.3 seconds
RetCode: 0
Status:  OK 
CheckDir: imageHTS.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings imageHTS_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/imageHTS.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘imageHTS/DESCRIPTION’ ... OK
* this is package ‘imageHTS’ 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘imageHTS’ can be installed ... [22s/23s] OK
* checking installed package size ... OK
* 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 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 ... NOTE
buildCellHTS: no visible global function definition for
  ‘convertWellCoordinates’
extractCells: no visible global function definition for ‘drawCircle’
getCellFtrsATH : <anonymous>: no visible global function definition for
  ‘computeFeatures.shape’
getCellFtrsATH : <anonymous>: no visible global function definition for
  ‘computeFeatures.moment’
getCellFtrsATH : <anonymous>: no visible global function definition for
  ‘computeFeatures.basic’
getCellFtrsATH : <anonymous>: no visible global function definition for
  ‘computeFeatures.haralick’
highlightSegmentation: no visible global function definition for
  ‘colorMode’
highlightSegmentation: no visible binding for global variable
  ‘Grayscale’
make.crown: no visible global function definition for ‘makeBrush’
makeCellHTS: no visible global function definition for ‘buildCellHTS2’
makeCellHTS: no visible global function definition for ‘name<-’
segmentATH : <anonymous>: no visible global function definition for
  ‘getFrame’
segmentATH : <anonymous>: no visible global function definition for
  ‘computeFeatures.basic’
segmentATH : <anonymous>: no visible global function definition for
  ‘computeFeatures.shape’
segmentRing: no visible global function definition for ‘makeBrush’
segmentRing: no visible global function definition for ‘thresh’
segmentRing: no visible global function definition for ‘drawCircle’
segmentWells: no visible global function definition for ‘getFrame’
* 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 files in ‘vignettes’ ... OK
* checking examples ... [87s/90s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
extractFeatures 24.110  0.056  24.370
countObjects    14.841  0.244  15.916
segmentWells     7.996  0.116   8.148
segmentYeastBF   5.401  0.064   5.712
* 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

NOTE: There were 2 notes.
See
  ‘/home/biocbuild/bbs-3.0-bioc/meat/imageHTS.Rcheck/00check.log’
for details.

imageHTS.Rcheck/00install.out:

* installing *source* package ‘imageHTS’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (imageHTS)

imageHTS.Rcheck/imageHTS-Ex.timings:

nameusersystemelapsed
collectCellFeatures0.0000.0000.001
countObjects14.841 0.24415.916
extractFeatures24.110 0.05624.370
fileHTS3.2760.0044.230
getImageConf1.6280.0041.637
getUnames4.3400.0084.360
getWellFeatures4.7280.0244.840
highlightSegmentation000
installCellPicker2.5050.0122.529
makeCellHTS0.0000.0000.001
parseDCF0.0040.0000.004
parseImageConf1.5520.0041.560
popCellPicker1.6400.0041.651
prw2uname0.0040.0000.005
readLearnTS000
segmentATH0.0040.0000.001
segmentWells7.9960.1168.148
segmentYeastBF5.4010.0645.712
summarizeWells0.0040.0000.001
zprime4.4240.0324.489