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 |
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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 imageHTS_1.16.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/imageHTS.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (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 ... [26s/27s] 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [102s/107s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
extractFeatures 25.970 1.355 27.824
countObjects 15.976 0.445 17.478
segmentWells 9.318 0.548 9.984
getWellFeatures 6.228 0.014 6.413
zprime 5.606 0.033 6.047
getUnames 5.532 0.040 5.690
segmentYeastBF 4.788 0.629 5.514
fileHTS 4.108 0.011 5.174
* 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
‘/Users/biocbuild/bbs-3.0-bioc/meat/imageHTS.Rcheck/00check.log’
for details.