BioC 3.1: CHECK report for imageHTS on petty

Package: imageHTS

Version: 1.18.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings imageHTS_1.18.2.tar.gz

StartedAt: 2015-10-08 23:47:33 -0700 (Thu, 08 Oct 2015)

EndedAt: 2015-10-08 23:53:10 -0700 (Thu, 08 Oct 2015)

EllapsedTime: 337.6 seconds

RetCode: 0

Status:  OK

CheckDir: imageHTS.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 imageHTS_1.18.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/imageHTS.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 ‘imageHTS/DESCRIPTION’ ... OK
* this is package ‘imageHTS’ version ‘1.18.2’
* 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/26s] 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 ... 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 ... [115s/116s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
extractFeatures 31.683  2.447  34.155
countObjects    16.335  0.769  17.341
segmentWells    10.787  0.961  11.756
getWellFeatures  6.970  0.011   6.983
zprime           6.557  0.073   6.636
segmentYeastBF   4.842  1.255   6.101
getUnames        5.930  0.009   5.942
fileHTS          5.237  0.068   6.260
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/imageHTS.Rcheck/00check.log’
for details.

* installing *source* package ‘imageHTS’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (imageHTS)

name	user	system	elapsed
collectCellFeatures	0.001	0.000	0.000
countObjects	16.335	0.769	17.341
extractFeatures	31.683	2.447	34.155
fileHTS	5.237	0.068	6.260
getImageConf	2.242	0.002	2.245
getUnames	5.930	0.009	5.942
getWellFeatures	6.970	0.011	6.983
highlightSegmentation	0.001	0.000	0.000
installCellPicker	3.251	0.010	3.260
makeCellHTS	0.002	0.000	0.002
parseDCF	0.005	0.001	0.005
parseImageConf	2.658	0.005	2.665
popCellPicker	1.910	0.001	1.910
prw2uname	0.005	0.001	0.005
readLearnTS	0.001	0.000	0.000
segmentATH	0.001	0.000	0.001
segmentWells	10.787	0.961	11.756
segmentYeastBF	4.842	1.255	6.101
summarizeWells	0.001	0.000	0.001
zprime	6.557	0.073	6.636