BioC 2.12: CHECK report for imageHTS on petty

Package: imageHTS

Version: 1.10.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch imageHTS_1.10.0.tar.gz

StartedAt: 2013-10-08 22:49:44 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 22:57:38 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 474.1 seconds

RetCode: 0

Status:  OK

CheckDir: imageHTS.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/imageHTS.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'imageHTS/DESCRIPTION' ... OK
* this is package 'imageHTS' version '1.10.0'
* 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 ... [32s/33s] OK
* checking installed package size ... OK
* 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [171s/174s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
extractFeatures   48.135  3.830  52.597
countObjects      28.177  1.057  29.945
segmentWells      15.112  1.685  16.856
segmentYeastBF     7.944  1.421   9.398
getWellFeatures    9.112  0.023   9.150
getUnames          7.973  0.085   8.094
fileHTS            7.317  0.038   8.866
zprime             6.761  0.024   6.800
installCellPicker  5.566  0.036   5.618
* 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
  '/Users/biocbuild/bbs-2.12-bioc/meat/imageHTS.Rcheck/00check.log'
for details.

* 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)

name	user	system	elapsed
collectCellFeatures	0.006	0.002	0.008
countObjects	28.177	1.057	29.945
extractFeatures	48.135	3.830	52.597
fileHTS	7.317	0.038	8.866
getImageConf	3.531	0.013	3.555
getUnames	7.973	0.085	8.094
getWellFeatures	9.112	0.023	9.150
highlightSegmentation	0.002	0.004	0.006
installCellPicker	5.566	0.036	5.618
makeCellHTS	0.006	0.010	0.016
parseDCF	0.008	0.006	0.014
parseImageConf	3.552	0.021	3.580
popCellPicker	3.696	0.013	3.719
prw2uname	0.012	0.011	0.023
readLearnTS	0.002	0.004	0.006
segmentATH	0.002	0.004	0.007
segmentWells	15.112	1.685	16.856
segmentYeastBF	7.944	1.421	9.398
summarizeWells	0.007	0.020	0.026
zprime	6.761	0.024	6.800