BioC 2.14: CHECK report for imageHTS on morelia

Package: imageHTS

Version: 1.14.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch imageHTS_1.14.1.tar.gz

StartedAt: 2014-10-07 23:34:38 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 23:39:52 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 314.3 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 --no-multiarch imageHTS_1.14.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/imageHTS.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin13.1.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘imageHTS/DESCRIPTION’ ... OK
* this is package ‘imageHTS’ version ‘1.14.1’
* 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 ... [23s/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 ... 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 ... [103s/105s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
extractFeatures 26.673  1.333  28.036
countObjects    17.459  0.471  17.947
segmentWells     9.204  0.633   9.883
getWellFeatures  6.338  0.011   6.354
getUnames        5.509  0.026   5.539
zprime           5.220  0.010   5.235
segmentYeastBF   4.478  0.521   5.003
fileHTS          4.329  0.012   5.876
* 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

NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-2.14-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	0.001	0.000	0.000
countObjects	17.459	0.471	17.947
extractFeatures	26.673	1.333	28.036
fileHTS	4.329	0.012	5.876
getImageConf	2.183	0.005	2.190
getUnames	5.509	0.026	5.539
getWellFeatures	6.338	0.011	6.354
highlightSegmentation	0.001	0.001	0.001
installCellPicker	3.050	0.011	3.064
makeCellHTS	0.001	0.000	0.001
parseDCF	0.003	0.001	0.003
parseImageConf	2.123	0.004	2.134
popCellPicker	2.198	0.003	2.203
prw2uname	0.004	0.000	0.004
readLearnTS	0.000	0.000	0.001
segmentATH	0.000	0.000	0.001
segmentWells	9.204	0.633	9.883
segmentYeastBF	4.478	0.521	5.003
summarizeWells	0.001	0.000	0.001
zprime	5.220	0.010	5.235