BioC 2.13: CHECK report for imageHTS on perceval

Package: imageHTS

Version: 1.12.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch imageHTS_1.12.0.tar.gz

StartedAt: 2014-04-05 02:06:57 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 02:15:32 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 515.3 seconds

RetCode: 0

Status:  OK

CheckDir: imageHTS.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/imageHTS.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘1.12.0’
* 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 ... [35s/36s] 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘imageHTS-introduction.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [165s/169s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
extractFeatures 42.514  3.675  46.778
countObjects    33.201  1.086  34.774
segmentWells    14.840  1.700  16.850
segmentYeastBF  11.007  1.264  12.439
getWellFeatures  7.801  0.044   8.059
getUnames        6.586  0.048   6.779
zprime           5.915  0.034   6.011
fileHTS          5.015  0.057   6.573
* 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 were 2 notes.
See
  ‘/Users/biocbuild/bbs-2.13-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	0.594	0.007	0.609
countObjects	33.201	1.086	34.774
extractFeatures	42.514	3.675	46.778
fileHTS	5.015	0.057	6.573
getImageConf	2.561	0.021	2.622
getUnames	6.586	0.048	6.779
getWellFeatures	7.801	0.044	8.059
highlightSegmentation	0.002	0.004	0.005
installCellPicker	3.994	0.034	4.108
makeCellHTS	0.006	0.012	0.024
parseDCF	0.008	0.006	0.014
parseImageConf	2.740	0.021	2.795
popCellPicker	2.656	0.015	2.709
prw2uname	0.009	0.008	0.017
readLearnTS	0.002	0.003	0.005
segmentATH	0.002	0.004	0.005
segmentWells	14.84	1.70	16.85
segmentYeastBF	11.007	1.264	12.439
summarizeWells	0.007	0.013	0.020
zprime	5.915	0.034	6.011