BioC 3.3: CHECK report for imageHTS on morelia

Package: imageHTS

Version: 1.21.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings imageHTS_1.21.2.tar.gz

StartedAt: 2016-04-21 04:04:18 -0700 (Thu, 21 Apr 2016)

EndedAt: 2016-04-21 04:08:35 -0700 (Thu, 21 Apr 2016)

EllapsedTime: 256.7 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_1.21.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/imageHTS.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* 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 ‘1.21.2’
* 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 ... [17s/18s] 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 ... [83s/85s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
extractFeatures 20.122  1.653  21.873
countObjects    11.412  0.557  12.137
segmentWells     8.181  0.787   9.104
getWellFeatures  5.717  0.010   5.765
zprime           5.028  0.033   5.072
fileHTS          3.852  0.036   5.348
* 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-3.3-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	0	0
countObjects	11.412	0.557	12.137
extractFeatures	20.122	1.653	21.873
fileHTS	3.852	0.036	5.348
getImageConf	1.990	0.004	2.004
getUnames	4.800	0.008	4.818
getWellFeatures	5.717	0.010	5.765
highlightSegmentation	0	0	0
installCellPicker	3.036	0.011	3.055
makeCellHTS	0.001	0.000	0.002
parseDCF	0.004	0.001	0.005
parseImageConf	1.784	0.002	1.792
popCellPicker	1.753	0.001	1.756
prw2uname	0.005	0.000	0.005
readLearnTS	0.001	0.000	0.000
segmentATH	0.001	0.000	0.001
segmentWells	8.181	0.787	9.104
segmentYeastBF	3.149	0.746	3.908
summarizeWells	0.001	0.000	0.001
zprime	5.028	0.033	5.072