BioC 3.2: CHECK report for imageHTS on zin1

Package: imageHTS

Version: 1.19.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings imageHTS_1.19.0.tar.gz

StartedAt: 2015-07-30 00:47:47 -0700 (Thu, 30 Jul 2015)

EndedAt: 2015-07-30 00:51:03 -0700 (Thu, 30 Jul 2015)

EllapsedTime: 196.3 seconds

RetCode: 0

Status:  OK

CheckDir: imageHTS.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings imageHTS_1.19.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/imageHTS.Rcheck’
* using R version 3.2.1 Patched (2015-07-20 r68705)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘imageHTS/DESCRIPTION’ ... OK
* this is package ‘imageHTS’ version ‘1.19.0’
* 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 ... [14s/14s] 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 ... [68s/72s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
extractFeatures 20.868  0.063  21.069
countObjects    11.012  0.064  11.068
segmentWells     6.177  0.000   6.389
getWellFeatures  3.928  0.000   5.078
* 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
  ‘/home/biocbuild/bbs-3.2-bioc/meat/imageHTS.Rcheck/00check.log’
for details.

* installing *source* package ‘imageHTS’ ...
** R
** inst
** preparing package for lazy loading
Warning: replacing previous import by ‘BiocGenerics::mad’ when loading ‘IRanges’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import by ‘BiocGenerics::mad’ when loading ‘IRanges’
* DONE (imageHTS)

name	user	system	elapsed
collectCellFeatures	0	0	0
countObjects	11.012	0.064	11.068
extractFeatures	20.868	0.063	21.069
fileHTS	2.831	0.004	3.831
getImageConf	1.392	0.012	1.535
getUnames	3.773	0.003	4.155
getWellFeatures	3.928	0.000	5.078
highlightSegmentation	0.001	0.000	0.000
installCellPicker	2.048	0.000	2.541
makeCellHTS	0.001	0.000	0.001
parseDCF	0.002	0.000	0.004
parseImageConf	1.314	0.000	1.334
popCellPicker	1.273	0.000	1.281
prw2uname	0.004	0.000	0.003
readLearnTS	0.000	0.004	0.001
segmentATH	0	0	0
segmentWells	6.177	0.000	6.389
segmentYeastBF	3.116	0.008	3.305
summarizeWells	0.001	0.000	0.000
zprime	3.393	0.000	3.669