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BioC 2.14: CHECK report for imageHTS on morelia

This page was generated on 2014-10-08 09:04:24 -0700 (Wed, 08 Oct 2014).

Package 410/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
imageHTS 1.14.1
Joseph Barry
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/imageHTS
Last Changed Rev: 94228 / Revision: 95116
Last Changed Date: 2014-09-18 01:28:07 -0700 (Thu, 18 Sep 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK 

Summary

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

Command output

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


* 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.

imageHTS.Rcheck/00install.out:

* 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)

imageHTS.Rcheck/imageHTS-Ex.timings:

nameusersystemelapsed
collectCellFeatures0.0010.0000.000
countObjects17.459 0.47117.947
extractFeatures26.673 1.33328.036
fileHTS4.3290.0125.876
getImageConf2.1830.0052.190
getUnames5.5090.0265.539
getWellFeatures6.3380.0116.354
highlightSegmentation0.0010.0010.001
installCellPicker3.0500.0113.064
makeCellHTS0.0010.0000.001
parseDCF0.0030.0010.003
parseImageConf2.1230.0042.134
popCellPicker2.1980.0032.203
prw2uname0.0040.0000.004
readLearnTS0.0000.0000.001
segmentATH0.0000.0000.001
segmentWells9.2040.6339.883
segmentYeastBF4.4780.5215.003
summarizeWells0.0010.0000.001
zprime5.2200.0105.235