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BioC 3.2: CHECK report for imageHTS on perceval

This page was generated on 2015-11-10 14:46:42 -0800 (Tue, 10 Nov 2015).

Package 523/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
imageHTS 1.20.0
Joseph Barry
Snapshot Date: 2015-11-09 16:24:09 -0800 (Mon, 09 Nov 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/imageHTS
Last Changed Rev: 109589 / Revision: 110496
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: imageHTS
Version: 1.20.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings imageHTS_1.20.0.tar.gz
StartedAt: 2015-11-10 06:05:15 -0800 (Tue, 10 Nov 2015)
EndedAt: 2015-11-10 06:09:43 -0800 (Tue, 10 Nov 2015)
EllapsedTime: 267.1 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 imageHTS_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/imageHTS.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* 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 ‘1.20.0’
* 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 ... [19s/19s] 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 ... [86s/86s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
extractFeatures 23.271  1.816  25.090
countObjects    13.419  0.623  14.044
segmentWells     7.300  0.848   8.148
* 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-3.2-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
collectCellFeatures0.0010.0000.001
countObjects13.419 0.62314.044
extractFeatures23.271 1.81625.090
fileHTS3.6900.0604.613
getImageConf1.6330.0011.635
getUnames4.1220.0024.125
getWellFeatures4.7700.0034.774
highlightSegmentation000
installCellPicker2.4870.0082.495
makeCellHTS0.0020.0000.002
parseDCF0.0030.0010.004
parseImageConf1.6460.0011.648
popCellPicker1.5890.0011.590
prw2uname0.0040.0000.005
readLearnTS000
segmentATH0.0010.0000.001
segmentWells7.3000.8488.148
segmentYeastBF3.6890.9924.681
summarizeWells0.0010.0000.001
zprime4.2780.0394.318