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CHECK report for imageHTS on merida2

This page was generated on 2019-04-09 13:25:22 -0400 (Tue, 09 Apr 2019).

Package 789/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
imageHTS 1.33.1
Joseph Barry
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/imageHTS
Branch: master
Last Commit: 58f564f
Last Changed Date: 2019-01-04 13:36:10 -0400 (Fri, 04 Jan 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK 

Summary

Package: imageHTS
Version: 1.33.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:imageHTS.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings imageHTS_1.33.1.tar.gz
StartedAt: 2019-04-09 01:37:07 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 01:40:40 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 213.5 seconds
RetCode: 0
Status:  OK 
CheckDir: imageHTS.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:imageHTS.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings imageHTS_1.33.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/imageHTS.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘imageHTS/DESCRIPTION’ ... OK
* this is package ‘imageHTS’ version ‘1.33.1’
* 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 ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
extractFeatures 14.418  0.735  15.292
countObjects     7.208  0.321   7.782
segmentWells     5.376  0.240   5.679
fileHTS          2.693  0.040   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-3.9-bioc/meat/imageHTS.Rcheck/00check.log’
for details.



Installation output

imageHTS.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL imageHTS
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘imageHTS’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (imageHTS)

Tests output


Example timings

imageHTS.Rcheck/imageHTS-Ex.timings

nameusersystemelapsed
collectCellFeatures0.0010.0000.001
countObjects7.2080.3217.782
extractFeatures14.418 0.73515.292
fileHTS2.6930.0405.348
getImageConf1.2940.0181.325
getUnames3.2260.0053.272
getWellFeatures4.0570.0084.115
highlightSegmentation0.0010.0000.000
installCellPicker2.0670.0112.103
makeCellHTS0.0010.0010.001
parseDCF0.0030.0000.004
parseImageConf1.2340.0021.245
popCellPicker1.2700.0021.284
prw2uname0.0050.0010.006
readLearnTS000
segmentATH000
segmentWells5.3760.2405.679
segmentYeastBF2.6070.5493.183
summarizeWells000
zprime3.3370.0323.388