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CHECK report for imageHTS on merida1

This page was generated on 2019-04-16 11:55:18 -0400 (Tue, 16 Apr 2019).

Package 765/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
imageHTS 1.32.1
Joseph Barry
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/imageHTS
Branch: RELEASE_3_8
Last Commit: e914c11
Last Changed Date: 2019-01-04 13:36:12 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: imageHTS
Version: 1.32.1
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_1.32.1.tar.gz
StartedAt: 2019-04-16 00:40:24 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 00:43:45 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 201.0 seconds
RetCode: 0
Status:  OK 
CheckDir: imageHTS.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /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_1.32.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/imageHTS.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.32.1’
* 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 12.161  1.192  13.420
countObjects     7.389  0.370   7.806
segmentWells     4.865  0.525   5.430
* 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-3.8-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/3.5/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
collectCellFeatures0.0000.0000.001
countObjects7.3890.3707.806
extractFeatures12.161 1.19213.420
fileHTS2.3810.0294.438
getImageConf1.1800.0021.187
getUnames2.8960.0132.926
getWellFeatures3.6250.0123.654
highlightSegmentation000
installCellPicker1.810.011.83
makeCellHTS000
parseDCF0.0100.0000.011
parseImageConf1.1690.0031.183
popCellPicker1.1420.0021.148
prw2uname0.0030.0000.004
readLearnTS000
segmentATH000
segmentWells4.8650.5255.430
segmentYeastBF2.7150.7703.522
summarizeWells000
zprime3.0520.0113.075