Package: FISHalyseR

Version: 1.18.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:FISHalyseR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings FISHalyseR_1.18.0.tar.gz

StartedAt: 2019-10-16 02:47:47 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 02:49:13 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 86.3 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: FISHalyseR.Rcheck

Warnings: 2

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:FISHalyseR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings FISHalyseR_1.18.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/FISHalyseR.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FISHalyseR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘FISHalyseR’ version ‘1.18.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘FISHalyseR’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘EBImage::abind’ by ‘abind::abind’ when loading ‘FISHalyseR’
See ‘/Users/biocbuild/bbs-3.9-bioc/meat/FISHalyseR.Rcheck/00install.out’ for details.
* 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 ... NOTE
computeIlluminationCorrection: warning in gblur(I, s = 5): partial
  argument match of 's' to 'sigma'
GetDistances: no visible global function definition for ‘na.exclude’
plotLabelMatrix: no visible global function definition for ‘jpeg’
plotLabelMatrix: no visible global function definition for ‘text’
plotLabelMatrix: no visible global function definition for ‘dev.off’
processFISH: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  dev.off jpeg na.exclude text write.table
Consider adding
  importFrom("grDevices", "dev.off", "jpeg")
  importFrom("graphics", "text")
  importFrom("stats", "na.exclude")
  importFrom("utils", "write.table")
to your NAMESPACE file.
* 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 ... WARNING
Found the following significant warnings:
  Warning: working directory was changed to ‘/private/tmp/Rtmp5dTNjTSampleFISH.jpg’, resetting
* 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: 2 WARNINGs, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/FISHalyseR.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL FISHalyseR
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘FISHalyseR’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘EBImage::abind’ by ‘abind::abind’ when loading ‘FISHalyseR’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘EBImage::abind’ by ‘abind::abind’ when loading ‘FISHalyseR’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘EBImage::abind’ by ‘abind::abind’ when loading ‘FISHalyseR’
** testing if installed package keeps a record of temporary installation path
* DONE (FISHalyseR)

name	user	system	elapsed
analyseParticles	0.340	0.080	0.423
calculateMaxEntropy	0.269	0.041	0.311
calculateThreshold	0.113	0.020	0.133
computeIlluminationCorrection	0.001	0.001	0.002