BioC 3.5: CHECK report for FISHalyseR on oaxaca

Package: FISHalyseR

Version: 1.9.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings FISHalyseR_1.9.0.tar.gz

StartedAt: 2017-03-04 02:44:41 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 02:45:37 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 55.6 seconds

RetCode: 0

Status:  OK

CheckDir: FISHalyseR.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings FISHalyseR_1.9.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/FISHalyseR.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.9.0’
* 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 ... 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 loading without being on the library search path ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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-3.5-bioc/meat/FISHalyseR.Rcheck/00check.log’
for details.

* installing *source* package ‘FISHalyseR’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (FISHalyseR)

name	user	system	elapsed
analyseParticles	0.437	0.041	0.478
calculateMaxEntropy	0.419	0.039	0.458
calculateThreshold	0.230	0.036	0.267
computeIlluminationCorrection	0.000	0.000	0.001