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CHECK report for FISHalyseR on machv2

This page was generated on 2020-10-17 11:58:28 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE FISHalyseR PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 598/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FISHalyseR 1.22.0
Karesh Arunakirinathan
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/FISHalyseR
Branch: RELEASE_3_11
Last Commit: d8d2370
Last Changed Date: 2020-04-27 14:48:03 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: FISHalyseR
Version: 1.22.0
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_1.22.0.tar.gz
StartedAt: 2020-10-17 01:09:33 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 01:10:35 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 61.7 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: FISHalyseR.Rcheck
Warnings: 2

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:FISHalyseR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings FISHalyseR_1.22.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/FISHalyseR.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.22.0’
* 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-3.11-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/RtmpyZ4lVPSampleFISH.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-3.11-bioc/meat/FISHalyseR.Rcheck/00check.log’
for details.



Installation output

FISHalyseR.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL FISHalyseR
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/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)

Tests output


Example timings

FISHalyseR.Rcheck/FISHalyseR-Ex.timings

nameusersystemelapsed
analyseParticles0.1520.0330.187
calculateMaxEntropy0.1580.0410.200
calculateThreshold0.1740.0430.218
computeIlluminationCorrection0.0000.0000.002