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CHECK report for FISHalyseR on tokay2

This page was generated on 2018-10-17 08:40:18 -0400 (Wed, 17 Oct 2018).

Package 490/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FISHalyseR 1.14.0
Karesh Arunakirinathan
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/FISHalyseR
Branch: RELEASE_3_7
Last Commit: 6ed71be
Last Changed Date: 2018-04-30 10:35:36 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: FISHalyseR
Version: 1.14.0
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:FISHalyseR.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings FISHalyseR_1.14.0.tar.gz
StartedAt: 2018-10-17 01:58:06 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 01:59:46 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 99.8 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: FISHalyseR.Rcheck
Warnings: 3

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:FISHalyseR.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings FISHalyseR_1.14.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/FISHalyseR.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'FISHalyseR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'FISHalyseR' version '1.14.0'
* 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 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 'C:/Users/biocbuild/bbs-3.7-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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... WARNING
Found the following significant warnings:
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpiinNjwSampleFISH.jpg', resetting
** running examples for arch 'x64' ... WARNING
Found the following significant warnings:
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp8ga5fqSampleFISH.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: 3 WARNINGs, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/FISHalyseR.Rcheck/00check.log'
for details.



Installation output

FISHalyseR.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/FISHalyseR_1.14.0.tar.gz && rm -rf FISHalyseR.buildbin-libdir && mkdir FISHalyseR.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=FISHalyseR.buildbin-libdir FISHalyseR_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL FISHalyseR_1.14.0.zip && rm FISHalyseR_1.14.0.tar.gz FISHalyseR_1.14.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  232k  100  232k    0     0  3978k      0 --:--:-- --:--:-- --:--:-- 4465k

install for i386

* installing *source* package 'FISHalyseR' ...
** 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
  converting help for package 'FISHalyseR'
    finding HTML links ... done
    analyseParticles                        html  
    calculateMaxEntropy                     html  
    calculateThreshold                      html  
    computeIlluminationCorrection           html  
    processFISH                             html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import 'EBImage::abind' by 'abind::abind' when loading 'FISHalyseR'
In R CMD INSTALL

install for x64

* installing *source* package 'FISHalyseR' ...
** testing if installed package can be loaded
Warning: replacing previous import 'EBImage::abind' by 'abind::abind' when loading 'FISHalyseR'
* MD5 sums
packaged installation of 'FISHalyseR' as FISHalyseR_1.14.0.zip
* DONE (FISHalyseR)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'FISHalyseR' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

FISHalyseR.Rcheck/examples_i386/FISHalyseR-Ex.timings

nameusersystemelapsed
analyseParticles0.230.060.35
calculateMaxEntropy0.280.170.46
calculateThreshold0.190.080.26
computeIlluminationCorrection0.010.000.02

FISHalyseR.Rcheck/examples_x64/FISHalyseR-Ex.timings

nameusersystemelapsed
analyseParticles0.200.080.28
calculateMaxEntropy0.340.110.45
calculateThreshold0.280.150.43
computeIlluminationCorrection000