Package: FISHalyseR

Version: 1.16.0

Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:FISHalyseR.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings FISHalyseR_1.16.0.tar.gz

StartedAt: 2019-04-13 02:13:38 -0400 (Sat, 13 Apr 2019)

EndedAt: 2019-04-13 02:16:11 -0400 (Sat, 13 Apr 2019)

EllapsedTime: 153.4 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: FISHalyseR.Rcheck

Warnings: 3

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### Running command:
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###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:FISHalyseR.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings FISHalyseR_1.16.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/FISHalyseR.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '1.16.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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-3.8-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-3.8-bioc/tmpdir/RtmpaimEU7SampleFISH.jpg', resetting
** running examples for arch 'x64' ... WARNING
Found the following significant warnings:
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp0sLfmiSampleFISH.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-3.8-bioc/meat/FISHalyseR.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/FISHalyseR_1.16.0.tar.gz && rm -rf FISHalyseR.buildbin-libdir && mkdir FISHalyseR.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=FISHalyseR.buildbin-libdir FISHalyseR_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL FISHalyseR_1.16.0.zip && rm FISHalyseR_1.16.0.tar.gz FISHalyseR_1.16.0.zip
###
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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_1.16.0.zip
* DONE (FISHalyseR)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'FISHalyseR' successfully unpacked and MD5 sums checked
In R CMD INSTALL