Package: spotSegmentation

Version: 1.52.0

Command: rm -rf spotSegmentation.buildbin-libdir spotSegmentation.Rcheck && mkdir spotSegmentation.buildbin-libdir spotSegmentation.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=spotSegmentation.buildbin-libdir spotSegmentation_1.52.0.tar.gz >spotSegmentation.Rcheck\00install.out 2>&1 && cp spotSegmentation.Rcheck\00install.out spotSegmentation-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=spotSegmentation.buildbin-libdir --install="check:spotSegmentation-install.out" --force-multiarch --no-vignettes --timings spotSegmentation_1.52.0.tar.gz

StartedAt: 2018-04-12 03:23:35 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 03:24:18 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 43.0 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: spotSegmentation.Rcheck

Warnings: 1

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### Running command:
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###   rm -rf spotSegmentation.buildbin-libdir spotSegmentation.Rcheck && mkdir spotSegmentation.buildbin-libdir spotSegmentation.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=spotSegmentation.buildbin-libdir spotSegmentation_1.52.0.tar.gz >spotSegmentation.Rcheck\00install.out 2>&1 && cp spotSegmentation.Rcheck\00install.out spotSegmentation-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=spotSegmentation.buildbin-libdir --install="check:spotSegmentation-install.out" --force-multiarch --no-vignettes --timings spotSegmentation_1.52.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/spotSegmentation.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'spotSegmentation/DESCRIPTION' ... OK
* this is package 'spotSegmentation' version '1.52.0'
* 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 'spotSegmentation' can be installed ... OK
* checking installed package size ... OK
* checking package 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: 'mclust'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plot.spotseg : plotSpotImage: no visible global function definition for
  'par'
plot.spotseg : plotSpotImage: no visible global function definition for
  'image'
plot.spotseg: no visible global function definition for 'postscript'
plotBlockImage: no visible global function definition for 'par'
plotBlockImage: no visible global function definition for 'image'
plotBlockImage: no visible global function definition for 'gray'
spotgrid : spotgridPeaks: no visible global function definition for
  'runif'
spotgrid : spotgridPeaks: no visible global function definition for
  'embed'
spotgrid: no visible global function definition for 'contour'
spotseg : spotseg1 : plotSpotImage: no visible global function
  definition for 'par'
spotseg : spotseg1 : plotSpotImage: no visible global function
  definition for 'image'
spotseg : spotseg1: no visible global function definition for
  'mclustBIC'
spotseg : spotseg1: no visible global function definition for 'hcE'
spotseg : spotseg1: no visible global function definition for 'frame'
spotseg: no visible global function definition for 'par'
spotseg: no visible global function definition for 'median'
Undefined global functions or variables:
  contour embed frame gray hcE image mclustBIC median par postscript
  runif
Consider adding
  importFrom("grDevices", "gray", "postscript")
  importFrom("graphics", "contour", "frame", "image", "par")
  importFrom("stats", "embed", "median", "runif")
to your NAMESPACE file.
* checking Rd files ... NOTE
prepare_Rd: plot.spotseg.Rd:23: Dropping empty section \author
prepare_Rd: plotBlockImage.Rd:20: Dropping empty section \author
prepare_Rd: spotgrid.Rd:21: Dropping empty section \details
prepare_Rd: spotgrid.Rd:33: Dropping empty section \note
prepare_Rd: spotgrid.Rd:34: Dropping empty section \author
prepare_Rd: spotseg.Rd:45: Dropping empty section \author
prepare_Rd: summary.spotseg.Rd:27: Dropping empty section \author
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
  'spotsegdoc.pdf'
Package has no Sweave vignette sources and no VignetteBuilder field.
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/spotSegmentation.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'spotSegmentation' ...
** R
** data
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'spotSegmentation'
    finding HTML links ... done
    plot.spotseg                            html  
    plotBlockImage                          html  
    spotSegTest                             html  
    spotgrid                                html  
    spotseg                                 html  
    summary.spotseg                         html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'spotSegmentation' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'spotSegmentation' as spotSegmentation_1.52.0.zip
* DONE (spotSegmentation)
In R CMD INSTALL
In R CMD INSTALL