Multiple platform build/check report for BioC 3.6 - CHECK report for plateCore on tokay1

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### Running command:
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###   rm -rf plateCore.buildbin-libdir plateCore.Rcheck && mkdir plateCore.buildbin-libdir plateCore.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=plateCore.buildbin-libdir plateCore_1.36.0.tar.gz >plateCore.Rcheck\00install.out 2>&1 && cp plateCore.Rcheck\00install.out plateCore-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=plateCore.buildbin-libdir --install="check:plateCore-install.out" --force-multiarch --no-vignettes --timings plateCore_1.36.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/plateCore.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 'plateCore/DESCRIPTION' ... OK
* this is package 'plateCore' version '1.36.0'
* 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 'plateCore' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'flowCore' 'lattice'
A package should be listed in only one of these fields.
* 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
Packages in Depends field not imported from:
  'flowViz' 'latticeExtra'
  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
panel.xyplot.flowPlate: warning in filterBoundary(filter =
  filter[[nm]], parameters = c(channel.x.name, channel.y.name), frame =
  frames[[nm]]): partial argument match of 'filter' to 'filter.object'
fixAutoFl,flowPlate: no visible binding for global variable
  'Sample.Type'
fpbind,flowPlate-flowPlate : <anonymous>: no visible binding for global
  variable 'name'
gutterPlot,flowPlate: no visible global function definition for 'plot'
mfiPlot,flowPlate: no visible global function definition for 'plot'
plotPlate,flowPlate: no visible global function definition for 'plot'
setControlGates,flowPlate: no visible binding for global variable
  'Sample.Type'
setControlGates,flowPlate: no visible binding for global variable
  'Channel'
setControlGates,flowPlate : <anonymous>: no visible binding for global
  variable 'Well.Id'
setControlGates,flowPlate : <anonymous>: no visible binding for global
  variable 'plateName'
setControlGates,flowPlate : <anonymous>: no visible binding for global
  variable 'name'
Undefined global functions or variables:
  Channel Sample.Type Well.Id name plateName plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic '[' and siglist 'flowPlate,ANY,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
summaryStats-methods 5.03      0    5.03
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
applyControlGates-methods 6.11   0.00    6.11
mfiPlot-methods           5.91   0.01    5.92
summaryStats-methods      5.64   0.02    5.66
* 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 WARNING, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/plateCore.Rcheck/00check.log'
for details.


install for i386

* installing *source* package 'plateCore' ...
** R
** data
** inst
** preparing package for lazy loading
No methods found in package 'flowStats' for request: '%on%' when loading 'plateCore'
** help
*** installing help indices
  converting help for package 'plateCore'
    finding HTML links ... done
    Subset-methods                          html  
    applyControlGates-methods               html  
    compensate-methods                      html  
    compensationSet                         html  
    densityplot-methods                     html  
    fixAutoFl-methods                       html  
    flowPlate-class                         html  
    finding level-2 HTML links ... done

    flowPlate-method                        html  
    fpbind-methods                          html  
    getGroups-methods                       html  
    gutterPlot-methods                      html  
    mfiPlot-methods                         html  
    on-methods                              html  
    panel.densityplot.flowPlate             html  
    panel.xyplot.flowPlate                  html  
    pbmcPlate                               html  
    plateCore-package                       html  
    plateSet-methods                        html  
    plotPlate-methods                       html  
    prepanel.densityplot.flowPlate          html  
    prepanel.xyplot.flowPlate               html  
    setControlGates-methods                 html  
    summaryStats-methods                    html  
    wellAnnotation-methods                  html  
    xyplot-methods                          html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in package 'flowStats' for request: '%on%' when loading 'plateCore'
In R CMD INSTALL

install for x64

* installing *source* package 'plateCore' ...
** testing if installed package can be loaded
No methods found in package 'flowStats' for request: '%on%' when loading 'plateCore'
* MD5 sums
packaged installation of 'plateCore' as plateCore_1.36.0.zip
* DONE (plateCore)
In R CMD INSTALL
In R CMD INSTALL

CHECK report for plateCore on tokay1

Summary

Command output

Installation output

Tests output

Example timings