Package: esetVis

Version: 1.10.0

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:esetVis.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings esetVis_1.10.0.tar.gz

StartedAt: 2019-10-16 03:35:07 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 03:39:55 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 287.6 seconds

RetCode: 0

Status:  OK

CheckDir: esetVis.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:esetVis.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings esetVis_1.10.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/esetVis.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'esetVis/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'esetVis' version '1.10.0'
* 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 'esetVis' can be installed ... OK
* 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
getMethodsInputObjectEsetVis: no visible binding for global variable
  'rowData'
getMethodsInputObjectEsetVis: no visible binding for global variable
  'colData'
getMethodsInputObjectEsetVis: no visible binding for global variable
  'assay'
getMethodsInputObjectEsetVis : : no visible global function
  definition for 'colData'
getMethodsInputObjectEsetVis : : no visible global function
  definition for 'rowData'
ggvisPlotEset: no visible global function definition for ':='
ggvisPlotEset: no visible binding for global variable 'fill'
ggvisPlotEset: no visible binding for global variable 'shape'
ggvisPlotEset: no visible binding for global variable 'size'
ggvisPlotEset: no visible binding for global variable 'opacity'
ggvisPlotEset: no visible global function definition for '%>%'
ggvisPlotEset: no visible global function definition for
  'scale_ordinal'
ggvisPlotEset: no visible global function definition for 'set_options'
Undefined global functions or variables:
  %>% := assay colData fill opacity rowData scale_ordinal set_options
  shape size
* 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' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
getGeneSetsForPlot 52.18   3.84   56.01
esetLda             6.76   0.30    7.06
esetSpectralMap     5.72   0.27    5.98
esetPlotWrapper     5.51   0.29    5.81
esetTsne            5.53   0.08    5.61
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
getGeneSetsForPlot 57.53   1.58   59.12
esetPlotWrapper     6.06   0.30    6.35
esetLda             5.94   0.19    6.13
esetSpectralMap     5.47   0.39    5.86
* 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 NOTE
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/esetVis.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/esetVis_1.10.0.tar.gz && rm -rf esetVis.buildbin-libdir && mkdir esetVis.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=esetVis.buildbin-libdir esetVis_1.10.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL esetVis_1.10.0.zip && rm esetVis_1.10.0.tar.gz esetVis_1.10.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
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100 43253  100 43253    0     0   322k      0 --:--:-- --:--:-- --:--:--  343k

install for i386

* installing *source* package 'esetVis' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'esetVis'
    finding HTML links ... done
    characterORexpressionOrCall-class       html  
    esetLda                                 html  
    finding level-2 HTML links ... done

    esetPlot-class                          html  
    esetPlotInteractive-class               html  
    esetPlotWrapper                         html  
    esetSpectralMap                         html  
    esetTsne                                html  
    formatManualScale                       html  
    formatOutput                            html  
    getAxesLimits-methods                   html  
    getCoordGeneSets                        html  
    getDataPlotSamplesWithAnnotation-methods
                                            html  
    getGeneSetsForPlot                      html  
    getMethodsInputObjectEsetVis            html  
    ggPlotEset                              html  
    ggplotEsetPlot-class                    html  
    ggvisEsetPlot-class                     html  
    ggvisPlotEset                           html  
    plotEset-methods                        html  
    plotTopElements                         html  
    rbokehEsetPlot-class                    html  
    rbokehPlotEset                          html  
    setFixElement                           html  
    setManualScale                          html  
    simpleCap                               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'esetVis' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'esetVis' as esetVis_1.10.0.zip
* DONE (esetVis)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'esetVis' successfully unpacked and MD5 sums checked