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CHECK report for esetVis on tokay1

This page was generated on 2019-04-13 11:26:50 -0400 (Sat, 13 Apr 2019).

Package 489/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
esetVis 1.8.0
Laure Cougnaud
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/esetVis
Branch: RELEASE_3_8
Last Commit: fc2bebc
Last Changed Date: 2018-10-30 11:42:01 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: esetVis
Version: 1.8.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:esetVis.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings esetVis_1.8.0.tar.gz
StartedAt: 2019-04-13 02:06:58 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 02:12:03 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 304.8 seconds
RetCode: 0
Status:  OK  
CheckDir: esetVis.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:esetVis.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings esetVis_1.8.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/esetVis.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 'esetVis/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'esetVis' version '1.8.0'
* 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 '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 : <anonymous>: no visible global function
  definition for 'colData'
getMethodsInputObjectEsetVis : <anonymous>: 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 53.52   3.86   57.37
esetLda             7.50   0.18    7.69
esetPlotWrapper     5.91   0.30    6.20
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
getGeneSetsForPlot 53.38   1.64   55.02
esetLda             5.19   0.11    5.29
* 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-3.8-bioc/meat/esetVis.Rcheck/00check.log'
for details.



Installation output

esetVis.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/esetVis_1.8.0.tar.gz && rm -rf esetVis.buildbin-libdir && mkdir esetVis.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=esetVis.buildbin-libdir esetVis_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL esetVis_1.8.0.zip && rm esetVis_1.8.0.tar.gz esetVis_1.8.0.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 42072  100 42072    0     0   678k      0 --:--:-- --:--:-- --:--:--  720k

install for i386

* installing *source* package 'esetVis' ...
** 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
In R CMD INSTALL

install for x64

* installing *source* package 'esetVis' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'esetVis' as esetVis_1.8.0.zip
* DONE (esetVis)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'esetVis' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

esetVis.Rcheck/examples_i386/esetVis-Ex.timings

nameusersystemelapsed
esetLda7.500.187.69
esetPlotWrapper5.910.306.20
esetSpectralMap4.520.254.76
esetTsne3.540.153.71
getGeneSetsForPlot53.52 3.8657.37

esetVis.Rcheck/examples_x64/esetVis-Ex.timings

nameusersystemelapsed
esetLda5.190.115.29
esetPlotWrapper4.550.364.91
esetSpectralMap4.090.164.25
esetTsne3.490.123.61
getGeneSetsForPlot53.38 1.6455.02