Package: gaucho

Version: 1.14.0

Command: rm -rf gaucho.buildbin-libdir gaucho.Rcheck && mkdir gaucho.buildbin-libdir gaucho.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=gaucho.buildbin-libdir gaucho_1.14.0.tar.gz >gaucho.Rcheck\00install.out 2>&1 && cp gaucho.Rcheck\00install.out gaucho-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=gaucho.buildbin-libdir --install="check:gaucho-install.out" --force-multiarch --no-vignettes --timings gaucho_1.14.0.tar.gz

StartedAt: 2018-04-12 00:07:47 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 00:12:34 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 286.8 seconds

RetCode: 0

Status:  OK

CheckDir: gaucho.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf gaucho.buildbin-libdir gaucho.Rcheck && mkdir gaucho.buildbin-libdir gaucho.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=gaucho.buildbin-libdir gaucho_1.14.0.tar.gz >gaucho.Rcheck\00install.out 2>&1 && cp gaucho.Rcheck\00install.out gaucho-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=gaucho.buildbin-libdir --install="check:gaucho-install.out" --force-multiarch --no-vignettes --timings gaucho_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/gaucho.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 'gaucho/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'gaucho' version '1.14.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'compiler' 'GA' 'graph' 'heatmap.plus' 'png' 'Rgraphviz'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'gaucho' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
Authors@R field gives more than one person with maintainer role:
  Alex Murison <Alexander.Murison@icr.ac.uk> [aut, cre]
  Christopher Wardell <Christopher.Wardell@icr.ac.uk> [aut, cre]
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
gaucho : generate_phylogeny_aware_individual: no visible global
  function definition for 'runif'
gaucho : phylo_mutate: no visible global function definition for
  'runif'
gauchoReport: no visible global function definition for 'write.table'
gauchoReport: no visible global function definition for 'png'
gauchoReport: no visible global function definition for 'dev.off'
gauchoReport: no visible global function definition for 'layout'
gauchoReport: no visible global function definition for 'par'
gauchoReport: no visible global function definition for 'plot.new'
gauchoReport: no visible global function definition for 'legend'
gauchoReport: no visible global function definition for 'barplot'
gauchoReport: no visible global function definition for 'as'
new_phylo: no visible global function definition for 'runif'
Undefined global functions or variables:
  as barplot dev.off layout legend par plot.new png runif write.table
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "barplot", "layout", "legend", "par",
             "plot.new")
  importFrom("methods", "as")
  importFrom("stats", "runif")
  importFrom("utils", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 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
gaucho       50.45   0.05   50.50
gauchoReport 44.64   0.00   44.66
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
gauchoReport 59.67   0.00   59.67
gaucho       57.49   0.05   57.53
* 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 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/gaucho.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'gaucho' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'gaucho'
    finding HTML links ... done
    BYB1_G07_pruned                         html  
    finding level-2 HTML links ... done

    gaucho                                  html  
    gauchoReport                            html  
    gaucho_hidden_data                      html  
    gaucho_simple_data                      html  
    gaucho_synth_data                       html  
    gaucho_synth_data_jittered              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'gaucho' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'gaucho' as gaucho_1.14.0.zip
* DONE (gaucho)
In R CMD INSTALL
In R CMD INSTALL