Package: genphen

Version: 1.6.0

Command: rm -rf genphen.buildbin-libdir genphen.Rcheck && mkdir genphen.buildbin-libdir genphen.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=genphen.buildbin-libdir genphen_1.6.0.tar.gz >genphen.Rcheck\00install.out 2>&1 && cp genphen.Rcheck\00install.out genphen-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=genphen.buildbin-libdir --install="check:genphen-install.out" --force-multiarch --no-vignettes --timings genphen_1.6.0.tar.gz

StartedAt: 2018-04-12 00:19:56 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 00:24:55 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 298.9 seconds

RetCode: 0

Status:  OK

CheckDir: genphen.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf genphen.buildbin-libdir genphen.Rcheck && mkdir genphen.buildbin-libdir genphen.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=genphen.buildbin-libdir genphen_1.6.0.tar.gz >genphen.Rcheck\00install.out 2>&1 && cp genphen.Rcheck\00install.out genphen-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=genphen.buildbin-libdir --install="check:genphen-install.out" --force-multiarch --no-vignettes --timings genphen_1.6.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/genphen.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 'genphen/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'genphen' version '1.6.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'randomForest' 'e1071' 'ggplot2' 'effsize' 'Biostrings' 'rjags'
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 'genphen' 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
** 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
getBayesianTtest : getDataList: no visible global function definition
  for 'sd'
getBayesianTtest : getEss: no visible global function definition for
  'effectiveSize'
getBayesianTtest: no visible global function definition for 'update'
getTTestScore: no visible global function definition for 't.test'
plotGenphenBayes: no visible binding for global variable 'g.1'
plotGenphenBayes: no visible binding for global variable 'site'
plotGenphenBayes: no visible binding for global variable 'g.2'
plotGenphenRfSvm: no visible binding for global variable 'ca.hdi.H'
plotGenphenRfSvm: no visible binding for global variable 'ca.hdi.L'
plotGenphenRfSvm: no visible global function definition for
  'terrain.colors'
plotManhattan: no visible binding for global variable 't.test.pvalue'
Undefined global functions or variables:
  ca.hdi.H ca.hdi.L effectiveSize g.1 g.2 sd site t.test t.test.pvalue
  terrain.colors update
Consider adding
  importFrom("grDevices", "terrain.colors")
  importFrom("stats", "sd", "t.test", "update")
to your NAMESPACE file.
* 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 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
plotGenphenBayes 21.61   0.06   22.25
runGenphenBayes  17.58   0.00   17.57
plotGenphenRfSvm 13.86   0.14   15.92
plotManhattan    13.61   0.05   13.66
runGenphenRf     12.45   0.34   12.80
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
runGenphenRf     19.28   0.42   19.70
plotGenphenBayes 18.78   0.04   20.09
plotManhattan    15.50   0.02   15.51
plotGenphenRfSvm 15.34   0.17   15.52
runGenphenBayes  12.25   0.00   12.25
* 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/genphen.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'genphen' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'genphen'
    finding HTML links ... done
    genotype.saap                           html  
    genotype.saap.msa                       html  
    genotype.snp                            html  
    genotype.snp.msa                        html  
    phenotype.saap                          html  
    phenotype.snp                           html  
    plotGenphenBayes                        html  
    plotGenphenRfSvm                        html  
    plotManhattan                           html  
    plotSpecificGenotype                    html  
    runGenphenBayes                         html  
    runGenphenRf                            html  
    runGenphenSvm                           html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'genphen' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'genphen' as genphen_1.6.0.zip
* DONE (genphen)
In R CMD INSTALL
In R CMD INSTALL