Package: pint

Version: 1.30.0

Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pint.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings pint_1.30.0.tar.gz

StartedAt: 2018-10-17 03:59:22 -0400 (Wed, 17 Oct 2018)

EndedAt: 2018-10-17 04:02:59 -0400 (Wed, 17 Oct 2018)

EllapsedTime: 216.6 seconds

RetCode: 0

Status:  OK

CheckDir: pint.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pint.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings pint_1.30.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/pint.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'pint/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'pint' version '1.30.0'
* 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 'pint' 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 ... NOTE
Packages in Depends field not imported from:
  'Matrix' 'methods' 'mvtnorm'
  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
W.effects: no visible global function definition for 'princomp'
W.effects: no visible global function definition for 'cor'
calculate.arm: no visible global function definition for 'as'
calculate.arm: no visible global function definition for 'new'
calculate.arm.sparse: no visible global function definition for 'new'
calculate.chr: no visible global function definition for 'new'
calculate.chr.sparse: no visible global function definition for 'new'
calculate.genome: no visible global function definition for 'new'
calculate.genome.sparse: no visible global function definition for
  'new'
imputation: no visible global function definition for 'rnorm'
imputation: no visible global function definition for 'sd'
join.top.regions: no visible global function definition for 'quantile'
plot.ChromosomeModels: no visible global function definition for 'par'
plot.ChromosomeModels: no visible global function definition for
  'abline'
plot.ChromosomeModels: no visible global function definition for
  'points'
plot.ChromosomeModels: no visible global function definition for 'text'
plot.ChromosomeModels: no visible global function definition for
  'lines'
plot.GeneDependencyModel: no visible global function definition for
  'gray'
plot.GeneDependencyModel: no visible global function definition for
  'par'
plot.GeneDependencyModel: no visible global function definition for
  'layout'
plot.GeneDependencyModel: no visible global function definition for
  'barplot'
plot.GeneDependencyModel: no visible global function definition for
  'legend'
plot.GeneDependencyModel: no visible global function definition for
  'mtext'
plot.GenomeModels: no visible global function definition for 'par'
plot.GenomeModels: no visible global function definition for 'abline'
plot.GenomeModels: no visible global function definition for 'points'
plot.GenomeModels: no visible global function definition for 'text'
plot.GenomeModels: no visible global function definition for 'lines'
plot.GenomeModels: no visible global function definition for 'axis'
summarize.region.parameters: no visible global function definition for
  'na.omit'
summarize.region.parameters: no visible global function definition for
  'cor'
z.effects: no visible global function definition for 'princomp'
coerce,GeneDependencyModel-DependencyModel: no visible global function
  definition for 'new'
coerce<-,GeneDependencyModel-DependencyModel: no visible global
  function definition for 'slot<-'
coerce<-,GeneDependencyModel-DependencyModel: no visible global
  function definition for 'slot'
getPArm,ChromosomeModels: no visible global function definition for
  'new'
getQArm,ChromosomeModels: no visible global function definition for
  'new'
Undefined global functions or variables:
  abline as axis barplot cor gray layout legend lines mtext na.omit new
  par points princomp quantile rnorm sd slot slot<- text
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "abline", "axis", "barplot", "layout", "legend",
             "lines", "mtext", "par", "points", "text")
  importFrom("methods", "as", "new", "slot", "slot<-")
  importFrom("stats", "cor", "na.omit", "princomp", "quantile", "rnorm",
             "sd")
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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
screen                    30.28   0.03   30.32
ChromosomeModels-class    25.00   0.03   25.04
GeneDependencyModel-class  6.64   0.00    6.66
plot                       6.17   0.01    6.18
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
screen                    34.76   0.05   34.81
ChromosomeModels-class    25.42   0.02   25.44
plot                       9.85   0.01    9.86
GeneDependencyModel-class  7.59   0.02    7.61
* 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-3.7-bioc/meat/pint.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/pint_1.30.0.tar.gz && rm -rf pint.buildbin-libdir && mkdir pint.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=pint.buildbin-libdir pint_1.30.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL pint_1.30.0.zip && rm pint_1.30.0.tar.gz pint_1.30.0.zip
###
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install for i386

* installing *source* package 'pint' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'pint'
    finding HTML links ... done
    ChromosomeModels-class                  html  
    GeneDependencyModel-class               html  
    finding level-2 HTML links ... done

    GenomeModels-class                      html  
    fit.byname                              html  
    geneCopyNum                             html  
    geneExp                                 html  
    get.neighboring.probes                  html  
    get.neighs                              html  
    join.top.regions                        html  
    order.feature.info                      html  
    pint.data                               html  
    plot                                    html  
    screen                                  html  
    summarize.region.parameters             html  
    window                                  html  
    z.effect                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'pint' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'pint' as pint_1.30.0.zip
* DONE (pint)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'pint' successfully unpacked and MD5 sums checked
In R CMD INSTALL