Package: PADOG

Version: 1.26.0

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PADOG.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings PADOG_1.26.0.tar.gz

StartedAt: 2019-10-16 05:47:42 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 05:55:08 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 445.1 seconds

RetCode: 0

Status:  OK

CheckDir: PADOG.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PADOG.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings PADOG_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/PADOG.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 'PADOG/DESCRIPTION' ... OK
* this is package 'PADOG' version '1.26.0'
* 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 'PADOG' 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
compPADOG: no visible global function definition for 'data'
compPADOG : padogF: no visible global function definition for
  'p.adjust'
compPADOG : gsaF: no visible global function definition for 'p.adjust'
compPADOG : : no visible global function definition for
  'complete.cases'
compPADOG : wi: no visible global function definition for 'wilcox.test'
compPADOG: no visible binding for global variable 'median'
compPADOG: no visible global function definition for 'colors'
compPADOG: no visible global function definition for 'par'
compPADOG: no visible global function definition for 'boxplot'
compPADOG: no visible global function definition for 'abline'
filteranot: no visible global function definition for 'model.matrix'
padog: no visible global function definition for 'quantile'
padog: no visible global function definition for 'sd'
padog : combFun: no visible global function definition for 'combn'
padog : gsScoreFun: no visible global function definition for
  'model.matrix'
padog : gsScoreFun : : no visible global function definition
  for 'na.omit'
padog: no visible global function definition for 'par'
padog: no visible global function definition for 'boxplot'
padog: no visible global function definition for 'points'
padog: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline boxplot colors combn complete.cases data median model.matrix
  na.omit p.adjust par points quantile sd wilcox.test
Consider adding
  importFrom("grDevices", "colors")
  importFrom("graphics", "abline", "boxplot", "par", "points")
  importFrom("stats", "complete.cases", "median", "model.matrix",
             "na.omit", "p.adjust", "quantile", "sd", "wilcox.test")
  importFrom("utils", "combn", "data")
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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
          user system elapsed
compPADOG 15.0   4.19  137.10
padog     10.9   0.82   23.26
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
compPADOG 14.62   3.87  139.86
padog     11.11   0.47   22.80
* 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/PADOG.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/PADOG_1.26.0.tar.gz && rm -rf PADOG.buildbin-libdir && mkdir PADOG.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=PADOG.buildbin-libdir PADOG_1.26.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL PADOG_1.26.0.zip && rm PADOG_1.26.0.tar.gz PADOG_1.26.0.zip
###
##############################################################################
##############################################################################


  % 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 38413  100 38413    0     0   536k      0 --:--:-- --:--:-- --:--:--  586k

install for i386

* installing *source* package 'PADOG' ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'PADOG'
    finding HTML links ... done
    compPADOG                               html  
    filteranot                              html  
    padog                                   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 'PADOG' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'PADOG' as PADOG_1.26.0.zip
* DONE (PADOG)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'PADOG' successfully unpacked and MD5 sums checked