Package: DMRforPairs

Version: 1.14.0

Command: rm -rf DMRforPairs.buildbin-libdir DMRforPairs.Rcheck && mkdir DMRforPairs.buildbin-libdir DMRforPairs.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DMRforPairs.buildbin-libdir DMRforPairs_1.14.0.tar.gz >DMRforPairs.Rcheck\00install.out 2>&1 && cp DMRforPairs.Rcheck\00install.out DMRforPairs-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=DMRforPairs.buildbin-libdir --install="check:DMRforPairs-install.out" --force-multiarch --no-vignettes --timings DMRforPairs_1.14.0.tar.gz

StartedAt: 2018-04-11 23:34:20 -0400 (Wed, 11 Apr 2018)

EndedAt: 2018-04-11 23:40:46 -0400 (Wed, 11 Apr 2018)

EllapsedTime: 386.3 seconds

RetCode: 0

Status:  OK

CheckDir: DMRforPairs.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf DMRforPairs.buildbin-libdir DMRforPairs.Rcheck && mkdir DMRforPairs.buildbin-libdir DMRforPairs.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DMRforPairs.buildbin-libdir DMRforPairs_1.14.0.tar.gz >DMRforPairs.Rcheck\00install.out 2>&1 && cp DMRforPairs.Rcheck\00install.out DMRforPairs-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=DMRforPairs.buildbin-libdir --install="check:DMRforPairs-install.out" --force-multiarch --no-vignettes --timings DMRforPairs_1.14.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/DMRforPairs.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 'DMRforPairs/DESCRIPTION' ... OK
* this is package 'DMRforPairs' version '1.14.0'
* 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 'DMRforPairs' 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
DMRforPairs: no visible global function definition for 'combn'
DMRforPairs: no visible global function definition for 'p.adjust'
calc_stats: no visible global function definition for 'combn'
calc_stats: no visible binding for global variable 'median'
calc_stats: no visible global function definition for 'wilcox.test'
calc_stats: no visible global function definition for 'kruskal.test'
export_data: no visible global function definition for 'write.table'
plot_annotate_probes: no visible global function definition for
  'rainbow'
plot_annotate_probes: no visible global function definition for 'png'
plot_annotate_probes: no visible global function definition for 'par'
plot_annotate_probes: no visible global function definition for 'plot'
plot_annotate_probes: no visible global function definition for 'lines'
plot_annotate_probes: no visible global function definition for
  'extendrange'
plot_annotate_probes: no visible global function definition for
  'dev.off'
plot_annotate_probes: no visible global function definition for 'pdf'
plot_annotate_probes: no visible global function definition for 'combn'
plot_annotate_probes: no visible global function definition for
  'legend'
plot_annotate_probes: no visible global function definition for 'axis'
plot_annotate_probes: no visible global function definition for 'box'
plot_annotate_probes: no visible global function definition for
  'seqlevels<-'
plot_annotate_probes: no visible global function definition for 'Rle'
plot_annotate_probes: no visible global function definition for
  'IRanges'
Undefined global functions or variables:
  IRanges Rle axis box combn dev.off extendrange kruskal.test legend
  lines median p.adjust par pdf plot png rainbow seqlevels<-
  wilcox.test write.table
Consider adding
  importFrom("grDevices", "dev.off", "extendrange", "pdf", "png",
             "rainbow")
  importFrom("graphics", "axis", "box", "legend", "lines", "par", "plot")
  importFrom("stats", "kruskal.test", "median", "p.adjust",
             "wilcox.test")
  importFrom("utils", "combn", "write.table")
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
** running examples for arch 'x64' ... OK
* 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-3.6-bioc/meat/DMRforPairs.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'DMRforPairs' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'DMRforPairs'
    finding HTML links ... done
    CL.methy                                html  
    DMRforPairs-package                     html  
    DMRforPairs                             html  
    calc_stats                              html  
    example_output_DMRforPairs              html  
    export_data                             html  
    merge_classes                           html  
    plot_annotate_custom_region             html  
    plot_annotate_gene                      html  
    plot_annotate_probes                    html  
    plot_annotate_region                    html  
    regionfinder                            html  
    testregion                              html  
    tune_parameters                         html  
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'DMRforPairs' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DMRforPairs' as DMRforPairs_1.14.0.zip
* DONE (DMRforPairs)
In R CMD INSTALL
In R CMD INSTALL