Package: EBSeqHMM

Version: 1.12.0

Command: rm -rf EBSeqHMM.buildbin-libdir EBSeqHMM.Rcheck && mkdir EBSeqHMM.buildbin-libdir EBSeqHMM.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=EBSeqHMM.buildbin-libdir EBSeqHMM_1.12.0.tar.gz >EBSeqHMM.Rcheck\00install.out 2>&1 && cp EBSeqHMM.Rcheck\00install.out EBSeqHMM-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=EBSeqHMM.buildbin-libdir --install="check:EBSeqHMM-install.out" --force-multiarch --no-vignettes --timings EBSeqHMM_1.12.0.tar.gz

StartedAt: 2018-04-11 23:42:07 -0400 (Wed, 11 Apr 2018)

EndedAt: 2018-04-11 23:43:34 -0400 (Wed, 11 Apr 2018)

EllapsedTime: 87.5 seconds

RetCode: 0

Status:  OK

CheckDir: EBSeqHMM.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf EBSeqHMM.buildbin-libdir EBSeqHMM.Rcheck && mkdir EBSeqHMM.buildbin-libdir EBSeqHMM.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=EBSeqHMM.buildbin-libdir EBSeqHMM_1.12.0.tar.gz >EBSeqHMM.Rcheck\00install.out 2>&1 && cp EBSeqHMM.Rcheck\00install.out EBSeqHMM-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=EBSeqHMM.buildbin-libdir --install="check:EBSeqHMM-install.out" --force-multiarch --no-vignettes --timings EBSeqHMM_1.12.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/EBSeqHMM.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 'EBSeqHMM/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'EBSeqHMM' version '1.12.0'
* 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 'EBSeqHMM' 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
EBHMMNBfun: no visible binding for global variable 'median'
EBHMMNBfun : <anonymous>: no visible global function definition for
  'quantile'
EBHMMNBfun: no visible global function definition for 'optim'
EBHMMNBfunForMulti: no visible binding for global variable 'median'
EBHMMNBfunForMulti : <anonymous>: no visible global function definition
  for 'quantile'
EBHMMNBfunForMulti: no visible global function definition for 'optim'
EBSeqHMMTest : <anonymous>: no visible global function definition for
  'quantile'
EBTest_ext: no visible global function definition for 'quantile'
EBTest_ext: no visible binding for global variable 'var'
PlotExp: no visible global function definition for 'plot'
PlotExp: no visible global function definition for 'axis'
PlotExp : <anonymous>: no visible global function definition for
  'median'
PlotExp: no visible global function definition for 'lines'
beta.mom: no visible global function definition for 'var'
Undefined global functions or variables:
  axis lines median optim plot quantile var
Consider adding
  importFrom("graphics", "axis", "lines", "plot")
  importFrom("stats", "median", "optim", "quantile", "var")
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/EBSeqHMM.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'EBSeqHMM' ...
** R
** data
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'EBSeqHMM'
    finding HTML links ... done
    EBHMMNBMultiEM_2chain                   html  
    EBHMMNBfun                              html  
    EBHMMNBfunForMulti                      html  
    EBSeqHMM-package                        html  
    EBSeqHMMTest                            html  
    EBTest_ext                              html  
    finding level-2 HTML links ... done

    GeneExampleData                         html  
    GetAllPaths                             html  
    GetConfidentCalls                       html  
    GetDECalls                              html  
    IsoExampleList                          html  
    LikefunNBHMM                            html  
    PlotExp                                 html  
    beta.mom                                html  
    f0                                      html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'EBSeqHMM' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'EBSeqHMM' as EBSeqHMM_1.12.0.zip
* DONE (EBSeqHMM)
In R CMD INSTALL
In R CMD INSTALL