Package: MergeMaid

Version: 2.50.0

Command: rm -rf MergeMaid.buildbin-libdir MergeMaid.Rcheck && mkdir MergeMaid.buildbin-libdir MergeMaid.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MergeMaid.buildbin-libdir MergeMaid_2.50.0.tar.gz >MergeMaid.Rcheck\00install.out 2>&1 && cp MergeMaid.Rcheck\00install.out MergeMaid-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=MergeMaid.buildbin-libdir --install="check:MergeMaid-install.out" --force-multiarch --no-vignettes --timings MergeMaid_2.50.0.tar.gz

StartedAt: 2018-04-12 01:12:47 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 01:15:06 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 139.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: MergeMaid.Rcheck

Warnings: 1

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### Running command:
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###   rm -rf MergeMaid.buildbin-libdir MergeMaid.Rcheck && mkdir MergeMaid.buildbin-libdir MergeMaid.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MergeMaid.buildbin-libdir MergeMaid_2.50.0.tar.gz >MergeMaid.Rcheck\00install.out 2>&1 && cp MergeMaid.Rcheck\00install.out MergeMaid-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=MergeMaid.buildbin-libdir --install="check:MergeMaid-install.out" --force-multiarch --no-vignettes --timings MergeMaid_2.50.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/MergeMaid.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 'MergeMaid/DESCRIPTION' ... OK
* this is package 'MergeMaid' version '2.50.0'
* 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 'MergeMaid' 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:
  'MASS' 'methods' 'survival'
  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
.dens.mergeExpressionSet: no visible global function definition for
  'density'
.fdr.mergeCor: no visible global function definition for '.getnull'
.fdr.mergeCor: no visible global function definition for 'approxfun'
.fdr.mergeCor: no visible global function definition for 'density'
.fdr.mergeCor: no visible global function definition for 'integrate'
.ic.plot : norm: no visible global function definition for 'sd'
.ic.plot: no visible global function definition for 'cov'
.icor : norm: no visible global function definition for 'sd'
.icor: no visible global function definition for 'cov'
.intcor : norm: no visible global function definition for 'sd'
.intcor: no visible global function definition for 'new'
.integ.cal : sziicor: no visible global function definition for 'cor'
.mergemodel: no visible global function definition for 'lm'
.mergemodel: no visible binding for global variable 'na.omit'
.mergemodel: no visible global function definition for 'coxph'
.mergemodel: no visible global function definition for 'sd'
.mergemodel: no visible global function definition for 'glm'
.mergemodel: no visible binding for global variable 'binomial'
.model.outcome: no visible global function definition for 'new'
.nullicornorm : norm: no visible global function definition for 'sd'
.nullicornorm: no visible global function definition for 'cov'
.nullicornorm : getone: no visible global function definition for
  'rnorm'
maxintcor: no visible global function definition for 'cov'
maxintcor: no visible global function definition for 'ginv'
mergeExprs: no visible global function definition for 'new'
mergeget: no visible global function definition for 'new'
subsetmES: no visible global function definition for 'new'
intersection,mergeExpressionSet: no visible global function definition
  for 'new'
Undefined global functions or variables:
  .getnull approxfun binomial cor cov coxph density ginv glm integrate
  lm na.omit new rnorm sd
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "approxfun", "binomial", "cor", "cov", "density",
             "glm", "integrate", "lm", "na.omit", "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 ... WARNING
Undocumented S4 methods:
  generic '[' and siglist 'mergeExpressionSet,ANY,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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
intcorDens               11.97   0.06   12.03
class.mergeExpressionSet  4.99   0.03    5.02
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
intcorDens               13.67   0.05   13.72
class.mergeExpressionSet  6.08   0.01    6.10
* 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 WARNING, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/MergeMaid.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'MergeMaid' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'MergeMaid'
    finding HTML links ... done
    class.mergeCoeff                        html  
    class.mergeCor                          html  
    class.mergeExpressionSet                html  
    intCor                                  html  
    intcorDens                              html  
    intersection                            html  
    mergeData                               html  
    mergeExprs                              html  
    modelOutcome                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'MergeMaid' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MergeMaid' as MergeMaid_2.50.0.zip
* DONE (MergeMaid)
In R CMD INSTALL
In R CMD INSTALL