Package: unifiedWMWqPCR

Version: 1.14.0

Command: rm -rf unifiedWMWqPCR.buildbin-libdir unifiedWMWqPCR.Rcheck && mkdir unifiedWMWqPCR.buildbin-libdir unifiedWMWqPCR.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=unifiedWMWqPCR.buildbin-libdir unifiedWMWqPCR_1.14.0.tar.gz >unifiedWMWqPCR.Rcheck\00install.out 2>&1 && cp unifiedWMWqPCR.Rcheck\00install.out unifiedWMWqPCR-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=unifiedWMWqPCR.buildbin-libdir --install="check:unifiedWMWqPCR-install.out" --force-multiarch --no-vignettes --timings unifiedWMWqPCR_1.14.0.tar.gz

StartedAt: 2018-04-12 03:45:31 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 03:46:52 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 80.8 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: unifiedWMWqPCR.Rcheck

Warnings: 3

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### Running command:
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###   rm -rf unifiedWMWqPCR.buildbin-libdir unifiedWMWqPCR.Rcheck && mkdir unifiedWMWqPCR.buildbin-libdir unifiedWMWqPCR.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=unifiedWMWqPCR.buildbin-libdir unifiedWMWqPCR_1.14.0.tar.gz >unifiedWMWqPCR.Rcheck\00install.out 2>&1 && cp unifiedWMWqPCR.Rcheck\00install.out unifiedWMWqPCR-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=unifiedWMWqPCR.buildbin-libdir --install="check:unifiedWMWqPCR-install.out" --force-multiarch --no-vignettes --timings unifiedWMWqPCR_1.14.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/unifiedWMWqPCR.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 'unifiedWMWqPCR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'unifiedWMWqPCR' 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 'unifiedWMWqPCR' 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
.uWMW: no visible global function definition for 'pnorm'
.volcano: no visible global function definition for 'text'
forestplot.internal: no visible global function definition for 'par'
forestplot.internal: no visible global function definition for 'abline'
forestplot.internal: no visible global function definition for
  'strheight'
forestplot.internal: no visible global function definition for
  'segments'
forestplot.internal: no visible global function definition for
  'polygon'
forestplot.internal: no visible global function definition for 'text'
forestplot.internal: no visible global function definition for 'axis'
forestplot.internal: no visible global function definition for 'mtext'
forestplot.internal: no visible global function definition for 'points'
sandwich1.f: no visible global function definition for 'na.omit'
sandwich2.f: no visible global function definition for 'na.omit'
sandwich3.f: no visible global function definition for 'na.omit'
getEstimate,uwmwRes: no visible global function definition for 'qnorm'
getEstimate,uwmwRes: no visible global function definition for 'plogis'
uWMW,qPCRset: no visible global function definition for 'exprs'
Undefined global functions or variables:
  abline axis exprs mtext na.omit par plogis pnorm points polygon qnorm
  segments strheight text
Consider adding
  importFrom("graphics", "abline", "axis", "mtext", "par", "points",
             "polygon", "segments", "strheight", "text")
  importFrom("stats", "na.omit", "plogis", "pnorm", "qnorm")
to your NAMESPACE file.
* 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 'uwmwRes,character'
  generic 'getEstimate' and siglist 'uwmwRes'
  generic 'sort' and siglist 'uwmwRes'
  generic 'type' and siglist 'uwmwRes'
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 ... WARNING
Codoc mismatches from documentation object 'type':
is.unsorted
  Code: function(x, na.rm = FALSE, strictly = FALSE)
  Docs: function(x, na.rm = FALSE, strictly = FALSE, ...)
  Argument names in docs not in code:
    ...

* checking Rd \usage sections ... WARNING
Objects in \usage without \alias in documentation object 'getEstimate':
  '\S4method{getEstimate}{uwmwRes}'

Undocumented arguments in documentation object 'unorder'
  'method'
Objects in \usage without \alias in documentation object 'unorder':
  '\S4method{sort}{uwmwRes}'

Undocumented arguments in documentation object 'type'
  '...'
Objects in \usage without \alias in documentation object 'type':
  '\S4method{type}{uwmwRes}'

Objects in \usage without \alias in documentation object 'uwmw_Extract':
  '\S4method{[}{uwmwRes,character}'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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: 3 WARNINGs, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/unifiedWMWqPCR.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'unifiedWMWqPCR' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'order' from package 'base' in package 'unifiedWMWqPCR'
** help
*** installing help indices
  converting help for package 'unifiedWMWqPCR'
    finding HTML links ... done
    NBdata                                  html  
    as.matrix.uwmwEstimate                  html  
    as.matrix.uwmwRes                       html  
    forestplot-methods                      html  
    getEstimate-methods                     html  
    plot                                    html  
    sort.uwmwRes                            html  
    uWMW-methods                            html  
    unifiedWMWqPCR-package                  html  
    uwmwEstimate-class                      html  
    uwmwRes-class                           html  
    uwmw_Accessors                          html  
    uwmw_Extract                            html  
    volcanopar                              html  
    volcanoplot-methods                     html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'unifiedWMWqPCR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'unifiedWMWqPCR' as unifiedWMWqPCR_1.14.0.zip
* DONE (unifiedWMWqPCR)
In R CMD INSTALL
In R CMD INSTALL