Multiple platform build/check report for BioC 3.6 - CHECK report for NormqPCR on tokay1

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### Running command:
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###   rm -rf NormqPCR.buildbin-libdir NormqPCR.Rcheck && mkdir NormqPCR.buildbin-libdir NormqPCR.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=NormqPCR.buildbin-libdir NormqPCR_1.24.0.tar.gz >NormqPCR.Rcheck\00install.out 2>&1 && cp NormqPCR.Rcheck\00install.out NormqPCR-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=NormqPCR.buildbin-libdir --install="check:NormqPCR-install.out" --force-multiarch --no-vignettes --timings NormqPCR_1.24.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/NormqPCR.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 'NormqPCR/DESCRIPTION' ... OK
* this is package 'NormqPCR' version '1.24.0'
* 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 'NormqPCR' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpodUOAF/R.INSTALL31006b8b72d/NormqPCR/man/ComputeNRQs.Rd:14: missing file link 'qPCRBatch'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpodUOAF/R.INSTALL31006b8b72d/NormqPCR/man/CqValues.Rd:23: missing file link 'CyclesSet'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/NormqPCR.Rcheck/00install.out' for details.
* 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
stabMeasureM: no visible global function definition for 'sd'
ComputeNRQs,qPCRBatch: no visible global function definition for 'effs'
ComputeNRQs,qPCRBatch: no visible global function definition for
  'se.effs'
CqValues,CyclesSet: no visible binding for global variable 'l5'
CqValues,CyclesSet: no visible global function definition for 'effs<-'
CqValues,CyclesSet: no visible global function definition for
  'se.effs<-'
combineTechReps,qPCRBatch: no visible binding for global variable
  'median'
combineTechRepsWithSD,qPCRBatch: no visible binding for global variable
  'sd'
combineTechRepsWithSD,qPCRBatch: no visible binding for global variable
  'median'
combineTechRepsWithSD,qPCRBatch: no visible binding for global variable
  'mad'
deltaDeltaCt,qPCRBatch: no visible global function definition for 'sd'
selectHKs,matrix: no visible global function definition for 'sd'
stabMeasureRho,matrix: no visible global function definition for
  'aggregate'
Undefined global functions or variables:
  aggregate effs effs<- l5 mad median sd se.effs se.effs<-
Consider adding
  importFrom("stats", "aggregate", "mad", "median", "sd")
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
Examples with CPU or elapsed time > 5s
          user system elapsed
CqValues 40.31   0.03   40.95
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
         user system elapsed
CqValues 47.8      0   47.95
* 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, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/NormqPCR.Rcheck/00check.log'
for details.


install for i386

* installing *source* package 'NormqPCR' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'NormqPCR'
    finding HTML links ... done
    Bladder                                 html  
    BladderRepro                            html  
    Colon                                   html  
    ComputeNRQs                             html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpodUOAF/R.INSTALL31006b8b72d/NormqPCR/man/ComputeNRQs.Rd:14: missing file link 'qPCRBatch'
    CqValues                                html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpodUOAF/R.INSTALL31006b8b72d/NormqPCR/man/CqValues.Rd:23: missing file link 'CyclesSet'
    NormqPCR-package                        html  
    combineTechReps                         html  
    combineTechRepsSD                       html  
    deltaCt                                 html  
    deltaDeltaCt                            html  
    geNorm                                  html  
    geomMean                                html  
    makeAllNAs                              html  
    makeAllNewVal                           html  
    replaceAboveCutOff                      html  
    replaceNAs                              html  
    selectHKs                               html  
    stabMeasureM                            html  
    stabMeasureRho                          html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'NormqPCR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'NormqPCR' as NormqPCR_1.24.0.zip
* DONE (NormqPCR)
In R CMD INSTALL
In R CMD INSTALL

CHECK report for NormqPCR on tokay1

Summary

Command output

Installation output

Tests output

Example timings