Multiple platform build/check report for BioC 3.6 - CHECK report for ImpulseDE2 on tokay1

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf ImpulseDE2.buildbin-libdir ImpulseDE2.Rcheck && mkdir ImpulseDE2.buildbin-libdir ImpulseDE2.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ImpulseDE2.buildbin-libdir ImpulseDE2_1.2.0.tar.gz >ImpulseDE2.Rcheck\00install.out 2>&1 && cp ImpulseDE2.Rcheck\00install.out ImpulseDE2-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=ImpulseDE2.buildbin-libdir --install="check:ImpulseDE2-install.out" --force-multiarch --no-vignettes --timings ImpulseDE2_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/ImpulseDE2.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 'ImpulseDE2/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ImpulseDE2' version '1.2.0'
* package encoding: UTF-8
* 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 'ImpulseDE2' 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
plotGenes: no visible global function definition for 'error'
plotGenes: no visible binding for global variable 'normCounts'
plotGenes: no visible binding for global variable 'Condition'
plotGenes: no visible binding for global variable 'Batch'
plotGenes: no visible binding for global variable 'value'
plotGenes: no visible binding for global variable 'BatchFit'
Undefined global functions or variables:
  Batch BatchFit Condition error normCounts value
* 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 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
updateDEAnalysis  27.01   0.00   27.01
plotHeatmap       26.87   0.03   26.91
plotGenes         20.39   0.05   20.45
fitSigmoidModels  13.98   0.04   14.03
get_accessors     13.38   0.00   13.38
runImpulseDE2     12.41   0.00   12.40
list_accession    11.95   0.02   11.97
writeReportToFile 11.74   0.00   11.74
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
plotHeatmap       29.17   0.01   29.18
updateDEAnalysis  27.16   0.04   27.19
plotGenes         25.27   0.02   25.28
get_accessors     17.47   0.03   17.50
fitSigmoidModels  17.32   0.03   17.36
writeReportToFile 14.82   0.01   14.84
runImpulseDE2     14.72   0.00   14.72
list_accession    14.00   0.01   14.02
* 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/ImpulseDE2.Rcheck/00check.log'
for details.


install for i386

* installing *source* package 'ImpulseDE2' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'ImpulseDE2'
    finding HTML links ... done
    ImpulseDE2Object-class                  html  
    append_strReport                        html  
    computeNormConst                        html  
    computeSizeFactors                      html  
    estimateImpulseParam                    html  
    estimateSigmoidParam                    html  
    evalImpulse                             html  
    evalImpulse_comp                        html  
    evalLogLikImpulse                       html  
    evalLogLikImpulse_comp                  html  
    evalLogLikMu                            html  
    evalLogLikMu_comp                       html  
    evalLogLikSigmoid                       html  
    evalLogLikSigmoid_comp                  html  
    evalSigmoid                             html  
    evalSigmoid_comp                        html  
    fitConstImpulse                         html  
    fitConstImpulseGene                     html  
    fitConstModel                           html  
    fitImpulseModel                         html  
    fitModels                               html  
    fitSigmoidGene                          html  
    fitSigmoidModel                         html  
    fitSigmoidModels                        html  
    get_accessors                           html  
    list_accession                          html  
    plotGenes                               html  
    plotHeatmap                             html  
    processData                             html  
    runDEAnalysis                           html  
    runDESeq2                               html  
    runImpulseDE2                           html  
    set_accessors                           html  
    simulateDataSetImpulseDE2               html  
    updateDEAnalysis                        html  
    writeReportToFile                       html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'ImpulseDE2' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ImpulseDE2' as ImpulseDE2_1.2.0.zip
* DONE (ImpulseDE2)
In R CMD INSTALL
In R CMD INSTALL

CHECK report for ImpulseDE2 on tokay1

Summary

Command output

Installation output

Tests output

Example timings