Package: pathVar

Version: 1.12.0

Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pathVar.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings pathVar_1.12.0.tar.gz

StartedAt: 2019-04-13 04:25:09 -0400 (Sat, 13 Apr 2019)

EndedAt: 2019-04-13 04:32:27 -0400 (Sat, 13 Apr 2019)

EllapsedTime: 437.9 seconds

RetCode: 0

Status:  OK

CheckDir: pathVar.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pathVar.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings pathVar_1.12.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/pathVar.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'pathVar/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'pathVar' version '1.12.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 'pathVar' 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
diagnosticsVarPlots: no visible binding for global variable 'avg'
diagnosticsVarPlots: no visible binding for global variable 'standDev'
diagnosticsVarPlots: no visible binding for global variable 'medAbsDev'
diagnosticsVarPlots: no visible binding for global variable 'cv'
diagnosticsVarPlotsTwoSample: no visible binding for global variable
  'avg'
diagnosticsVarPlotsTwoSample: no visible binding for global variable
  'standDev'
diagnosticsVarPlotsTwoSample: no visible binding for global variable
  'medAbsDev'
diagnosticsVarPlotsTwoSample: no visible binding for global variable
  'cv'
pathVarOneSample: no visible binding for global variable 'APval'
pathVarOneSample: no visible binding for global variable
  'PercOfGenesInPway'
pathVarTwoSamplesCont: no visible binding for global variable 'APval'
pathVarTwoSamplesCont: no visible binding for global variable
  'PercOfGenesInPway'
pathVarTwoSamplesDisc: no visible binding for global variable 'APval'
pathVarTwoSamplesDisc: no visible binding for global variable
  'PercOfGenesInPway'
plotAllTwoSampleDistributionCounts: no visible binding for global
  variable 'Cluster'
plotAllTwoSampleDistributionCounts: no visible binding for global
  variable 'Number_of_genes'
plotOneSample: no visible binding for global variable 'Cluster'
plotOneSample: no visible binding for global variable 'Number_of_genes'
plotTwoSamplesCont: no visible binding for global variable 'PwayName'
plotTwoSamplesCont: no visible binding for global variable
  'NumOfGenesFromDataSetInPathway'
plotTwoSamplesCont: no visible binding for global variable 'value'
plotTwoSamplesCont: no visible binding for global variable
  '..density..'
plotTwoSamplesCont: no visible binding for global variable 'group'
plotTwoSamplesDisc: no visible binding for global variable 'Cluster'
plotTwoSamplesDisc: no visible binding for global variable
  'Number_of_genes'
sigOneSample: no visible binding for global variable 'APval'
sigOneSample: no visible binding for global variable 'PwayName'
sigTwoSamplesCont: no visible binding for global variable 'APval'
sigTwoSamplesCont: no visible binding for global variable 'PwayName'
sigTwoSamplesDisc: no visible binding for global variable 'APval'
sigTwoSamplesDisc: no visible binding for global variable 'PwayName'
Undefined global functions or variables:
  ..density.. APval Cluster NumOfGenesFromDataSetInPathway
  Number_of_genes PercOfGenesInPway PwayName avg cv group medAbsDev
  standDev 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                                    user system elapsed
sigPway                            66.22   0.01   66.24
diagnosticsVarPlotsTwoSample       19.14   2.12   21.27
diagnosticsVarPlots                10.32   0.44   10.75
plotAllTwoSampleDistributionCounts  5.62   0.05    5.68
pathVar-package                     4.99   0.03    5.02
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                                    user system elapsed
sigPway                            79.52   0.06   79.58
diagnosticsVarPlots                34.55   3.56   38.11
diagnosticsVarPlotsTwoSample       23.16   2.58   26.32
plotAllTwoSampleDistributionCounts  8.74   0.02    8.75
pathVar-package                     7.61   0.00    7.62
saveAsPDF                           7.17   0.00    7.17
plotPway                            6.73   0.00    6.73
pathVarTwoSamplesCont               6.24   0.00    6.23
getGenes                            6.06   0.00    6.07
pathVarOneSample                    5.53   0.02    5.55
* 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-3.8-bioc/meat/pathVar.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/pathVar_1.12.0.tar.gz && rm -rf pathVar.buildbin-libdir && mkdir pathVar.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=pathVar.buildbin-libdir pathVar_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL pathVar_1.12.0.zip && rm pathVar_1.12.0.tar.gz pathVar_1.12.0.zip
###
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install for i386

* installing *source* package 'pathVar' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'pathVar'
    finding HTML links ... done
    bock                                    html  
    diagnosticsVarPlots                     html  
    diagnosticsVarPlotsTwoSample            html  
    geneDistributionSet-class               html  
    geneDistributionSet2-class              html  
    geneDistributionSet3-class              html  
    geneSet-class                           html  
    getGenes                                html  
    makeDBList                              html  
    pathVar-package                         html  
    pathVarOneSample                        html  
    pathVarTwoSamplesCont                   html  
    pathVarTwoSamplesDisc                   html  
    plotAllTwoSampleDistributionCounts      html  
    plotPway                                html  
    pways.kegg                              html  
    pways.reactome                          html  
    saveAsPDF                               html  
    sigPway                                 html  
    significantPathway-class                html  
    significantPathway2-class               html  
    significantPathway3-class               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'pathVar' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'pathVar' as pathVar_1.12.0.zip
* DONE (pathVar)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'pathVar' successfully unpacked and MD5 sums checked
In R CMD INSTALL