Package: facopy

Version: 1.13.0

Command: rm -rf facopy.buildbin-libdir facopy.Rcheck && mkdir facopy.buildbin-libdir facopy.Rcheck && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=facopy.buildbin-libdir facopy_1.13.0.tar.gz >facopy.Rcheck\00install.out 2>&1 && cp facopy.Rcheck\00install.out facopy-install.out && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --library=facopy.buildbin-libdir --install="check:facopy-install.out" --force-multiarch --install=check:facopy.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings facopy_1.13.0.tar.gz

StartedAt: 2018-03-04 02:12:19 -0500 (Sun, 04 Mar 2018)

EndedAt: 2018-03-04 02:16:49 -0500 (Sun, 04 Mar 2018)

EllapsedTime: 270.7 seconds

RetCode: 0

Status:  OK

CheckDir: facopy.Rcheck

Warnings: 0

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### Running command:
###
###   rm -rf facopy.buildbin-libdir facopy.Rcheck && mkdir facopy.buildbin-libdir facopy.Rcheck && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=facopy.buildbin-libdir facopy_1.13.0.tar.gz >facopy.Rcheck\00install.out 2>&1 && cp facopy.Rcheck\00install.out facopy-install.out  &&  C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --library=facopy.buildbin-libdir --install="check:facopy-install.out" --force-multiarch --install=check:facopy.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings facopy_1.13.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/facopy.Rcheck'
* using R Under development (unstable) (2018-01-28 r74175)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'facopy/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'facopy' version '1.13.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'cgdsr' 'coin' 'ggplot2' 'gridExtra' 'facopy.annot' 'grid'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'facopy' 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
Package in Depends field not imported from: 'grid'
  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
.aggregateInt: no visible global function definition for 'data'
.checkFullModel: no visible global function definition for 'formula'
.enrichment: no visible global function definition for 'phyper'
.enrichment: no visible global function definition for 'p.adjust'
.enrichment: no visible global function definition for 'write.table'
.enrichment: no visible global function definition for 'data'
.enrichment: no visible global function definition for 'pdf'
.enrichment: no visible global function definition for 'dev.off'
.enrichment : <anonymous>: no visible global function definition for
  'heat.colors'
.facopyPlotInt: no visible global function definition for 'data'
.getFacopyAnnot: no visible global function definition for 'data'
.graphPathway: no visible global function definition for 'mtext'
.makeArmsInt: no visible global function definition for 'data'
.makeCor : <anonymous>: no visible global function definition for 'lm'
.plotArm: no visible global function definition for 'data'
.plotVicinityInt: no visible global function definition for 'par'
.plotVicinityInt : makeAb: no visible global function definition for
  'abline'
.plotVicinityInt: no visible global function definition for 'layout'
.plotVicinityInt: no visible global function definition for 'plot.new'
.plotVicinityInt: no visible global function definition for
  'plot.window'
.plotVicinityInt: no visible global function definition for 'grid'
.plotVicinityInt: no visible global function definition for 'quantile'
.plotVicinityInt: no visible global function definition for 'rect'
.plotVicinityInt: no visible global function definition for 'title'
.plotVicinityInt: no visible global function definition for 'axis'
.plotVicinityInt: no visible global function definition for 'mtext'
.plotVicinityInt: no visible global function definition for 'legend'
.plotVicinityInt: no visible global function definition for 'image'
.readFromGAP: no visible global function definition for 'read.table'
.readFromInt: no visible global function definition for 'read.delim'
.refcols: no visible global function definition for 'colorRampPalette'
addFeatures: no visible global function definition for 'read.table'
addVariables: no visible global function definition for 'read.table'
alterationSummary: no visible global function definition for
  'write.table'
calculateCor: no visible global function definition for 'read.table'
facopy : doMultinom: no visible global function definition for
  'formula'
facopy : doMultinom: no visible global function definition for 'anova'
facopy: no visible global function definition for 'formula'
facopy: no visible global function definition for 'glm'
facopy: no visible global function definition for 'binomial'
facopy: no visible global function definition for 'anova'
facopyEnrichment: no visible global function definition for 'data'
plotPCA: no visible global function definition for 'points'
plotPCA: no visible global function definition for 'legend'
plotPCA: no visible global function definition for 'image'
plotPCA: no visible global function definition for 'quantile'
variableCor: no visible global function definition for 'combn'
variableCor: no visible global function definition for 'chisq.test'
variableCor: no visible global function definition for 'fisher.test'
variableCor: no visible global function definition for 'cor.test'
variableCor: no visible global function definition for 'oneway.test'
variableCor: no visible global function definition for 'kruskal.test'
variableCor: no visible global function definition for 'write.table'
variableSummary : wilcoxtest: no visible global function definition for
  'wilcox.test'
variableSummary : cortest: no visible global function definition for
  'cor.test'
variableSummary: no visible global function definition for 'combn'
variableSummary: no visible global function definition for
  'write.table'
Undefined global functions or variables:
  abline anova axis binomial chisq.test colorRampPalette combn cor.test
  data dev.off fisher.test formula glm grid heat.colors image
  kruskal.test layout legend lm mtext oneway.test p.adjust par pdf
  phyper plot.new plot.window points quantile read.delim read.table
  rect title wilcox.test write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.off", "heat.colors",
             "pdf")
  importFrom("graphics", "abline", "axis", "grid", "image", "layout",
             "legend", "mtext", "par", "plot.new", "plot.window",
             "points", "rect", "title")
  importFrom("stats", "anova", "binomial", "chisq.test", "cor.test",
             "fisher.test", "formula", "glm", "kruskal.test", "lm",
             "oneway.test", "p.adjust", "phyper", "quantile",
             "wilcox.test")
  importFrom("utils", "combn", "data", "read.delim", "read.table",
             "write.table")
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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
facopyPlot   10.12   0.03   10.22
calculateCor  4.91   2.25    8.68
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
facopyPlot   6.54   0.03    6.58
calculateCor 3.19   1.85    6.33
* 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 NOTEs
See
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/facopy.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   rm -rf facopy.buildbin-libdir && mkdir facopy.buildbin-libdir  && C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/facopy_1.13.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --build --library=facopy.buildbin-libdir --merge-multiarch facopy_1.13.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL facopy_1.13.0.zip  && rm facopy_1.13.0.tar.gz facopy_1.13.0.zip
###
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install for i386

* installing *source* package 'facopy' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'facopy'
    finding HTML links ... done
    addFeatures                             html  
    addVariables                            html  
    alterationSummary                       html  
    calculateCor                            html  
    facopy-package                          html  
    facopy                                  html  
    finding level-2 HTML links ... done

    facopyEnrichment                        html  
    facopyInfo-class                        html  
    facopyPlot                              html  
    getFacopyInfo                           html  
    myCalls                                 html  
    myStudy                                 html  
    myVariables                             html  
    plotBar                                 html  
    plotHist                                html  
    plotPCA                                 html  
    plotZoom                                html  
    preview                                 html  
    readCNData                              html  
    variableCor                             html  
    variableSummary                         html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'facopy' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'facopy' as facopy_1.13.0.zip
* DONE (facopy)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'facopy' successfully unpacked and MD5 sums checked
In R CMD INSTALL