Package: CAFE

Version: 1.14.0

Command: rm -rf CAFE.buildbin-libdir CAFE.Rcheck && mkdir CAFE.buildbin-libdir CAFE.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CAFE.buildbin-libdir CAFE_1.14.0.tar.gz >CAFE.Rcheck\00install.out 2>&1 && cp CAFE.Rcheck\00install.out CAFE-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=CAFE.buildbin-libdir --install="check:CAFE-install.out" --force-multiarch --no-vignettes --timings CAFE_1.14.0.tar.gz

StartedAt: 2018-04-11 22:38:32 -0400 (Wed, 11 Apr 2018)

EndedAt: 2018-04-11 22:46:04 -0400 (Wed, 11 Apr 2018)

EllapsedTime: 451.8 seconds

RetCode: 0

Status:  OK

CheckDir: CAFE.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf CAFE.buildbin-libdir CAFE.Rcheck && mkdir CAFE.buildbin-libdir CAFE.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CAFE.buildbin-libdir CAFE_1.14.0.tar.gz >CAFE.Rcheck\00install.out 2>&1 && cp CAFE.Rcheck\00install.out CAFE-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=CAFE.buildbin-libdir --install="check:CAFE-install.out" --force-multiarch --no-vignettes --timings CAFE_1.14.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/CAFE.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 'CAFE/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CAFE' 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 'CAFE' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
Armchisqr: no visible global function definition for 'chisq.test'
ArmfisherExact: no visible global function definition for 'fisher.test'
ProcessCels: no visible global function definition for 'download.file'
ProcessCels: no visible global function definition for 'read.table'
ProcessCels: no visible global function definition for 'txtProgressBar'
ProcessCels: no visible global function definition for
  'setTxtProgressBar'
ProcessCels: no visible global function definition for 'na.omit'
allBandsOnChrom: no visible global function definition for
  'fisher.test'
allBandsOnChromChi: no visible global function definition for
  'chisq.test'
armStats: no visible global function definition for 'p.adjust'
bandStats: no visible global function definition for 'p.adjust'
chisqr: no visible global function definition for 'chisq.test'
chromosomeStats: no visible global function definition for 'p.adjust'
discontPlot: no visible global function definition for 'png'
discontPlot: no visible global function definition for 'dev.off'
discontPlot: no visible global function definition for 'data'
facetPlot: no visible global function definition for 'png'
facetPlot: no visible global function definition for 'dev.off'
facetPlot: no visible global function definition for 'na.omit'
fisher.method: no visible global function definition for 'pchisq'
fisherExact: no visible global function definition for 'fisher.test'
makelevels: no visible global function definition for 'na.omit'
rawPlot: no visible global function definition for 'png'
rawPlot: no visible global function definition for 'dev.off'
rawPlot: no visible global function definition for 'data'
slidPlot: no visible global function definition for 'png'
slidPlot: no visible global function definition for 'dev.off'
slidPlot: no visible global function definition for 'data'
Undefined global functions or variables:
  chisq.test data dev.off download.file fisher.test na.omit p.adjust
  pchisq png read.table setTxtProgressBar txtProgressBar
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("stats", "chisq.test", "fisher.test", "na.omit", "p.adjust",
             "pchisq")
  importFrom("utils", "data", "download.file", "read.table",
             "setTxtProgressBar", "txtProgressBar")
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
facetPlot  6.2    0.3     6.5
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
          user system elapsed
facetPlot 5.86   0.25    6.11
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.R'
 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/CAFE.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'CAFE' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'CAFE'
    finding HTML links ... done
    CAFE-package                            html  
    CAFE                                    html  
    ProcessCels                             html  
    armStats                                html  
    bandStats                               html  
    chromosomeStats                         html  
    cliSubset                               html  
    discontPlot                             html  
    discontSmooth                           html  
    facetPlot                               html  
    fisher.method                           html  
    guiSubset                               html  
    rawPlot                                 html  
    slidPlot                                html  
    slidSmooth                              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'CAFE' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CAFE' as CAFE_1.14.0.zip
* DONE (CAFE)
In R CMD INSTALL
In R CMD INSTALL

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> #BiocGenerics:::testPackage("CAFE")
> 
> proc.time()
   user  system elapsed 
   0.23    0.03    0.25 

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> #BiocGenerics:::testPackage("CAFE")
> 
> proc.time()
   user  system elapsed 
   0.26    0.01    0.28