Package: DFP

Version: 1.40.0

Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DFP.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings DFP_1.40.0.tar.gz

StartedAt: 2019-04-13 01:47:37 -0400 (Sat, 13 Apr 2019)

EndedAt: 2019-04-13 01:49:22 -0400 (Sat, 13 Apr 2019)

EllapsedTime: 105.0 seconds

RetCode: 0

Status:  OK

CheckDir: DFP.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:DFP.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings DFP_1.40.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/DFP.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 'DFP/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'DFP' version '1.40.0'
* 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 'DFP' 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
'library' or 'require' call to 'Biobase' which was already attached by Depends.
  Please remove these calls from your code.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plotDiscriminantFuzzyPattern: warning in matrix(x, nr = ly, nc = lx,
  byrow = TRUE): partial argument match of 'nr' to 'nrow'
plotDiscriminantFuzzyPattern: warning in matrix(x, nr = ly, nc = lx,
  byrow = TRUE): partial argument match of 'nc' to 'ncol'
plotDiscriminantFuzzyPattern: warning in matrix(y, nr = ly, nc = lx):
  partial argument match of 'nr' to 'nrow'
plotDiscriminantFuzzyPattern: warning in matrix(y, nr = ly, nc = lx):
  partial argument match of 'nc' to 'ncol'
.plotGeneMF: no visible global function definition for 'curve'
.plotGeneMF: no visible binding for global variable 'x'
.plotGeneMF: no visible global function definition for 'abline'
.plotGeneMF: no visible global function definition for 'palette'
.plotGeneMF: no visible global function definition for 'rainbow'
.plotGeneMF: no visible global function definition for 'legend'
calculateFuzzyPatterns: no visible global function definition for
  'head'
discretizeExpressionValues: no visible global function definition for
  'head'
discriminantFuzzyPattern: no visible global function definition for
  'head'
plotDiscriminantFuzzyPattern: no visible global function definition for
  'image'
plotDiscriminantFuzzyPattern: no visible global function definition for
  'par'
plotDiscriminantFuzzyPattern: no visible global function definition for
  'axis'
plotDiscriminantFuzzyPattern: no visible global function definition for
  'text'
plotMembershipFunctions: no visible global function definition for
  'par'
readCSV: no visible global function definition for 'read.table'
readCSV: no visible global function definition for 'head'
Undefined global functions or variables:
  abline axis curve head image legend palette par rainbow read.table
  text x
Consider adding
  importFrom("grDevices", "palette", "rainbow")
  importFrom("graphics", "abline", "axis", "curve", "image", "legend",
             "par", "text")
  importFrom("utils", "head", "read.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
** running examples for arch 'x64' ... 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-3.8-bioc/meat/DFP.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/DFP_1.40.0.tar.gz && rm -rf DFP.buildbin-libdir && mkdir DFP.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DFP.buildbin-libdir DFP_1.40.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL DFP_1.40.0.zip && rm DFP_1.40.0.tar.gz DFP_1.40.0.zip
###
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install for i386

* installing *source* package 'DFP' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'DFP'
    finding HTML links ... done
    DFP-internal                            html  
    DFP-package                             html  
    ExpressionLevel-class                   html  
    HighExpressionLevel-class               html  
    LowExpressionLevel-class                html  
    MediumExpressionLevel-class             html  
    calculateDiscriminantFuzzyPattern       html  
    calculateFuzzyPatterns                  html  
    calculateMembershipFunctions            html  
    discretizeExpressionValues              html  
    discriminantFuzzyPattern                html  
    plotDiscriminantFuzzyPattern            html  
    plotMembershipFunctions                 html  
    readCSV                                 html  
    rmadataset                              html  
    show-methods                            html  
    showDiscreteValues                      html  
    showFuzzyPatterns                       html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'DFP' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DFP' as DFP_1.40.0.zip
* DONE (DFP)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'DFP' successfully unpacked and MD5 sums checked
In R CMD INSTALL