Package: phenoDist

Version: 1.27.0

Command: rm -rf phenoDist.buildbin-libdir phenoDist.Rcheck && mkdir phenoDist.buildbin-libdir phenoDist.Rcheck && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=phenoDist.buildbin-libdir phenoDist_1.27.0.tar.gz >phenoDist.Rcheck\00install.out 2>&1 && cp phenoDist.Rcheck\00install.out phenoDist-install.out && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --library=phenoDist.buildbin-libdir --install="check:phenoDist-install.out" --force-multiarch --no-vignettes --timings phenoDist_1.27.0.tar.gz

StartedAt: 2018-01-09 01:54:21 -0500 (Tue, 09 Jan 2018)

EndedAt: 2018-01-09 02:00:30 -0500 (Tue, 09 Jan 2018)

EllapsedTime: 368.6 seconds

RetCode: 0

Status:  OK

CheckDir: phenoDist.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf phenoDist.buildbin-libdir phenoDist.Rcheck && mkdir phenoDist.buildbin-libdir phenoDist.Rcheck && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=phenoDist.buildbin-libdir phenoDist_1.27.0.tar.gz >phenoDist.Rcheck\00install.out 2>&1 && cp phenoDist.Rcheck\00install.out phenoDist-install.out  &&  C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --library=phenoDist.buildbin-libdir --install="check:phenoDist-install.out" --force-multiarch --no-vignettes --timings phenoDist_1.27.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/phenoDist.Rcheck'
* using R Under development (unstable) (2018-01-02 r74023)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'phenoDist/DESCRIPTION' ... OK
* this is package 'phenoDist' version '1.27.0'
* checking package namespace information ... NOTE
  Namespace with empty importFrom: 'e1071'
* 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 'phenoDist' 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 ... NOTE
'library' or 'require' call to 'MASS' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
PDMByFactorAnalysis: no visible global function definition for
  'collectCellFeatures'
PDMByFactorAnalysis: no visible global function definition for
  'factanal'
PDMByKS: no visible global function definition for
  'collectCellFeatures'
PDMByKS: no visible global function definition for 'uname2prw'
PDMByKS : <anonymous>: no visible global function definition for
  'getUnames'
PDMByKS : <anonymous> : <anonymous>: no visible global function
  definition for 'collectCellFeatures'
PDMByKS : <anonymous>: no visible global function definition for
  'collectCellFeatures'
PDMByKS : <anonymous>: no visible global function definition for
  'uname2prw'
PDMByKS : <anonymous> : <anonymous> : <anonymous>: no visible global
  function definition for 'ks.test'
PDMByKS : <anonymous> : <anonymous>: no visible global function
  definition for 'median'
PDMBySvmAccuracy: no visible global function definition for
  'collectCellFeatures'
PDMBySvmAccuracy : <anonymous>: no visible global function definition
  for 'collectCellFeatures'
PDMBySvmAccuracy : <anonymous> : <anonymous>: no visible global
  function definition for 'svm'
PDMBySvmWeightVector: no visible global function definition for
  'collectCellFeatures'
PDMBySvmWeightVector: no visible global function definition for
  'uname2prw'
PDMBySvmWeightVector : <anonymous>: no visible global function
  definition for 'getUnames'
PDMBySvmWeightVector : <anonymous> : <anonymous>: no visible global
  function definition for 'collectCellFeatures'
PDMBySvmWeightVector : <anonymous>: no visible global function
  definition for 'collectCellFeatures'
PDMBySvmWeightVector : <anonymous>: no visible global function
  definition for 'uname2prw'
PDMBySvmWeightVector : <anonymous> : <anonymous>: no visible global
  function definition for 'svm'
PDMBySvmWeightVector : <anonymous>: no visible binding for global
  variable 'median'
PDMByWellAvg: no visible global function definition for 'prcomp'
PDMByWellAvg: no visible global function definition for 'dist'
PDMByWellAvg: no visible global function definition for 'cor'
PDMByWellAvg: no visible global function definition for 'cov'
PDMByWellAvg : <anonymous>: no visible global function definition for
  'mahalanobis'
cleanDistMatrix: no visible global function definition for
  'getWellFeatures'
clusterDist: no visible global function definition for
  'getWellFeatures'
clusterDist: no visible global function definition for 'as.dist'
ctlSeparatn: no visible global function definition for
  'getWellFeatures'
ctlSeparatn: no visible global function definition for 'zprime'
distToNeg : <anonymous>: no visible global function definition for
  'uname2prw'
distToNeg : <anonymous>: no visible global function definition for
  'getUnames'
enrichAnalysis : <anonymous>: no visible global function definition for
  'new'
enrichAnalysis : <anonymous>: no visible global function definition for
  'hyperGTest'
getBadWells: no visible global function definition for 'prw2uname'
getReplicate: no visible global function definition for 'uname2prw'
getReplicate: no visible global function definition for 'getUnames'
repCorr: no visible global function definition for 'getUnames'
repCorr: no visible global function definition for 'cor'
repDistRank : <anonymous>: no visible global function definition for
  'median'
Undefined global functions or variables:
  as.dist collectCellFeatures cor cov dist factanal getUnames
  getWellFeatures hyperGTest ks.test mahalanobis median new prcomp
  prw2uname svm uname2prw zprime
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "as.dist", "cor", "cov", "dist", "factanal",
             "ks.test", "mahalanobis", "median", "prcomp")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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
distToNeg            44.20   0.04   44.34
PDMBySvmWeightVector 11.20   0.09   11.30
PDMBySvmAccuracy      9.30   0.10    9.39
PDMByKS               4.72   0.18    9.32
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
distToNeg            57.05   0.06   57.11
PDMBySvmWeightVector 11.77   0.10   11.86
PDMBySvmAccuracy      9.89   0.06    9.95
PDMByKS               4.87   0.16    8.20
* 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/phenoDist.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'phenoDist' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'phenoDist'
    finding HTML links ... done
    PDMByFactorAnalysis                     html  
    PDMByKS                                 html  
    PDMBySvmAccuracy                        html  
    PDMBySvmWeightVector                    html  
    PDMByWellAvg                            html  
    clusterDist                             html  
    ctlSeparatn                             html  
    distToNeg                               html  
    enrichAnalysis                          html  
    repCorr                                 html  
    repDistRank                             html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'phenoDist' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'phenoDist' as phenoDist_1.27.0.zip
* DONE (phenoDist)
In R CMD INSTALL
In R CMD INSTALL