Package: phenoDist

Version: 1.27.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings phenoDist_1.27.0.tar.gz

StartedAt: 2018-01-09 01:06:24 -0500 (Tue, 09 Jan 2018)

EndedAt: 2018-01-09 01:11:55 -0500 (Tue, 09 Jan 2018)

EllapsedTime: 330.8 seconds

RetCode: 0

Status:  OK

CheckDir: phenoDist.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings phenoDist_1.27.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/phenoDist.Rcheck’
* using R Under development (unstable) (2017-12-04 r73829)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... 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
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
distToNeg            95.830  0.688  99.692
PDMBySvmWeightVector 14.360  0.200  14.887
PDMBySvmAccuracy     10.198  0.114  10.532
PDMByKS               4.919  0.246  16.943
PDMByFactorAnalysis   1.848  0.123   9.516
PDMByWellAvg          0.922  0.027   5.136
* 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
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/phenoDist.Rcheck/00check.log’
for details.

* installing *source* package ‘phenoDist’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (phenoDist)

name	user	system	elapsed
PDMByFactorAnalysis	1.848	0.123	9.516
PDMByKS	4.919	0.246	16.943
PDMBySvmAccuracy	10.198	0.114	10.532
PDMBySvmWeightVector	14.360	0.200	14.887
PDMByWellAvg	0.922	0.027	5.136
clusterDist	0.758	0.017	0.788
ctlSeparatn	0	0	0
distToNeg	95.830	0.688	99.692
enrichAnalysis	0.001	0.000	0.001
repCorr	0	0	0
repDistRank	0.000	0.000	0.001