Package: phenoDist

Version: 1.26.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings phenoDist_1.26.0.tar.gz

StartedAt: 2018-01-09 01:57:37 -0500 (Tue, 09 Jan 2018)

EndedAt: 2018-01-09 02:01:47 -0500 (Tue, 09 Jan 2018)

EllapsedTime: 250.4 seconds

RetCode: 0

Status:  OK

CheckDir: phenoDist.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings phenoDist_1.26.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/phenoDist.Rcheck’
* using R version 3.4.3 (2017-11-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘phenoDist/DESCRIPTION’ ... OK
* this is package ‘phenoDist’ version ‘1.26.0’
* 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 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            49.188  0.012  49.231
PDMBySvmWeightVector 12.648  0.016  12.678
PDMBySvmAccuracy      8.124  0.004   8.137
PDMByKS               5.816  0.208  23.094
PDMByFactorAnalysis   2.020  0.100  10.600
PDMByWellAvg          1.648  0.028   7.273
* 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
  ‘/home/biocbuild/bbs-3.6-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	2.02	0.10	10.60
PDMByKS	5.816	0.208	23.094
PDMBySvmAccuracy	8.124	0.004	8.137
PDMBySvmWeightVector	12.648	0.016	12.678
PDMByWellAvg	1.648	0.028	7.273
clusterDist	0.572	0.008	0.579
ctlSeparatn	0	0	0
distToNeg	49.188	0.012	49.231
enrichAnalysis	0	0	0
repCorr	0	0	0
repDistRank	0	0	0