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BioC 3.4: CHECK report for phenoDist on malbec1

This page was generated on 2017-04-15 16:10:15 -0400 (Sat, 15 Apr 2017).

Package 915/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
phenoDist 1.22.0
Xian Zhang
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/phenoDist
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: phenoDist
Version: 1.22.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings phenoDist_1.22.0.tar.gz
StartedAt: 2017-04-15 00:23:51 -0400 (Sat, 15 Apr 2017)
EndedAt: 2017-04-15 00:28:12 -0400 (Sat, 15 Apr 2017)
EllapsedTime: 260.4 seconds
RetCode: 0
Status:  OK 
CheckDir: phenoDist.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings phenoDist_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/phenoDist.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.22.0’
* 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            68.840  0.020  68.897
PDMBySvmWeightVector 12.656  0.024  12.687
PDMBySvmAccuracy      8.136  0.016   8.160
PDMByKS               5.664  0.076  15.599
PDMByFactorAnalysis   1.524  0.044   7.227
* 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-3.4-bioc/meat/phenoDist.Rcheck/00check.log’
for details.


phenoDist.Rcheck/00install.out:

* 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)

phenoDist.Rcheck/phenoDist-Ex.timings:

nameusersystemelapsed
PDMByFactorAnalysis1.5240.0447.227
PDMByKS 5.664 0.07615.599
PDMBySvmAccuracy8.1360.0168.160
PDMBySvmWeightVector12.656 0.02412.687
PDMByWellAvg1.440.002.61
clusterDist0.1240.0000.122
ctlSeparatn000
distToNeg68.840 0.02068.897
enrichAnalysis0.0000.0000.001
repCorr000
repDistRank000