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BioC 3.0: CHECK report for phenoDist on perceval

This page was generated on 2015-04-10 09:55:26 -0700 (Fri, 10 Apr 2015).

Package 656/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
phenoDist 1.14.0
Xian Zhang
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/phenoDist
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ OK ] OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: phenoDist
Version: 1.14.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch phenoDist_1.14.0.tar.gz
StartedAt: 2015-04-10 04:45:57 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 04:56:02 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 605.8 seconds
RetCode: 0
Status:  OK 
CheckDir: phenoDist.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch phenoDist_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/phenoDist.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘phenoDist/DESCRIPTION’ ... OK
* this is package ‘phenoDist’ version ‘1.14.0’
* checking package namespace information ... OK
* 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 ... [36s/37s] 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.
Package in Depends field not imported from: ‘e1071’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
cleanDistMatrix: no visible global function definition for
  ‘getWellFeatures’
clusterDist: no visible global function definition for
  ‘getWellFeatures’
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
  ‘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’
PDMByFactorAnalysis: no visible global function definition for
  ‘collectCellFeatures’
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’
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’
repCorr: no visible global function definition for ‘getUnames’
* 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 ... [219s/250s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
distToNeg            151.939  1.037 153.101
PDMBySvmWeightVector  19.835  0.195  20.038
PDMBySvmAccuracy      11.326  0.105  11.454
PDMByKS                9.810  0.406  29.131
PDMByFactorAnalysis    3.387  0.180  12.992
* 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

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-3.0-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
PDMByFactorAnalysis 3.387 0.18012.992
PDMByKS 9.810 0.40629.131
PDMBySvmAccuracy11.326 0.10511.454
PDMBySvmWeightVector19.835 0.19520.038
PDMByWellAvg1.4440.0333.238
clusterDist0.9550.0320.988
ctlSeparatn0.0000.0000.001
distToNeg151.939 1.037153.101
enrichAnalysis000
repCorr0.0000.0010.000
repDistRank0.0010.0000.000