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BioC 3.4: CHECK report for phenoDist on tokay1

This page was generated on 2017-04-15 16:16:25 -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: rm -rf phenoDist.buildbin-libdir phenoDist.Rcheck && mkdir phenoDist.buildbin-libdir phenoDist.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=phenoDist.buildbin-libdir phenoDist_1.22.0.tar.gz >phenoDist.Rcheck\00install.out 2>&1 && cp phenoDist.Rcheck\00install.out phenoDist-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=phenoDist.buildbin-libdir --install="check:phenoDist-install.out" --force-multiarch --no-vignettes --timings phenoDist_1.22.0.tar.gz
StartedAt: 2017-04-15 00:03:25 -0400 (Sat, 15 Apr 2017)
EndedAt: 2017-04-15 00:10:31 -0400 (Sat, 15 Apr 2017)
EllapsedTime: 425.8 seconds
RetCode: 0
Status:  OK  
CheckDir: phenoDist.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf phenoDist.buildbin-libdir phenoDist.Rcheck && mkdir phenoDist.buildbin-libdir phenoDist.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=phenoDist.buildbin-libdir phenoDist_1.22.0.tar.gz >phenoDist.Rcheck\00install.out 2>&1 && cp phenoDist.Rcheck\00install.out phenoDist-install.out  && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=phenoDist.buildbin-libdir --install="check:phenoDist-install.out" --force-multiarch --no-vignettes --timings phenoDist_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/phenoDist.Rcheck'
* using R version 3.3.3 (2017-03-06)
* 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 '1.22.0'
* 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 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            68.48   0.03   68.53
PDMBySvmWeightVector 15.88   0.10   16.00
PDMBySvmAccuracy      9.84   0.06    9.91
PDMByKS               6.67   0.08    9.55
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
distToNeg            74.82   0.03   74.84
PDMBySvmWeightVector 12.90   0.06   12.97
PDMBySvmAccuracy      9.34   0.03    9.37
PDMByKS               6.02   0.10    9.75
* 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-3.4-bioc/meat/phenoDist.Rcheck/00check.log'
for details.


phenoDist.Rcheck/00install.out:


install for i386

* 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

install for x64

* installing *source* package 'phenoDist' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'phenoDist' as phenoDist_1.22.0.zip
* DONE (phenoDist)

phenoDist.Rcheck/examples_i386/phenoDist-Ex.timings:

nameusersystemelapsed
PDMByFactorAnalysis1.630.063.97
PDMByKS6.670.089.55
PDMBySvmAccuracy9.840.069.91
PDMBySvmWeightVector15.88 0.1016.00
PDMByWellAvg1.890.032.71
clusterDist0.670.010.69
ctlSeparatn000
distToNeg68.48 0.0368.53
enrichAnalysis000
repCorr000
repDistRank000

phenoDist.Rcheck/examples_x64/phenoDist-Ex.timings:

nameusersystemelapsed
PDMByFactorAnalysis1.560.013.67
PDMByKS6.020.109.75
PDMBySvmAccuracy9.340.039.37
PDMBySvmWeightVector12.90 0.0612.97
PDMByWellAvg1.780.092.75
clusterDist0.110.000.11
ctlSeparatn000
distToNeg74.82 0.0374.84
enrichAnalysis000
repCorr000
repDistRank000