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BioC 3.4: CHECK report for HELP on tokay1

This page was generated on 2017-04-15 16:15:39 -0400 (Sat, 15 Apr 2017).

Package 587/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HELP 1.32.0
Reid F. Thompson
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/HELP
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: HELP
Version: 1.32.0
Command: rm -rf HELP.buildbin-libdir HELP.Rcheck && mkdir HELP.buildbin-libdir HELP.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=HELP.buildbin-libdir HELP_1.32.0.tar.gz >HELP.Rcheck\00install.out 2>&1 && cp HELP.Rcheck\00install.out HELP-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=HELP.buildbin-libdir --install="check:HELP-install.out" --force-multiarch --no-vignettes --timings HELP_1.32.0.tar.gz
StartedAt: 2017-04-14 22:57:30 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 22:58:18 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 48.0 seconds
RetCode: 0
Status:  OK  
CheckDir: HELP.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf HELP.buildbin-libdir HELP.Rcheck && mkdir HELP.buildbin-libdir HELP.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=HELP.buildbin-libdir HELP_1.32.0.tar.gz >HELP.Rcheck\00install.out 2>&1 && cp HELP.Rcheck\00install.out HELP-install.out  && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=HELP.buildbin-libdir --install="check:HELP-install.out" --force-multiarch --no-vignettes --timings HELP_1.32.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/HELP.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 'HELP/DESCRIPTION' ... OK
* this is package 'HELP' version '1.32.0'
* 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 whether package 'HELP' 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
Package in Depends field not imported from: 'methods'
  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
calcTm: no visible global function definition for 'data'
calcTm: no visible binding for global variable
  'base.stacking.thermodynamics'
readSampleKey: no visible global function definition for 'read.table'
calcGC,ExpressionSet: no visible global function definition for
  'validObject'
calcGC,ExpressionSet: no visible global function definition for
  'callGeneric'
calcGC,ExpressionSet: no visible global function definition for 'new'
calcPrototype,ExpressionSet: no visible global function definition for
  'validObject'
calcPrototype,ExpressionSet: no visible global function definition for
  'callGeneric'
calcPrototype,vector: no visible global function definition for
  'callGeneric'
calcTm,ExpressionSet: no visible global function definition for
  'validObject'
calcTm,ExpressionSet: no visible global function definition for
  'callGeneric'
calcTm,ExpressionSet: no visible global function definition for 'new'
calcTm,character: no visible binding for global variable
  'base.stacking.thermodynamics'
combineData,ExpressionSet-missing-missing: no visible global function
  definition for 'validObject'
combineData,ExpressionSet-missing-missing: no visible global function
  definition for 'callGeneric'
combineData,ExpressionSet-vector-missing: no visible global function
  definition for 'validObject'
combineData,ExpressionSet-vector-missing: no visible global function
  definition for 'callGeneric'
combineData,matrix-vector-missing: no visible global function
  definition for 'callGeneric'
combineData,vector-missing-missing: no visible global function
  definition for 'callGeneric'
combineData,vector-missing-vector: no visible global function
  definition for 'callGeneric'
combineData,vector-vector-missing: no visible global function
  definition for 'callGeneric'
combineData,vector-vector-vector: no visible global function definition
  for 'callGeneric'
createWiggle,ExpressionSet-matrix: no visible global function
  definition for 'validObject'
createWiggle,ExpressionSet-matrix: no visible global function
  definition for 'callGeneric'
createWiggle,ExpressionSet-missing: no visible global function
  definition for 'validObject'
createWiggle,ExpressionSet-missing: no visible global function
  definition for 'callGeneric'
createWiggle,matrix-matrix: no visible global function definition for
  'rainbow'
createWiggle,matrix-matrix: no visible global function definition for
  'col2rgb'
createWiggle,vector-matrix: no visible global function definition for
  'callGeneric'
getFeatures,AnnotatedDataFrame-NULL: no visible global function
  definition for 'validObject'
getFeatures,AnnotatedDataFrame-missing: no visible global function
  definition for 'validObject'
getFeatures,AnnotatedDataFrame-vector: no visible global function
  definition for 'validObject'
getFeatures,AnnotatedDataFrame-vector: no visible global function
  definition for 'callGeneric'
getFeatures,ExpressionSet-NULL: no visible global function definition
  for 'validObject'
getFeatures,ExpressionSet-missing: no visible global function
  definition for 'validObject'
getFeatures,ExpressionSet-vector: no visible global function definition
  for 'validObject'
getFeatures,ExpressionSet-vector: no visible global function definition
  for 'callGeneric'
getFeatures,vector-vector: no visible global function definition for
  'callGeneric'
getSamples,ExpressionSet-NULL: no visible global function definition
  for 'validObject'
getSamples,ExpressionSet-missing: no visible global function definition
  for 'validObject'
getSamples,ExpressionSet-vector: no visible global function definition
  for 'validObject'
getSamples,ExpressionSet-vector: no visible global function definition
  for 'callGeneric'
getSamples,vector-vector: no visible global function definition for
  'callGeneric'
plotBins,ExpressionSet-ExpressionSet: no visible global function
  definition for 'validObject'
plotBins,ExpressionSet-ExpressionSet: no visible global function
  definition for 'callGeneric'
plotBins,ExpressionSet-missing: no visible global function definition
  for 'validObject'
plotBins,ExpressionSet-missing: no visible global function definition
  for 'callGeneric'
plotBins,ExpressionSet-vector: no visible global function definition
  for 'validObject'
plotBins,ExpressionSet-vector: no visible global function definition
  for 'callGeneric'
plotBins,matrix-missing: no visible global function definition for
  'callGeneric'
plotBins,vector-ExpressionSet: no visible global function definition
  for 'validObject'
plotBins,vector-ExpressionSet: no visible global function definition
  for 'callGeneric'
plotBins,vector-vector: no visible global function definition for
  'rainbow'
plotBins,vector-vector: no visible global function definition for
  'quantile'
plotBins,vector-vector: no visible global function definition for
  'layout'
plotBins,vector-vector: no visible global function definition for
  'plot'
plotBins,vector-vector: no visible global function definition for
  'axis'
plotBins,vector-vector: no visible global function definition for
  'rect'
plotBins,vector-vector: no visible global function definition for
  'density'
plotBins,vector-vector: no visible global function definition for
  'lines'
plotChip,ExpressionSet-ExpressionSet-missing: no visible global
  function definition for 'validObject'
plotChip,ExpressionSet-ExpressionSet-missing: no visible global
  function definition for 'callGeneric'
plotChip,ExpressionSet-missing-missing: no visible global function
  definition for 'validObject'
plotChip,ExpressionSet-missing-missing: no visible global function
  definition for 'callGeneric'
plotChip,ExpressionSet-vector-missing: no visible global function
  definition for 'validObject'
plotChip,ExpressionSet-vector-missing: no visible global function
  definition for 'callGeneric'
plotChip,matrix-missing-missing: no visible global function definition
  for 'callGeneric'
plotChip,vector-vector-ExpressionSet: no visible global function
  definition for 'validObject'
plotChip,vector-vector-ExpressionSet: no visible global function
  definition for 'callGeneric'
plotChip,vector-vector-vector: no visible global function definition
  for 'rainbow'
plotChip,vector-vector-vector: no visible global function definition
  for 'quantile'
plotChip,vector-vector-vector: no visible global function definition
  for 'plot'
plotChip,vector-vector-vector: no visible global function definition
  for 'rect'
plotFeature,ExpressionSet-missing: no visible global function
  definition for 'callGeneric'
plotFeature,ExpressionSet-vector: no visible global function definition
  for 'validObject'
plotFeature,ExpressionSet-vector: no visible global function definition
  for 'callGeneric'
plotFeature,matrix-vector: no visible global function definition for
  'par'
plotFeature,matrix-vector: no visible global function definition for
  'median'
plotFeature,matrix-vector: no visible global function definition for
  'mad'
plotFeature,matrix-vector: no visible global function definition for
  'layout'
plotFeature,matrix-vector: no visible global function definition for
  'density'
plotFeature,matrix-vector: no visible global function definition for
  'plot'
plotFeature,matrix-vector: no visible global function definition for
  'points'
plotFeature,matrix-vector: no visible global function definition for
  'abline'
plotPairs,ExpressionSet: no visible global function definition for
  'validObject'
plotPairs,ExpressionSet: no visible global function definition for
  'callGeneric'
plotPairs,matrix: no visible global function definition for 'par'
plotPairs,matrix: no visible global function definition for 'hclust'
plotPairs,matrix: no visible global function definition for 'dist'
plotPairs,matrix: no visible global function definition for 'cutree'
plotPairs,matrix: no visible global function definition for 'rainbow'
plotPairs,matrix : plot.pairs.upper: no visible global function
  definition for 'par'
plotPairs,matrix : plot.pairs.upper: no visible global function
  definition for 'points'
plotPairs,matrix : plot.pairs.upper: no visible global function
  definition for 'cor'
plotPairs,matrix : plot.pairs.upper: no visible global function
  definition for 'lowess'
plotPairs,matrix : plot.pairs.upper: no visible global function
  definition for 'lines'
plotPairs,matrix : plot.pairs.upper: no visible global function
  definition for 'text'
plotPairs,matrix: no visible global function definition for 'layout'
plotPairs,matrix: no visible global function definition for 'pairs'
plotPairs,matrix: no visible global function definition for 'plot'
plotPairs,matrix: no visible global function definition for 'points'
plotPairs,matrix: no visible global function definition for 'abline'
plotPairs,matrix: no visible global function definition for 'text'
plotPairs,matrix : draw.tree: no visible global function definition for
  'points'
plotPairs,matrix: no visible global function definition for
  'as.dendrogram'
quantileNormalize,ExpressionSet-ExpressionSet: no visible global
  function definition for 'validObject'
quantileNormalize,ExpressionSet-ExpressionSet: no visible global
  function definition for 'callGeneric'
quantileNormalize,ExpressionSet-missing: no visible global function
  definition for 'validObject'
quantileNormalize,ExpressionSet-missing: no visible global function
  definition for 'callGeneric'
quantileNormalize,ExpressionSet-vector: no visible global function
  definition for 'validObject'
quantileNormalize,ExpressionSet-vector: no visible global function
  definition for 'callGeneric'
quantileNormalize,matrix-missing: no visible global function definition
  for 'callGeneric'
quantileNormalize,vector-ExpressionSet: no visible global function
  definition for 'validObject'
quantileNormalize,vector-ExpressionSet: no visible global function
  definition for 'callGeneric'
quantileNormalize,vector-vector: no visible global function definition
  for 'quantile'
readDesign,character-character-ExpressionSet: no visible global
  function definition for 'validObject'
readDesign,character-character-ExpressionSet: no visible global
  function definition for 'read.table'
readDesign,character-character-ExpressionSet: no visible global
  function definition for 'new'
readDesign,vector-missing-missing: no visible global function
  definition for 'callGeneric'
readDesign,vector-missing-missing: no visible global function
  definition for 'new'
readDesign,vector-vector-missing: no visible global function definition
  for 'callGeneric'
readDesign,vector-vector-missing: no visible global function definition
  for 'new'
readPairs,character-character-ExpressionSet: no visible global function
  definition for 'validObject'
readPairs,character-character-ExpressionSet: no visible global function
  definition for 'read.table'
readPairs,character-character-ExpressionSet: no visible global function
  definition for 'new'
readPairs,vector-missing-missing: no visible global function definition
  for 'callGeneric'
readPairs,vector-missing-missing: no visible global function definition
  for 'new'
readPairs,vector-vector-missing: no visible global function definition
  for 'callGeneric'
readPairs,vector-vector-missing: no visible global function definition
  for 'new'
Undefined global functions or variables:
  abline as.dendrogram axis base.stacking.thermodynamics callGeneric
  col2rgb cor cutree data density dist hclust layout lines lowess mad
  median new pairs par plot points quantile rainbow read.table rect
  text validObject
Consider adding
  importFrom("grDevices", "col2rgb", "rainbow")
  importFrom("graphics", "abline", "axis", "layout", "lines", "pairs",
             "par", "plot", "points", "rect", "text")
  importFrom("methods", "callGeneric", "new", "validObject")
  importFrom("stats", "as.dendrogram", "cor", "cutree", "density",
             "dist", "hclust", "lowess", "mad", "median", "quantile")
  importFrom("utils", "data", "read.table")
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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.4-bioc/meat/HELP.Rcheck/00check.log'
for details.

HELP.Rcheck/00install.out:


install for i386

* installing *source* package 'HELP' ...
** R
** data
** demo
** 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 'HELP' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'HELP' as HELP_1.32.0.zip
* DONE (HELP)

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

nameusersystemelapsed
base.stacking.thermodynamics0.020.000.02
calcGC000
calcPrototype0.030.000.03
calcTm000
combineData000
createWiggle000
exprs2000
fuzzyMatches0.020.000.02
getFeatures0.050.000.05
getSamples0.030.000.03
plotBins0.060.020.08
plotChip0.110.000.10
plotFeature0.060.000.07
plotPairs0.320.000.31
quantileNormalize0.030.000.03
readDesign0.100.000.09
readPairs0.060.000.06
readSampleKey000

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

nameusersystemelapsed
base.stacking.thermodynamics0.010.010.03
calcGC000
calcPrototype0.040.000.03
calcTm0.010.000.01
combineData0.020.000.02
createWiggle000
exprs2000
fuzzyMatches0.010.000.01
getFeatures0.050.020.07
getSamples0.030.000.03
plotBins0.080.000.08
plotChip0.120.000.12
plotFeature0.070.000.06
plotPairs0.370.000.38
quantileNormalize0.060.000.06
readDesign0.070.010.08
readPairs0.110.000.11
readSampleKey0.010.000.01