Multiple platform build/check report for BioC 3.7 - CHECK report for HELP on tokay2

Package: HELP

Version: 1.38.0

Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:HELP.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings HELP_1.38.0.tar.gz

StartedAt: 2018-10-17 02:40:23 -0400 (Wed, 17 Oct 2018)

EndedAt: 2018-10-17 02:41:19 -0400 (Wed, 17 Oct 2018)

EllapsedTime: 55.8 seconds

RetCode: 0

Status: OK

CheckDir: HELP.Rcheck

Warnings: 0

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:HELP.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings HELP_1.38.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/HELP.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* 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 '1.38.0'
* 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
* 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 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 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-3.7-bioc/meat/HELP.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/HELP_1.38.0.tar.gz && rm -rf HELP.buildbin-libdir && mkdir HELP.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=HELP.buildbin-libdir HELP_1.38.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL HELP_1.38.0.zip && rm HELP_1.38.0.tar.gz HELP_1.38.0.zip
###
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100  281k  100  281k    0     0  4536k      0 --:--:-- --:--:-- --:--:-- 5218k

install for i386

* installing *source* package 'HELP' ...
** R
** data
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'HELP'
    finding HTML links ... done
    base.stacking.thermodynamics            html  
    calcGC-methods                          html  
    calcGC                                  html  
    calcPrototype-methods                   html  
    calcPrototype                           html  
    calcTm-methods                          html  
    calcTm                                  html  
    combineData-methods                     html  
    combineData                             html  
    createWiggle-methods                    html  
    createWiggle                            html  
    exprs2-methods                          html  
    exprs2                                  html  
    fuzzyMatches-methods                    html  
    fuzzyMatches                            html  
    getFeatures-methods                     html  
    getFeatures                             html  
    getSamples-methods                      html  
    getSamples                              html  
    plotBins-methods                        html  
    plotBins                                html  
    plotChip-methods                        html  
    plotChip                                html  
    plotFeature-methods                     html  
    plotFeature                             html  
    plotPairs-methods                       html  
    plotPairs                               html  
    quantileNormalize-methods               html  
    quantileNormalize                       html  
    readDesign-methods                      html  
    readDesign                              html  
    readPairs-methods                       html  
    readPairs                               html  
    readSampleKey                           html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'HELP' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'HELP' as HELP_1.38.0.zip
* DONE (HELP)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'HELP' successfully unpacked and MD5 sums checked
In R CMD INSTALL

CHECK report for HELP on tokay2

Summary

Command output

Installation output

Tests output

Example timings