[Bioc-devel] How to debug for the warnings?

Mon May 2 23:53:34 CEST 2016

Hi All,

I got some warnings when check. However, I could not see any details for that warnings. How could I debug for these kind of warnings? Thank you.

* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/ChIPpeakAnno.Rcheck’
* using R version 3.3.0 RC (2016-04-25 r70549)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ChIPpeakAnno/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChIPpeakAnno’ version ‘3.5.18’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘grid’ ‘IRanges’ ‘Biostrings’ ‘GenomicRanges’ ‘S4Vectors’
  ‘VennDiagram’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘ChIPpeakAnno’ can be installed ... [20s/22s] OK
* checking installed package size ... NOTE
  installed size is 19.4Mb
  sub-directories of 1Mb or more:
    data     12.7Mb
    extdata   5.2Mb
* 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 dependencies in R code ... NOTE

* checking S3 generic/method consistency ... WARNING

See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... WARNING

The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
* checking foreign function calls ... NOTE

See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
BED2RangedData: no visible global function definition for 'read.delim'
GFF2RangedData: no visible global function definition for 'read.delim'
addGeneIDs : is.installed: no visible global function definition for
  'installed.packages'
binOverFeature: no visible global function definition for 'par'
binOverFeature : plotErrBar: no visible global function definition for
  'segments'
binOverFeature : plotErrBar: no visible global function definition for
  'par'
binOverFeature : <anonymous>: no visible global function definition for
  'plot'
binOverFeature : <anonymous>: no visible global function definition for
  'abline'
binOverFeature : <anonymous>: no visible global function definition for
  'axis'
buildBindingDistribution: no visible global function definition for
  'boxplot.stats'
buildBindingDistribution: no visible global function definition for
  'hist'
df2GRanges : <anonymous>: no visible global function definition for
  'rgb'
egOrgMap: no visible global function definition for 'adist'
featureAlignedDistribution: no visible global function definition for
  'matplot'
featureAlignedDistribution: no visible global function definition for
  'axis'
featureAlignedDistribution: no visible global function definition for
  'legend'
featureAlignedHeatmap: no visible global function definition for
  'colorRampPalette'
featureAlignedHeatmap : areColors : <anonymous>: no visible global
  function definition for 'col2rgb'
findOverlappingPeaks : <anonymous>: no visible binding for global
  variable 'data'
makeVennDiagram : plotVenn: no visible global function definition for
  'par'
makeVennDiagram : plotVenn: no visible global function definition for
  'plot.new'
mergePlusMinusPeaks: no visible global function definition for
  'read.table'
mergePlusMinusPeaks: no visible global function definition for
  'write.table'
newAnnoGR: no visible global function definition for 'setNames'
oligoSummary : subgroupMotif: no visible global function definition for
  'adist'
oligoSummary : subgroupMotif : <anonymous>: no visible global function
  definition for 'combn'
oligoSummary : subgroupMotif : <anonymous> : <anonymous>: no visible
  global function definition for 'combn'
oligoSummary: no visible global function definition for 'adist'
oligoSummary: no visible global function definition for 'hclust'
oligoSummary: no visible global function definition for 'kmeans'
oligoSummary: no visible global function definition for 'as.dendrogram'
oligoSummary: no visible binding for global variable 'nobs'
pie1: no visible global function definition for 'as.graphicsAnnot'
pie1: no visible global function definition for 'plot.new'
pie1: no visible global function definition for 'par'
pie1: no visible global function definition for 'dev.hold'
pie1: no visible global function definition for 'dev.flush'
pie1: no visible global function definition for 'plot.window'
pie1: no visible global function definition for 'polygon'
pie1: no visible global function definition for 'lines'
pie1: no visible global function definition for 'text'
pie1: no visible global function definition for 'title'
randPeaks: no visible global function definition for 'rexp'
summarizePatternInPeaks: no visible global function definition for
  'write.table'
toGRanges,character: no visible global function definition for
  'read.table'
toGRanges,connection: no visible global function definition for
  'read.table'
Undefined global functions or variables:
  abline adist as.dendrogram as.graphicsAnnot axis boxplot.stats
  col2rgb colorRampPalette combn data dev.flush dev.hold hclust hist
  installed.packages kmeans legend lines matplot nobs par plot plot.new
  plot.window polygon read.delim read.table rexp rgb segments setNames
  text title write.table
Consider adding
  importFrom("grDevices", "as.graphicsAnnot", "boxplot.stats", "col2rgb",
             "colorRampPalette", "dev.flush", "dev.hold", "rgb")
  importFrom("graphics", "abline", "axis", "hist", "legend", "lines",
             "matplot", "par", "plot", "plot.new", "plot.window",
             "polygon", "segments", "text", "title")
  importFrom("stats", "as.dendrogram", "hclust", "kmeans", "nobs",
             "rexp", "setNames")
  importFrom("utils", "adist", "combn", "data", "installed.packages",
             "read.delim", "read.table", "write.table")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING

All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING

* checking Rd \usage sections ... NOTE

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... [46s/52s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
findEnhancers 17.907  0.052  18.037
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [48s/49s]
 [48s/50s] 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: 4 WARNINGs, 6 NOTEs
See
  ‘/home/biocbuild/bbs-3.3-bioc/meat/ChIPpeakAnno.Rcheck/00check.log’
for details.

Yours Sincerely,

Jianhong Ou

TEL: 508-856-5379
LRB 608
Bioinformatician of Bioinformatics core at
Department of Molecular, Cell and Cancer Biology
364 Plantation Street Worcester,
MA 01605

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