[Bioc-devel] How to debug for the warnings?
Martin Morgan
martin.morgan at roswellpark.org
Tue May 3 00:33:51 CEST 2016
On 05/02/2016 05:53 PM, Ou, Jianhong wrote:
> 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.
Please see this thread
https://stat.ethz.ch/pipermail/bioc-devel/2016-May/009205.html
and update BiocInstaller (from svn)
svn co
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/BiocInstaller
>
>
> * 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
>
> [[alternative HTML version deleted]]
>
>
>
> _______________________________________________
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> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
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