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BioC 3.5: CHECK report for methyAnalysis on oaxaca

This page was generated on 2017-03-04 16:44:28 -0500 (Sat, 04 Mar 2017).

Package 774/1339HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
methyAnalysis 1.17.1
Pan Du , Lei Huang , Gang Feng
Snapshot Date: 2017-03-03 17:15:47 -0500 (Fri, 03 Mar 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/methyAnalysis
Last Changed Rev: 125808 / Revision: 127142
Last Changed Date: 2017-01-09 22:51:22 -0500 (Mon, 09 Jan 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ WARNINGS ] OK 

Summary

Package: methyAnalysis
Version: 1.17.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings methyAnalysis_1.17.1.tar.gz
StartedAt: 2017-03-04 05:41:20 -0800 (Sat, 04 Mar 2017)
EndedAt: 2017-03-04 05:54:25 -0800 (Sat, 04 Mar 2017)
EllapsedTime: 785.6 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: methyAnalysis.Rcheck
Warnings: 2

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings methyAnalysis_1.17.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/methyAnalysis.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘methyAnalysis/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘methyAnalysis’ version ‘1.17.1’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘grid’ ‘BiocGenerics’ ‘IRanges’ ‘GenomeInfoDb’ ‘GenomicRanges’
  ‘Biobase’ ‘org.Hs.eg.db’
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 ‘methyAnalysis’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘IRanges’ ‘GenomicRanges’ ‘Biobase’
A package should be listed in only one of these fields.
* 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 ... WARNING
'::' or ':::' import not declared from: 'bigmemoryExtras'
Packages in Depends field not imported from:
  'grid' 'org.Hs.eg.db'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Missing or unexported object: 'GenomicRanges::overlapsAny'
Unexported objects imported by ':::' calls:
  'Gviz:::.parMappings' 'Gviz:::.setupTextSize' 'Gviz:::.z2icol'
  'Gviz:::setStacks'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... WARNING
  'assayElement<-' '\S4method{assayElement<-}{SummarizedExperiment}'
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.estimateTrackHeight: no visible global function definition for
  'convertY'
.estimateTrackHeight: no visible global function definition for 'unit'
.identifySigProbe: no visible global function definition for 'rowMax'
MethyLumiM2GenoSet: no visible global function definition for 'fData'
MethyLumiM2GenoSet: no visible global function definition for
  'metadata'
MethyLumiM2GenoSet: no visible global function definition for 'mcols<-'
annotateDMRInfo: no visible global function definition for
  'elementNROWS'
annotateDMRInfo: no visible global function definition for 'values'
annotateGRanges: no visible global function definition for
  'elementNROWS'
annotateGRanges: no visible global function definition for 'values'
annotateGRanges: no visible global function definition for 'resize'
annotateGRanges: no visible global function definition for 'values<-'
annotateGRanges: no visible global function definition for 'flank'
annotateGRanges: no visible global function definition for 'nearest'
annotateGRanges: no visible global function definition for
  'findOverlaps'
annotateGRanges: no visible global function definition for 'queryHits'
annotateGRanges: no visible global function definition for
  'subjectHits'
buildAnnotationTracks: no visible global function definition for
  'values<-'
buildAnnotationTracks: no visible global function definition for
  'DataFrame'
buildAnnotationTracks: no visible global function definition for
  'values'
checkChrName: no visible global function definition for 'ranges<-'
createTranscriptTrack: no visible global function definition for
  'values'
detectDMR.slideWin: no visible global function definition for
  'values<-'
estimateCMR.methylation: no visible global function definition for
  'findOverlaps'
estimateCMR.methylation: no visible global function definition for
  'mcols'
estimateCMR.methylation: no visible global function definition for
  'values'
estimateMethySeq: no visible global function definition for 'slice'
estimateMethySeq: no visible global function definition for 'DataFrame'
estimateMethySeq: no visible global function definition for
  'findOverlaps'
estimateMethySeq: no visible global function definition for 'values<-'
estimateMethySeq: no visible global function definition for 'values'
filterBisulfiteVariant: no visible global function definition for
  'slice'
filterBisulfiteVariant: no visible global function definition for
  'findOverlaps'
getContinuousRegion: no visible global function definition for
  'values<-'
getContinuousRegion: no visible global function definition for 'values'
getContinuousRegion: no visible global function definition for 'reduce'
getCoverage: no visible global function definition for 'values<-'
getCoverage: no visible global function definition for 'DataFrame'
getCoverage: no visible global function definition for 'values'
getMethyProbeLocation: no visible global function definition for
  'features'
getMethyProbeLocation: no visible global function definition for
  'values<-'
getMethyProbeLocation: no visible global function definition for
  'DataFrame'
getMethyProbeLocation: no visible global function definition for 'keys'
heatmapByChromosome: no visible global function definition for
  'pushViewport'
heatmapByChromosome: no visible global function definition for
  'viewport'
heatmapByChromosome: no visible global function definition for
  'grid.layout'
heatmapByChromosome: no visible global function definition for
  'popViewport'
heatmapByChromosome: no visible global function definition for
  'convertX'
heatmapByChromosome: no visible global function definition for 'unit'
heatmapByChromosome: no visible global function definition for
  'convertY'
heatmapByChromosome: no visible global function definition for
  'grid.rect'
heatmapByChromosome: no visible global function definition for 'gpar'
heatmapByChromosome: no visible global function definition for
  'grid.lines'
identifyCpG: no visible global function definition for 'matchPattern'
identifySigDMR: no visible global function definition for 'values'
identifySigDMR: no visible global function definition for 'values<-'
identifySigDMR: no visible global function definition for
  'subsetByOverlaps'
plotHeatmapByGene: no visible global function definition for
  'grid.newpage'
plotHeatmapByGene: no visible global function definition for
  'pushViewport'
plotHeatmapByGene: no visible global function definition for 'viewport'
plotHeatmapByGene: no visible global function definition for
  'grid.layout'
plotHeatmapByGene: no visible global function definition for
  'popViewport'
plotHeatmapByGene: no visible global function definition for
  'grid.rect'
plotHeatmapByGene: no visible global function definition for 'gpar'
plotHeatmapByGene: no visible global function definition for
  'grid.segments'
plotHeatmapByGene: no visible global function definition for 'convertX'
plotHeatmapByGene: no visible global function definition for 'unit'
plotHeatmapByGene: no visible global function definition for
  'grid.text'
plotHeatmapByGene: no visible global function definition for 'convertY'
plotMethylationHeatmapByGene : <anonymous>: no visible global function
  definition for 'grid.newpage'
plotMethylationHeatmapByGene : <anonymous>: no visible global function
  definition for 'pushViewport'
plotMethylationHeatmapByGene : <anonymous>: no visible global function
  definition for 'viewport'
plotMethylationHeatmapByGene : <anonymous>: no visible global function
  definition for 'grid.layout'
plotMethylationHeatmapByGene : <anonymous>: no visible global function
  definition for 'popViewport'
plotMethylationHeatmapByGene : <anonymous>: no visible global function
  definition for 'grid.rect'
plotMethylationHeatmapByGene : <anonymous>: no visible global function
  definition for 'gpar'
plotMethylationHeatmapByGene : <anonymous>: no visible global function
  definition for 'grid.segments'
plotMethylationHeatmapByGene : <anonymous>: no visible global function
  definition for 'convertX'
plotMethylationHeatmapByGene : <anonymous>: no visible global function
  definition for 'unit'
plotMethylationHeatmapByGene : <anonymous>: no visible global function
  definition for 'grid.text'
plotMethylationHeatmapByGene : <anonymous>: no visible global function
  definition for 'convertY'
plotTracksWithDataTrackInfo : <anonymous>: no visible global function
  definition for 'values'
plotTracksWithDataTrackInfo: no visible global function definition for
  'grid.newpage'
plotTracksWithDataTrackInfo: no visible global function definition for
  'pushViewport'
plotTracksWithDataTrackInfo: no visible global function definition for
  'viewport'
plotTracksWithDataTrackInfo: no visible global function definition for
  'grid.layout'
plotTracksWithDataTrackInfo: no visible global function definition for
  'convertX'
plotTracksWithDataTrackInfo: no visible global function definition for
  'unit'
plotTracksWithDataTrackInfo : <anonymous>: no visible global function
  definition for 'convertX'
plotTracksWithDataTrackInfo : <anonymous>: no visible global function
  definition for 'unit'
plotTracksWithDataTrackInfo: no visible global function definition for
  'popViewport'
plotTracksWithDataTrackInfo: no visible global function definition for
  'convertY'
plotTracksWithDataTrackInfo: no visible global function definition for
  'grid.text'
plotTracksWithDataTrackInfo: no visible global function definition for
  'gpar'
plotTracksWithDataTrackInfo: no visible global function definition for
  'grid.rect'
transcriptDb2GeneRegionTrackByGene: no visible global function
  definition for 'values'
updateMethyGenoSet: no visible global function definition for 'mcols<-'
coerce,MethyGenoSet-MethyLumiM: no visible global function definition
  for 'mcols'
coerce,MethyGenoSet-MethyLumiM: no visible global function definition
  for 'fData<-'
Undefined global functions or variables:
  DataFrame convertX convertY elementNROWS fData fData<- features
  findOverlaps flank gpar grid.layout grid.lines grid.newpage grid.rect
  grid.segments grid.text keys matchPattern mcols mcols<- metadata
  nearest popViewport pushViewport queryHits ranges<- reduce resize
  rowMax slice subjectHits subsetByOverlaps unit values values<-
  viewport
* checking Rd files ... NOTE
prepare_Rd: estimateCMR.methylation.Rd:35-36: Dropping empty section \details
prepare_Rd: estimateCMR.methylation.Rd:45-47: Dropping empty section \examples
prepare_Rd: estimateMethySeq.Rd:33-35: Dropping empty section \details
prepare_Rd: estimateMethySeq.Rd:44-46: Dropping empty section \seealso
prepare_Rd: estimateMethySeq.Rd:47-49: Dropping empty section \examples
prepare_Rd: filterBisulfiteVariant.Rd:51-52: Dropping empty section \examples
prepare_Rd: getCoverage.Rd:35-36: Dropping empty section \examples
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
plotMethylationHeatmapByGene 44.352  1.615 158.049
plotHeatmapByGene            22.771  0.801  72.694
MethyLumiM2GenoSet           21.283  0.760  22.370
plotTracksWithDataTrackInfo  20.937  0.692  21.738
heatmapByChromosome          18.788  0.705  19.952
buildAnnotationTracks        16.523  0.781 100.951
createTranscriptTrack        15.405  0.603  16.213
annotateDMRInfo               5.693  0.306   6.001
* 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 WARNINGs, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/methyAnalysis.Rcheck/00check.log’
for details.

methyAnalysis.Rcheck/00install.out:

* installing *source* package ‘methyAnalysis’ ...
** R
** data
** inst
** preparing package for lazy loading
No methods found in "genoset" for requests: toGenomeOrder
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "genoset" for requests: toGenomeOrder
* DONE (methyAnalysis)

methyAnalysis.Rcheck/methyAnalysis-Ex.timings:

nameusersystemelapsed
MethyGenoSet-class0.0790.0030.083
MethyLumiM2GenoSet21.283 0.76022.370
annotateDMRInfo5.6930.3066.001
annotateGRanges3.0180.1563.175
buildAnnotationTracks 16.523 0.781100.951
checkChrName0.0960.0050.102
createTranscriptTrack15.405 0.60316.213
detectDMR.slideWin0.5120.0200.532
exampleMethyGenoSet0.1060.0060.113
export.DMRInfo2.2710.1532.424
export.methyGenoSet0.1440.0090.154
getContinuousRegion0.4310.0230.453
heatmapByChromosome18.788 0.70519.952
identifyCpG0.0010.0010.000
identifySigDMR0.6690.0170.686
plotHeatmapByGene22.771 0.80172.694
plotMethylationHeatmapByGene 44.352 1.615158.049
plotTracksWithDataTrackInfo20.937 0.69221.738
smoothMethyData0.3000.0140.313