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BioC 3.5: CHECK report for methyAnalysis on veracruz2

This page was generated on 2017-08-16 13:30:30 -0400 (Wed, 16 Aug 2017).

Package 802/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
methyAnalysis 1.18.0
Pan Du , Lei Huang , Gang Feng
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/methyAnalysis
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 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
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: methyAnalysis
Version: 1.18.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings methyAnalysis_1.18.0.tar.gz
StartedAt: 2017-08-16 05:12:38 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 05:23:51 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 673.3 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_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/methyAnalysis.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.18.0’
* 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 39.703  1.220  83.799
buildAnnotationTracks        25.218  1.049  72.144
plotHeatmapByGene            24.821  0.661  47.787
MethyLumiM2GenoSet           22.332  0.677  24.102
heatmapByChromosome          20.788  0.536  22.225
createTranscriptTrack        17.970  0.524  19.012
plotTracksWithDataTrackInfo  16.435  0.464  17.676
annotateDMRInfo               5.480  0.337   5.983
* 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-class0.0900.0070.097
MethyLumiM2GenoSet22.332 0.67724.102
annotateDMRInfo5.4800.3375.983
annotateGRanges3.7160.1063.935
buildAnnotationTracks25.218 1.04972.144
checkChrName0.0840.0050.091
createTranscriptTrack17.970 0.52419.012
detectDMR.slideWin0.4690.0110.490
exampleMethyGenoSet0.0900.0060.100
export.DMRInfo2.4900.1422.709
export.methyGenoSet0.1650.0090.177
getContinuousRegion0.5090.0100.534
heatmapByChromosome20.788 0.53622.225
identifyCpG0.0010.0000.001
identifySigDMR0.6010.0120.624
plotHeatmapByGene24.821 0.66147.787
plotMethylationHeatmapByGene39.703 1.22083.799
plotTracksWithDataTrackInfo16.435 0.46417.676
smoothMethyData0.3350.0130.353