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BioC 3.3: CHECK report for methyAnalysis on morelia

This page was generated on 2016-04-21 13:23:36 -0700 (Thu, 21 Apr 2016).

Package 701/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
methyAnalysis 1.13.3
Pan Du
Snapshot Date: 2016-04-20 17:20:35 -0700 (Wed, 20 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/methyAnalysis
Last Changed Rev: 115835 / Revision: 116626
Last Changed Date: 2016-04-05 16:11:19 -0700 (Tue, 05 Apr 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: methyAnalysis
Version: 1.13.3
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings methyAnalysis_1.13.3.tar.gz
StartedAt: 2016-04-21 04:54:27 -0700 (Thu, 21 Apr 2016)
EndedAt: 2016-04-21 05:03:52 -0700 (Thu, 21 Apr 2016)
EllapsedTime: 565.8 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: methyAnalysis.Rcheck
Warnings: 3

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings methyAnalysis_1.13.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/methyAnalysis.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* 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 ‘1.13.3’
* 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 ... [31s/32s] WARNING
Found the following significant warnings:
  Warning: multiple methods tables found for ‘colMeans’
  Warning: multiple methods tables found for ‘colSums’
  Warning: multiple methods tables found for ‘rowMeans’
  Warning: multiple methods tables found for ‘rowSums’
See ‘/Users/biocbuild/bbs-3.3-bioc/meat/methyAnalysis.Rcheck/00install.out’ for details.
* 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:
  ‘GenomicRanges’ ‘IRanges’ ‘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'
createTranscriptTrack: no visible global function definition for
  'overlapsAny'
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'
estimateMethySeq: no visible global function definition for
  'overlapsAny'
filterBisulfiteVariant: no visible global function definition for
  'slice'
filterBisulfiteVariant: no visible global function definition for
  'overlapsAny'
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
  'overlapsAny'
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'
transcriptDb2GeneRegionTrackByGene: no visible global function
  definition for 'overlapsAny'
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 overlapsAny 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 ... NOTE
Package unavailable to check Rd xrefs: ‘bigmemoryExtras’
* 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 ... [158s/252s] OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
plotMethylationHeatmapByGene 33.999  1.740  72.337
MethyLumiM2GenoSet           18.034  0.653  18.953
plotHeatmapByGene            16.159  0.871  34.992
buildAnnotationTracks        14.569  0.949  53.648
plotTracksWithDataTrackInfo  14.383  0.856  15.331
heatmapByChromosome          14.294  0.845  15.223
createTranscriptTrack        12.590  0.800  13.401
* 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: 3 WARNINGs, 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.3-bioc/meat/methyAnalysis.Rcheck/00check.log’
for details.

methyAnalysis.Rcheck/00install.out:

* installing *source* package ‘methyAnalysis’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning: multiple methods tables found for ‘colMeans’
Warning: multiple methods tables found for ‘colSums’
Warning: multiple methods tables found for ‘rowMeans’
Warning: multiple methods tables found for ‘rowSums’
No methods found in "GenomicRanges" for requests: overlapsAny
No methods found in "genoset" for requests: rowRanges, rowRanges<-, toGenomeOrder
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: multiple methods tables found for ‘colMeans’
Warning: multiple methods tables found for ‘colSums’
Warning: multiple methods tables found for ‘rowMeans’
Warning: multiple methods tables found for ‘rowSums’
No methods found in "GenomicRanges" for requests: overlapsAny
No methods found in "genoset" for requests: rowRanges, rowRanges<-, toGenomeOrder
* DONE (methyAnalysis)

methyAnalysis.Rcheck/methyAnalysis-Ex.timings:

nameusersystemelapsed
MethyGenoSet-class0.1100.0070.118
MethyLumiM2GenoSet18.034 0.65318.953
annotateDMRInfo3.9330.2954.231
annotateGRanges2.0080.2152.225
buildAnnotationTracks14.569 0.94953.648
checkChrName0.0920.0070.098
createTranscriptTrack12.590 0.80013.401
detectDMR.slideWin0.4890.0130.502
exampleMethyGenoSet0.1100.0070.118
export.DMRInfo2.6360.1982.836
export.methyGenoSet0.2050.0120.235
getContinuousRegion0.4680.0120.481
heatmapByChromosome14.294 0.84515.223
identifyCpG0.0010.0010.001
identifySigDMR0.8330.0420.876
plotHeatmapByGene16.159 0.87134.992
plotMethylationHeatmapByGene33.999 1.74072.337
plotTracksWithDataTrackInfo14.383 0.85615.331
smoothMethyData0.3680.0100.379