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BioC 3.3: CHECK report for methyAnalysis on moscato2

This page was generated on 2016-10-13 12:50:51 -0700 (Thu, 13 Oct 2016).

Package 701/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
methyAnalysis 1.14.0
Pan Du
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/methyAnalysis
Last Changed Rev: 117079 / Revision: 122332
Last Changed Date: 2016-05-03 14:20:18 -0700 (Tue, 03 May 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  ERROR 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  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 UNNEEDED, same version exists in internal repository

Summary

Package: methyAnalysis
Version: 1.14.0
Command: rm -rf methyAnalysis.buildbin-libdir methyAnalysis.Rcheck && mkdir methyAnalysis.buildbin-libdir methyAnalysis.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=methyAnalysis.buildbin-libdir methyAnalysis_1.14.0.tar.gz >methyAnalysis.Rcheck\00install.out 2>&1 && cp methyAnalysis.Rcheck\00install.out methyAnalysis-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=methyAnalysis.buildbin-libdir --install="check:methyAnalysis-install.out" --force-multiarch --no-vignettes --timings methyAnalysis_1.14.0.tar.gz
StartedAt: 2016-10-13 06:07:37 -0700 (Thu, 13 Oct 2016)
EndedAt: 2016-10-13 06:31:05 -0700 (Thu, 13 Oct 2016)
EllapsedTime: 1408.1 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: methyAnalysis.Rcheck
Warnings: 3

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf methyAnalysis.buildbin-libdir methyAnalysis.Rcheck && mkdir methyAnalysis.buildbin-libdir methyAnalysis.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=methyAnalysis.buildbin-libdir methyAnalysis_1.14.0.tar.gz >methyAnalysis.Rcheck\00install.out 2>&1 && cp methyAnalysis.Rcheck\00install.out methyAnalysis-install.out  && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=methyAnalysis.buildbin-libdir --install="check:methyAnalysis-install.out" --force-multiarch --no-vignettes --timings methyAnalysis_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.3-bioc/meat/methyAnalysis.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'methyAnalysis/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'methyAnalysis' version '1.14.0'
* 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 whether package 'methyAnalysis' can be installed ... 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 'E:/biocbld/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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                              user system elapsed
plotMethylationHeatmapByGene 58.05   0.52   97.86
buildAnnotationTracks        30.93   1.06  155.28
plotHeatmapByGene            26.22   0.25   44.82
plotTracksWithDataTrackInfo  22.63   0.26   22.94
MethyLumiM2GenoSet           22.22   0.30   48.69
heatmapByChromosome          21.78   0.14   22.26
createTranscriptTrack        18.77   0.07   18.87
annotateDMRInfo               6.01   0.14   13.78
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                              user system elapsed
plotMethylationHeatmapByGene 57.83   1.01  107.92
buildAnnotationTracks        31.83   1.67  103.64
plotHeatmapByGene            28.18   0.43   52.46
MethyLumiM2GenoSet           23.73   0.39   24.14
heatmapByChromosome          23.74   0.29   24.09
plotTracksWithDataTrackInfo  21.72   0.34   22.28
createTranscriptTrack        21.24   0.05   21.30
annotateDMRInfo               5.87   0.15    6.66
* 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
  'E:/biocbld/bbs-3.3-bioc/meat/methyAnalysis.Rcheck/00check.log'
for details.

methyAnalysis.Rcheck/00install.out:


install for i386

* 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

install for x64

* installing *source* package 'methyAnalysis' ...
** 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
* MD5 sums
packaged installation of 'methyAnalysis' as methyAnalysis_1.14.0.zip
* DONE (methyAnalysis)

methyAnalysis.Rcheck/examples_i386/methyAnalysis-Ex.timings:

nameusersystemelapsed
MethyGenoSet-class0.120.000.12
MethyLumiM2GenoSet22.22 0.3048.69
annotateDMRInfo 6.01 0.1413.78
annotateGRanges3.090.113.20
buildAnnotationTracks 30.93 1.06155.28
checkChrName0.110.020.13
createTranscriptTrack18.77 0.0718.87
detectDMR.slideWin0.570.020.59
exampleMethyGenoSet0.130.000.13
export.DMRInfo3.010.023.60
export.methyGenoSet0.370.000.38
getContinuousRegion0.670.000.67
heatmapByChromosome21.78 0.1422.26
identifyCpG000
identifySigDMR0.750.000.75
plotHeatmapByGene26.22 0.2544.82
plotMethylationHeatmapByGene58.05 0.5297.86
plotTracksWithDataTrackInfo22.63 0.2622.94
smoothMethyData0.450.000.45

methyAnalysis.Rcheck/examples_x64/methyAnalysis-Ex.timings:

nameusersystemelapsed
MethyGenoSet-class0.120.000.12
MethyLumiM2GenoSet23.73 0.3924.14
annotateDMRInfo5.870.156.66
annotateGRanges3.910.114.03
buildAnnotationTracks 31.83 1.67103.64
checkChrName0.140.020.15
createTranscriptTrack21.24 0.0521.30
detectDMR.slideWin0.600.010.61
exampleMethyGenoSet0.180.000.18
export.DMRInfo3.650.054.50
export.methyGenoSet0.280.000.34
getContinuousRegion0.610.000.61
heatmapByChromosome23.74 0.2924.09
identifyCpG000
identifySigDMR1.280.001.28
plotHeatmapByGene28.18 0.4352.46
plotMethylationHeatmapByGene 57.83 1.01107.92
plotTracksWithDataTrackInfo21.72 0.3422.28
smoothMethyData0.450.020.46