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CHECK report for methyAnalysis on tokay2

This page was generated on 2019-10-16 12:26:51 -0400 (Wed, 16 Oct 2019).

Package 977/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
methyAnalysis 1.26.0
Pan Du , Lei Huang , Gang Feng
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/methyAnalysis
Branch: RELEASE_3_9
Last Commit: 8cd0711
Last Changed Date: 2019-05-02 11:53:38 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 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
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: methyAnalysis
Version: 1.26.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:methyAnalysis.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings methyAnalysis_1.26.0.tar.gz
StartedAt: 2019-10-16 05:07:23 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 05:24:32 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 1029.6 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: methyAnalysis.Rcheck
Warnings: 3

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:methyAnalysis.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings methyAnalysis_1.26.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/methyAnalysis.Rcheck'
* using R version 3.6.1 (2019-07-05)
* 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 '1.26.0'
* 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:
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpof7WmX/R.INSTALL2902e761c24/methyAnalysis/man/MethyGenoSet-class.Rd:34: file link 'GenoSet' in package 'genoset' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpof7WmX/R.INSTALL2902e761c24/methyAnalysis/man/MethyGenoSet-class.Rd:36: file link 'GenoSet' in package 'genoset' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpof7WmX/R.INSTALL2902e761c24/methyAnalysis/man/MethyGenoSet-class.Rd:46: file link 'GenoSet' in package 'genoset' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpof7WmX/R.INSTALL2902e761c24/methyAnalysis/man/MethyGenoSet-class.Rd:51: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpof7WmX/R.INSTALL2902e761c24/methyAnalysis/man/MethyGenoSet-class.Rd:57: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpof7WmX/R.INSTALL2902e761c24/methyAnalysis/man/MethyGenoSet-class.Rd:58: file link 'colData' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpof7WmX/R.INSTALL2902e761c24/methyAnalysis/man/MethyGenoSet-class.Rd:86: file link 'GenoSet' in package 'genoset' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpof7WmX/R.INSTALL2902e761c24/methyAnalysis/man/MethyGenoSet-class.Rd:91: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpof7WmX/R.INSTALL2902e761c24/methyAnalysis/man/MethyGenoSet-class.Rd:92: file link 'GenoSet' in package 'genoset' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpof7WmX/R.INSTALL2902e761c24/methyAnalysis/man/MethyGenoSet-class.Rd:92: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpof7WmX/R.INSTALL2902e761c24/methyAnalysis/man/MethyGenoSet-class.Rd:100: file link 'GenoSet' in package 'genoset' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpof7WmX/R.INSTALL2902e761c24/methyAnalysis/man/MethyGenoSet-class.Rd:100: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpof7WmX/R.INSTALL2902e761c24/methyAnalysis/man/asBigMatrix-methods.Rd:15: file link 'GenoSet' in package 'genoset' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.9-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:
  '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
* 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'
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 : : no visible global function
  definition for 'grid.newpage'
plotMethylationHeatmapByGene : : no visible global function
  definition for 'pushViewport'
plotMethylationHeatmapByGene : : no visible global function
  definition for 'viewport'
plotMethylationHeatmapByGene : : no visible global function
  definition for 'grid.layout'
plotMethylationHeatmapByGene : : no visible global function
  definition for 'popViewport'
plotMethylationHeatmapByGene : : no visible global function
  definition for 'grid.rect'
plotMethylationHeatmapByGene : : no visible global function
  definition for 'gpar'
plotMethylationHeatmapByGene : : no visible global function
  definition for 'grid.segments'
plotMethylationHeatmapByGene : : no visible global function
  definition for 'convertX'
plotMethylationHeatmapByGene : : no visible global function
  definition for 'unit'
plotMethylationHeatmapByGene : : no visible global function
  definition for 'grid.text'
plotMethylationHeatmapByGene : : no visible global function
  definition for 'convertY'
plotTracksWithDataTrackInfo : : 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 : : no visible global function
  definition for 'convertX'
plotTracksWithDataTrackInfo : : 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 ... 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                              user system elapsed
plotMethylationHeatmapByGene 35.19   0.71   61.69
buildAnnotationTracks        20.74   0.61   47.86
MethyLumiM2GenoSet           17.78   3.19   39.92
heatmapByChromosome          20.59   0.17   20.98
plotTracksWithDataTrackInfo  17.22   0.29   17.95
plotHeatmapByGene            17.02   0.09   30.86
createTranscriptTrack        11.91   0.11   12.02
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                              user system elapsed
plotMethylationHeatmapByGene 34.26   0.31   62.11
MethyLumiM2GenoSet           22.54   0.41   22.94
heatmapByChromosome          17.75   0.09   18.06
buildAnnotationTracks        15.53   0.44   43.66
plotHeatmapByGene            15.71   0.08   29.60
plotTracksWithDataTrackInfo  14.11   0.21   14.54
createTranscriptTrack        13.35   0.02   13.36
annotateDMRInfo               4.94   0.20    5.14
* 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
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/methyAnalysis.Rcheck/00check.log'
for details.

Installation output

methyAnalysis.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/methyAnalysis_1.26.0.tar.gz && rm -rf methyAnalysis.buildbin-libdir && mkdir methyAnalysis.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=methyAnalysis.buildbin-libdir methyAnalysis_1.26.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL methyAnalysis_1.26.0.zip && rm methyAnalysis_1.26.0.tar.gz methyAnalysis_1.26.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  958k  100  958k    0     0  14.0M      0 --:--:-- --:--:-- --:--:-- 15.8M

install for i386

* installing *source* package 'methyAnalysis' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
No methods found in package 'genoset' for request: 'toGenomeOrder' when loading 'methyAnalysis'
** help
*** installing help indices
  converting help for package 'methyAnalysis'
    finding HTML links ... done
    MethyGenoSet-class                      html  
    finding level-2 HTML links ... done

Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpof7WmX/R.INSTALL2902e761c24/methyAnalysis/man/MethyGenoSet-class.Rd:34: file link 'GenoSet' in package 'genoset' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpof7WmX/R.INSTALL2902e761c24/methyAnalysis/man/MethyGenoSet-class.Rd:36: file link 'GenoSet' in package 'genoset' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpof7WmX/R.INSTALL2902e761c24/methyAnalysis/man/MethyGenoSet-class.Rd:46: file link 'GenoSet' in package 'genoset' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpof7WmX/R.INSTALL2902e761c24/methyAnalysis/man/MethyGenoSet-class.Rd:51: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpof7WmX/R.INSTALL2902e761c24/methyAnalysis/man/MethyGenoSet-class.Rd:57: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpof7WmX/R.INSTALL2902e761c24/methyAnalysis/man/MethyGenoSet-class.Rd:58: file link 'colData' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpof7WmX/R.INSTALL2902e761c24/methyAnalysis/man/MethyGenoSet-class.Rd:86: file link 'GenoSet' in package 'genoset' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpof7WmX/R.INSTALL2902e761c24/methyAnalysis/man/MethyGenoSet-class.Rd:91: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpof7WmX/R.INSTALL2902e761c24/methyAnalysis/man/MethyGenoSet-class.Rd:92: file link 'GenoSet' in package 'genoset' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpof7WmX/R.INSTALL2902e761c24/methyAnalysis/man/MethyGenoSet-class.Rd:92: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpof7WmX/R.INSTALL2902e761c24/methyAnalysis/man/MethyGenoSet-class.Rd:100: file link 'GenoSet' in package 'genoset' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpof7WmX/R.INSTALL2902e761c24/methyAnalysis/man/MethyGenoSet-class.Rd:100: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
    MethyLumiM2GenoSet                      html  
    annotateDMRInfo                         html  
    annotateGRanges                         html  
    asBigMatrix-methods                     html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpof7WmX/R.INSTALL2902e761c24/methyAnalysis/man/asBigMatrix-methods.Rd:15: file link 'GenoSet' in package 'genoset' does not exist and so has been treated as a topic
    buildAnnotationTracks                   html  
    checkChrName                            html  
    createTranscriptTrack                   html  
    detectDMR.slideWin                      html  
    estimateCMR.methylation                 html  
    estimateMethySeq                        html  
    exampleMethyGenoSet                     html  
    export.DMRInfo                          html  
    export.methyGenoSet                     html  
    filterBisulfiteVariant                  html  
    getContinuousRegion                     html  
    getCoverage                             html  
    heatmapByChromosome                     html  
    identifyCpG                             html  
    identifySigDMR                          html  
    plotHeatmapByGene                       html  
    plotMethylationHeatmapByGene            html  
    plotTracksWithDataTrackInfo             html  
    smoothMethyData                         html  
    updateMethyGenoSet                      html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
No methods found in package 'genoset' for request: 'toGenomeOrder' when loading 'methyAnalysis'
** testing if installed package can be loaded from final location
No methods found in package 'genoset' for request: 'toGenomeOrder' when loading 'methyAnalysis'
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'methyAnalysis' ...
** testing if installed package can be loaded
No methods found in package 'genoset' for request: 'toGenomeOrder' when loading 'methyAnalysis'
* MD5 sums
packaged installation of 'methyAnalysis' as methyAnalysis_1.26.0.zip
* DONE (methyAnalysis)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'methyAnalysis' successfully unpacked and MD5 sums checked

Tests output

Example timings

methyAnalysis.Rcheck/examples_i386/methyAnalysis-Ex.timings

nameusersystemelapsed
MethyGenoSet-class0.180.020.19
MethyLumiM2GenoSet17.78 3.1939.92
annotateDMRInfo3.731.174.91
annotateGRanges2.250.162.40
buildAnnotationTracks20.74 0.6147.86
checkChrName0.120.010.14
createTranscriptTrack11.91 0.1112.02
detectDMR.slideWin0.360.000.36
exampleMethyGenoSet0.120.020.14
export.DMRInfo2.520.092.65
export.methyGenoSet0.450.020.47
getContinuousRegion0.550.010.57
heatmapByChromosome20.59 0.1720.98
identifyCpG000
identifySigDMR0.450.020.47
plotHeatmapByGene17.02 0.0930.86
plotMethylationHeatmapByGene35.19 0.7161.69
plotTracksWithDataTrackInfo17.22 0.2917.95
smoothMethyData0.250.020.27

methyAnalysis.Rcheck/examples_x64/methyAnalysis-Ex.timings

nameusersystemelapsed
MethyGenoSet-class0.140.020.15
MethyLumiM2GenoSet22.54 0.4122.94
annotateDMRInfo4.940.205.14
annotateGRanges1.550.171.72
buildAnnotationTracks15.53 0.4443.66
checkChrName0.120.030.15
createTranscriptTrack13.35 0.0213.36
detectDMR.slideWin0.500.030.53
exampleMethyGenoSet0.140.010.16
export.DMRInfo2.640.023.91
export.methyGenoSet0.360.000.36
getContinuousRegion0.550.000.55
heatmapByChromosome17.75 0.0918.06
identifyCpG000
identifySigDMR0.480.000.48
plotHeatmapByGene15.71 0.0829.60
plotMethylationHeatmapByGene34.26 0.3162.11
plotTracksWithDataTrackInfo14.11 0.2114.54
smoothMethyData0.310.010.33