methyAnalysis 1.12.0
Pan Du
| Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/methyAnalysis | | Last Changed Rev: 109589 / Revision: 109947 | | Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015) |
| linux1.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |  |
| windows1.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | [ WARNINGS ] | OK | |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | WARNINGS | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | WARNINGS | OK | |
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### Running command:
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### rm -rf methyAnalysis.buildbin-libdir methyAnalysis.Rcheck && mkdir methyAnalysis.buildbin-libdir methyAnalysis.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=methyAnalysis.buildbin-libdir methyAnalysis_1.12.0.tar.gz >methyAnalysis.Rcheck\00install.out 2>&1 && cp methyAnalysis.Rcheck\00install.out methyAnalysis-install.out && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=methyAnalysis.buildbin-libdir --install="check:methyAnalysis-install.out" --force-multiarch --no-vignettes --timings methyAnalysis_1.12.0.tar.gz
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* using log directory 'C:/biocbld/bbs-3.2-bioc/meat/methyAnalysis.Rcheck'
* using R version 3.2.2 Patched (2015-08-16 r69094)
* 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 '1.12.0'
* 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 ... 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:
'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.
Unexported objects imported by ':::' calls:
'Gviz:::.parMappings' 'Gviz:::.setupTextSize' 'Gviz:::.z2icol'
'Gviz:::setStacks' 'genoset:::initGenoSet'
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
identifyCpG: warning in GRanges(seqname = rep(seqname, mLen_cg), ranges
= IRanges(start = start(cg_matches), end = end(cg_matches)), strand =
rep("+", mLen_cg), pattern = rep(pattern, mLen_cg)): partial argument
match of 'seqname' to 'seqnames'
.estimateTrackHeight: no visible global function definition for
'convertY'
.estimateTrackHeight: no visible global function definition for 'unit'
.identifySigProbe: no visible global function definition for 'rowMax'
MethyGenoSet: no visible global function definition for
'assayDataElementNames'
MethyLumiM2GenoSet: no visible global function definition for 'fData'
MethyLumiM2GenoSet: no visible global function definition for
'metadata'
MethyLumiM2GenoSet: no visible global function definition for
'assayDataElementNames'
MethyLumiM2GenoSet: no visible global function definition for
'assayDataElement'
MethyLumiM2GenoSet: no visible global function definition for 'fData<-'
annotateDMRInfo: no visible global function definition for
'elementLengths'
annotateDMRInfo: no visible global function definition for 'values'
annotateGRanges: no visible global function definition for
'elementLengths'
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
'fData'
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'
export.methyGenoSet: no visible global function definition for
'assayDataElement'
export.methyGenoSet: no visible global function definition for
'assayDataElementNames'
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
'assayDataElement<-'
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'
asBigMatrix,GenoSet : .local: no visible global function definition for
'assayDataElement'
asBigMatrix,GenoSet : .local: no visible global function definition for
'assayDataElementNames'
asBigMatrix,GenoSet : .local: no visible global function definition for
'assayDataElement<-'
asBigMatrix,GenoSet : .local: no visible global function definition for
'fData<-'
asBigMatrix,GenoSet : .local: no visible global function definition for
'fData'
coerce,GenoSet-MethyGenoSet: no visible global function definition for
'assayDataElementNames'
coerce,GenoSet-MethyGenoSet: no visible global function definition for
'assayDataElement'
coerce,GenoSet-MethyGenoSet: no visible global function definition for
'fData<-'
coerce,GenoSet-MethyGenoSet: no visible global function definition for
'fData'
coerce,MethyGenoSet-MethyLumiM: no visible global function definition
for 'fData'
coerce,MethyGenoSet-MethyLumiM: no visible global function definition
for 'phenoData'
coerce,MethyGenoSet-MethyLumiM: no visible global function definition
for 'fData<-'
detection,MethyGenoSet: no visible global function definition for
'assayDataElementNames'
detection,MethyGenoSet: no visible global function definition for
'assayDataElement'
detection<-,MethyGenoSet: no visible global function definition for
'storageMode<-'
detection<-,MethyGenoSet: no visible global function definition for
'assayDataElementReplace'
exprs,MethyGenoSet: no visible global function definition for
'assayDataElementNames'
exprs,MethyGenoSet: no visible global function definition for
'assayDataElement'
exprs<-,MethyGenoSet-ANY: no visible global function definition for
'storageMode<-'
exprs<-,MethyGenoSet-ANY: no visible global function definition for
'assayDataElementReplace'
methylated,MethyGenoSet: no visible global function definition for
'assayDataElementNames'
methylated,MethyGenoSet: no visible global function definition for
'assayDataElement'
methylated<-,MethyGenoSet-ANY: no visible global function definition
for 'storageMode<-'
methylated<-,MethyGenoSet-ANY: no visible global function definition
for 'assayDataElementReplace'
unmethylated,MethyGenoSet: no visible global function definition for
'assayDataElementNames'
unmethylated,MethyGenoSet: no visible global function definition for
'assayDataElement'
unmethylated<-,MethyGenoSet-ANY: no visible global function definition
for 'storageMode<-'
unmethylated<-,MethyGenoSet-ANY: no visible global function definition
for 'assayDataElementReplace'
* 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 ... WARNING
Codoc mismatches from documentation object 'estimateCMR.methylation':
estimateCMR.methylation
Code: function(cmr, methyGenoSet, estimateFun = mean, probeAnnotation
= NULL, selectGeneElement = c("exon1", "promoter"),
mc.cores = min(12, detectCores()))
Docs: function(cmr, methyGenoSet, tx2probe.corList = NULL,
estimateFun = mean, probeAnnotation = NULL,
selectGeneElement = c("exon1", "promoter"), mc.cores =
min(12, detectCores()))
Argument names in docs not in code:
tx2probe.corList
Mismatches in argument names (first 3):
Position: 3 Code: estimateFun Docs: tx2probe.corList
Position: 4 Code: probeAnnotation Docs: estimateFun
Position: 5 Code: selectGeneElement Docs: probeAnnotation
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'estimateCMR.methylation'
'tx2probe.corList'
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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' ... [258s] WARNING
Found the following significant warnings:
Warning: 'pData' is deprecated.
Warning: 'pData' is deprecated.
Warning: 'pData' is deprecated.
Warning: 'pData' is deprecated.
Warning: 'pData' is deprecated.
Warning: 'pData' is deprecated.
Warning: 'pData' is deprecated.
Warning: 'pData' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
user system elapsed
plotMethylationHeatmapByGene 33.17 0.59 69.08
buildAnnotationTracks 19.77 1.33 56.47
plotHeatmapByGene 15.94 0.36 33.47
heatmapByChromosome 14.87 0.28 15.33
plotTracksWithDataTrackInfo 14.55 0.38 15.14
MethyLumiM2GenoSet 13.98 0.50 32.65
createTranscriptTrack 12.00 0.20 12.22
** running examples for arch 'x64' ... [253s] WARNING
Found the following significant warnings:
Warning: 'pData' is deprecated.
Warning: 'pData' is deprecated.
Warning: 'pData' is deprecated.
Warning: 'pData' is deprecated.
Warning: 'pData' is deprecated.
Warning: 'pData' is deprecated.
Warning: 'pData' is deprecated.
Warning: 'pData' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
user system elapsed
plotMethylationHeatmapByGene 36.06 0.53 73.65
buildAnnotationTracks 21.61 1.58 61.00
MethyLumiM2GenoSet 17.96 0.33 18.28
plotHeatmapByGene 16.50 0.14 33.50
plotTracksWithDataTrackInfo 13.83 0.25 14.25
heatmapByChromosome 13.79 0.16 14.30
createTranscriptTrack 11.29 0.17 11.45
* 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: 5 WARNINGs, 5 NOTEs
See
'C:/biocbld/bbs-3.2-bioc/meat/methyAnalysis.Rcheck/00check.log'
for details.