methyAnalysis 1.8.0
Pan Du
| Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/methyAnalysis | | Last Changed Rev: 95439 / Revision: 102249 | | Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | OK | [ WARNINGS ] | |
| moscato1 | Windows Server 2008 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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### /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings methyAnalysis_1.8.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/methyAnalysis.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-linux-gnu (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 ‘1.8.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
‘grid’ ‘BiocGenerics’ ‘S4Vectors’ ‘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 ... [45s/48s] 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
* 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
.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
‘assayDataElementNames’
MethyLumiM2GenoSet: no visible global function definition for
‘assayDataElement’
MethyLumiM2GenoSet: no visible global function definition for ‘fData<-’
annotateGRanges: no visible global function definition for ‘resize’
annotateGRanges: no visible global function definition for ‘flank’
annotateGRanges: no visible global function definition for ‘nearest’
annotateGRanges: no visible global function definition for
‘findOverlaps’
checkChrName: no visible global function definition for ‘ranges<-’
estimateCMR.methylation: no visible global function definition for
‘findOverlaps’
estimateCMR.methylation: no visible global function definition for
‘fData’
export.methyGenoSet: no visible global function definition for
‘assayDataElement’
export.methyGenoSet: no visible global function definition for
‘assayDataElementNames’
getContinuousRegion: no visible global function definition for ‘reduce’
getMethyProbeLocation: no visible global function definition for
‘features’
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’
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: 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’
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
* 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 ... 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 ... [188s/250s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
MethyLumiM2GenoSet 33.510 0.256 34.702
plotMethylationHeatmapByGene 30.894 0.260 53.891
plotHeatmapByGene 15.801 0.100 26.360
buildAnnotationTracks 13.869 0.216 40.329
annotateDMRInfo 13.801 0.160 14.370
export.DMRInfo 13.109 0.032 13.440
heatmapByChromosome 11.960 0.088 12.468
plotTracksWithDataTrackInfo 11.077 0.088 11.327
createTranscriptTrack 9.585 0.120 9.890
annotateGRanges 8.160 0.032 8.212
* 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
WARNING: There were 2 warnings.
NOTE: There were 5 notes.
See
‘/home/biocbuild/bbs-3.0-bioc/meat/methyAnalysis.Rcheck/00check.log’
for details.