| Back to the "Multiple platform build/check report" | A B C D E F G H I J K L M N O P Q [R] S T U V W X Y Z |
This page was generated on 2016-04-23 10:14:43 -0700 (Sat, 23 Apr 2016).
| Package 900/1103 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||
| RnBeads 1.2.2 Fabian Mueller
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ WARNINGS ] |  | |||||
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | WARNINGS | OK | | |||||
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | WARNINGS | OK | |
| Package: RnBeads |
| Version: 1.2.2 |
| Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings RnBeads_1.2.2.tar.gz |
| StartedAt: 2016-04-23 04:56:52 -0700 (Sat, 23 Apr 2016) |
| EndedAt: 2016-04-23 05:02:59 -0700 (Sat, 23 Apr 2016) |
| EllapsedTime: 367.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: RnBeads.Rcheck |
| Warnings: 5 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings RnBeads_1.2.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/RnBeads.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RnBeads/DESCRIPTION’ ... OK
* this is package ‘RnBeads’ version ‘1.2.2’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
‘BiocGenerics’ ‘GenomicRanges’ ‘MASS’ ‘RColorBrewer’ ‘cluster’ ‘ff’
‘fields’ ‘ggplot2’ ‘gplots’ ‘gridExtra’ ‘limma’ ‘matrixStats’
‘illuminaio’ ‘methylumi’ ‘plyr’
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 ‘RnBeads’ can be installed ... [29s/29s] WARNING
Found the following significant warnings:
Warning: replacing previous import ‘gridExtra::combine’ by ‘methylumi::combine’ when loading ‘RnBeads’
See ‘/home/biocbuild/bbs-3.2-bioc/meat/RnBeads.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
installed size is 6.3Mb
sub-directories of 1Mb or more:
R 1.2Mb
bin 1.0Mb
doc 3.2Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... WARNING
Subdirectory ‘data’ contains no data sets.
* 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: ‘GLAD’
'library' or 'require' calls not declared from:
‘GLAD’ ‘IlluminaHumanMethylation450kanno.ilmn12.hg19’ ‘scales’
'library' or 'require' calls in package code:
‘Category’ ‘GLAD’ ‘GOstats’ ‘Gviz’
‘IlluminaHumanMethylation450kanno.ilmn12.hg19’
‘IlluminaHumanMethylation450kmanifest’ ‘RefFreeEWAS’ ‘annotate’
‘biomaRt’ ‘doParallel’ ‘foreach’ ‘isva’ ‘minfi’ ‘nlme’ ‘quadprog’
‘scales’ ‘sva’ ‘wateRmelon’
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported objects imported by ':::' calls:
‘Gviz:::.getBMFeatureMap’ ‘doParallel:::.options’
‘grDevices:::.smoothScatterCalcDensity’
‘minfi:::.default.450k.annotation’ ‘minfi:::.extractFromRGSet450k’
‘minfi:::.normalizeFunnorm450k’
See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
‘CONTROL.TARGETS.SAMPLE.INDEPENDENT’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.stopImplicitCluster: no visible global function definition for
‘stopCluster’
MethyLumiSet2RnBeadSet: no visible global function definition for
‘phenoData’
MethyLumiSet2RnBeadSet: no visible global function definition for
‘assayDataElementNames’
MethyLumiSet2RnBeadSet: no visible global function definition for
‘featureNames’
MethyLumiSet2RnBeadSet: no visible global function definition for
‘varLabels’
MethyLumiSet2RnBeadSet: no visible global function definition for
‘featureData’
add.negative.control.boxplot: no visible global function definition for
‘samples’
add.qc.barplots: no visible global function definition for ‘samples’
add.seq.coverage.histograms: no visible global function definition for
‘samples’
add.seq.coverage.plot: no visible global function definition for
‘samples’
add.seq.coverage.violins: no visible global function definition for
‘samples’
add.snp.barplot: no visible global function definition for ‘samples’
add.snp.distances: no visible global function definition for
‘grid.draw’
addReportPlots.diffMeth.bin.region.volcano: no visible binding for
global variable ‘combinedRank’
addReportPlots.diffMeth.bin.site.volcano: no visible binding for global
variable ‘mean.diff’
addReportPlots.diffMeth.bin.site.volcano: no visible binding for global
variable ‘diffmeth.p.val’
addReportPlots.diffMeth.bin.site.volcano: no visible binding for global
variable ‘combinedRank’
addReportPlots.diffMeth.bin.site.volcano: no visible binding for global
variable ‘mean.quot.log2’
addReportPlots.diffMeth.bin.site.volcano: no visible binding for global
variable ‘diffmeth.p.adj.fdr’
append.cpg.stats : cpg.stats: no visible global function definition for
‘DataFrame’
append.cpg.stats: no visible global function definition for ‘%dopar%’
append.cpg.stats: no visible global function definition for ‘foreach’
append.cpg.stats: no visible binding for global variable ‘chrom’
computeDiffTab.default.region: no visible global function definition
for ‘%dopar%’
computeDiffTab.default.region: no visible global function definition
for ‘foreach’
computeDiffTab.default.region: no visible binding for global variable
‘i’
create.densityScatter: no visible binding for global variable
‘..density..’
create.diffMeth.bin.dens.dmp.scatter: no visible binding for global
variable ‘mean.g1’
create.diffMeth.bin.dens.dmp.scatter: no visible binding for global
variable ‘mean.g2’
create.diffMeth.bin.dens.dmp.scatter: no visible binding for global
variable ‘color’
create.diffMeth.bin.dens.dmp.scatter: no visible binding for global
variable ‘plotOrder’
create.diffMeth.bin.dens.dmr.scatter: no visible binding for global
variable ‘mean.mean.g1’
create.diffMeth.bin.dens.dmr.scatter: no visible binding for global
variable ‘mean.mean.g2’
create.diffMeth.bin.dens.dmr.scatter: no visible binding for global
variable ‘color’
create.diffMeth.bin.dens.dmr.scatter: no visible binding for global
variable ‘plotOrder’
create.ucsc.track.hub: no visible global function definition for
‘samples’
data.frame2GRanges: no visible global function definition for
‘seqlevels<-’
data.frame2GRanges: no visible global function definition for
‘genome<-’
estimateProportionsCP: no visible global function definition for ‘lme’
estimateProportionsCP: no visible global function definition for
‘getVarCov’
get.adjustment.variables: no visible global function definition for
‘samples’
get.comparison.info : rm.na.from.adj.tab: no visible global function
definition for ‘samples’
get.components.isva: no visible global function definition for ‘DoISVA’
get.components.sva: no visible global function definition for ‘sva’
get.cpg.stats: no visible global function definition for
‘dinucleotideFrequency’
get.cpg.stats: no visible global function definition for
‘letterFrequency’
get.dataset.matrix: no visible global function definition for ‘samples’
get.diffmeth.tab.col.desc.list.txt: no visible binding for global
variable ‘report’
get.diffmeth.tab.col.desc.list.txt: no visible binding for global
variable ‘refText’
get.diffmeth.tab.col.desc.list.txt: no visible binding for global
variable ‘diffmeth’
getCGCounts : <anonymous>: no visible global function definition for
‘ChrNumeric’
getGLADProfiles: no visible global function definition for ‘samples’
getGLADProfiles : <anonymous>: no visible global function definition
for ‘as.profileCGH’
getGLADProfiles : <anonymous>: no visible global function definition
for ‘daglad’
getMergeList: no visible global function definition for ‘samples’
groupPermutationP.site.parallel: no visible global function definition
for ‘%dopar%’
groupPermutationP.site.parallel: no visible global function definition
for ‘foreach’
inferWBCbyLme: no visible global function definition for ‘lme’
inferWBCbyLme: no visible global function definition for ‘getVarCov’
intensities.by.color: no visible global function definition for
‘samples’
intensities.by.color: no visible binding for global variable
‘IlluminaHumanMethylation450kmanifest’
limmaP: no visible binding for global variable ‘group1’
limmaP: no visible binding for global variable ‘group2’
locus.profile.get.base.tracks: no visible global function definition
for ‘useMart’
locus.profile.get.base.tracks: no visible global function definition
for ‘IdeogramTrack’
locus.profile.get.base.tracks: no visible global function definition
for ‘GenomeAxisTrack’
locus.profile.get.base.tracks: no visible global function definition
for ‘BiomartGeneRegionTrack’
locus.profile.get.base.tracks: no visible global function definition
for ‘UcscTrack’
locus.profile.get.methylation.track.heatmap: no visible global function
definition for ‘DataTrack’
locus.profile.get.methylation.track.smooth: no visible global function
definition for ‘DataTrack’
methylumi.intensities.by.color: no visible global function definition
for ‘featureNames’
methylumi.intensities.by.color: no visible binding for global variable
‘IlluminaHumanMethylation450kmanifest’
methylumi.intensities.by.color: no visible global function definition
for ‘assayDataElement’
parallel.setup: no visible global function definition for
‘registerDoParallel’
parallel.setup: no visible global function definition for
‘getDoParWorkers’
plot.heatmap.pc.correlations: no visible global function definition for
‘melt’
plot.heatmap.pc.correlations: no visible global function definition for
‘grid.draw’
plot.heatmap.pc.pvalues: no visible global function definition for
‘melt’
plot.heatmap.pc.pvalues: no visible global function definition for
‘grid.draw’
plot.heatmap.rand: no visible global function definition for ‘melt’
plot.heatmap.symm: no visible global function definition for ‘melt’
plot.heatmap.symm: no visible global function definition for
‘grid.draw’
plotCGHProfile: no visible global function definition for ‘ChrNumeric’
projectWBC: no visible global function definition for ‘solve.QP’
read.GS.report: no visible global function definition for
‘featureNames’
read.idat.files: no visible binding for global variable ‘barcode’
refFreeEWASP: no visible global function definition for ‘EstDimRMT’
refFreeEWASP: no visible global function definition for
‘RefFreeEwasModel’
refFreeEWASP: no visible global function definition for
‘PairsBootRefFreeEwasModel’
refFreeEWASP: no visible global function definition for
‘BootRefFreeEwasModel’
rnb.RnBSet.to.GRangesList: no visible global function definition for
‘samples’
rnb.RnBSet.to.bed: no visible global function definition for ‘samples’
rnb.RnBSet.to.bedGraph: no visible global function definition for
‘samples’
rnb.execute.dreduction: no visible global function definition for
‘samples’
rnb.execute.filter.summary.internal: no visible global function
definition for ‘samples’
rnb.execute.normalization: no visible global function definition for
‘samples’
rnb.execute.normalization: no visible global function definition for
‘phenoData’
rnb.execute.normalization: no visible global function definition for
‘phenoData<-’
rnb.execute.normalization: no visible global function definition for
‘RGChannelSet’
rnb.execute.normalization: no visible global function definition for
‘preprocessSWAN’
rnb.execute.normalization: no visible global function definition for
‘getMeth’
rnb.execute.normalization: no visible global function definition for
‘getUnmeth’
rnb.execute.normalization: no visible global function definition for
‘featureNames’
rnb.execute.normalization: no visible global function definition for
‘%dopar%’
rnb.execute.normalization: no visible global function definition for
‘foreach’
rnb.execute.normalization: no visible global function definition for
‘mapToGenome’
rnb.execute.normalization: no visible global function definition for
‘addSex’
rnb.execute.normalization: no visible global function definition for
‘getSex’
rnb.execute.normalization: no visible global function definition for
‘getCN’
rnb.execute.quality: no visible global function definition for
‘samples’
rnb.execute.quality : <anonymous>: no visible global function
definition for ‘samples’
rnb.export.to.ewasher: no visible global function definition for
‘samples’
rnb.get.reliability.counts.per.sample: no visible global function
definition for ‘samples’
rnb.plot.beta.density.group: no visible binding for global variable
‘group’
rnb.plot.biseq.coverage: no visible global function definition for
‘samples’
rnb.plot.biseq.coverage.hist: no visible global function definition for
‘samples’
rnb.plot.control.barplot: no visible global function definition for
‘samples’
rnb.plot.control.barplot: no visible binding for global variable
‘Target’
rnb.plot.control.barplot: no visible binding for global variable
‘Index’
rnb.plot.control.barplot: no visible binding for global variable ‘ID’
rnb.plot.control.barplot: no visible binding for global variable
‘Address’
rnb.plot.control.barplot: no visible binding for global variable
‘Intensity’
rnb.plot.control.barplot: no visible global function definition for
‘grid.draw’
rnb.plot.control.boxplot: no visible binding for global variable
‘Probe’
rnb.plot.control.boxplot: no visible binding for global variable
‘Intensity’
rnb.plot.control.boxplot: no visible global function definition for
‘grid.draw’
rnb.plot.ct.heatmap: no visible binding for global variable ‘x’
rnb.plot.ct.heatmap: no visible binding for global variable ‘y’
rnb.plot.ct.heatmap: no visible binding for global variable ‘v’
rnb.plot.ct.heatmap: no visible global function definition for
‘grid.draw’
rnb.plot.locus.profile: no visible global function definition for
‘plotTracks’
rnb.plot.marker.fstat: no visible binding for global variable ‘x’
rnb.plot.marker.fstat: no visible binding for global variable ‘y’
rnb.plot.marker.fstat: no visible global function definition for
‘muted’
rnb.plot.negative.boxplot: no visible global function definition for
‘samples’
rnb.plot.negative.boxplot: no visible binding for global variable
‘numeric.names’
rnb.plot.negative.boxplot: no visible binding for global variable
‘type’
rnb.plot.negative.boxplot: no visible binding for global variable
‘types’
rnb.plot.negative.boxplot: no visible binding for global variable
‘Sample’
rnb.plot.negative.boxplot: no visible binding for global variable
‘Intensity’
rnb.plot.negative.boxplot: no visible global function definition for
‘grid.draw’
rnb.plot.num.sites.covg: no visible global function definition for
‘samples’
rnb.plot.num.sites.covg : <anonymous>: no visible global function
definition for ‘samples’
rnb.plot.num.sites.covg: no visible binding for global variable
‘numSites’
rnb.plot.num.sites.covg: no visible binding for global variable
‘covgMedian’
rnb.plot.num.sites.covg: no visible binding for global variable
‘covgPercLow’
rnb.plot.num.sites.covg: no visible binding for global variable
‘covgPercUp’
rnb.plot.num.sites.covg: no visible binding for global variable ‘comma’
rnb.plot.region.profile.density: no visible binding for global variable
‘relative.coord’
rnb.plot.region.profile.density: no visible binding for global variable
‘..density..’
rnb.plot.region.profiles : <anonymous>: no visible global function
definition for ‘samples’
rnb.plot.region.profiles: no visible binding for global variable
‘relative.coord’
rnb.plot.region.profiles: no visible binding for global variable
‘group’
rnb.plot.region.site.density: no visible binding for global variable
‘relative.coord’
rnb.plot.sentrix.distributions: no visible global function definition
for ‘samples’
rnb.plot.sentrix.distributions: no visible binding for global variable
‘Slide’
rnb.plot.snp.barplot: no visible global function definition for
‘samples’
rnb.plot.snp.boxplot: no visible global function definition for
‘samples’
rnb.plot.snp.boxplot: no visible binding for global variable ‘SNP’
rnb.plot.snp.boxplot: no visible binding for global variable
‘Beta.values’
rnb.plot.snp.heatmap: no visible global function definition for
‘samples’
rnb.run.preprocessing : logger.completed.filtering: no visible global
function definition for ‘samples’
rnb.sample.summary.table: no visible global function definition for
‘samples’
rnb.section.clustering : <anonymous> : <anonymous>: no visible global
function definition for ‘samples’
rnb.section.clustering: no visible global function definition for
‘samples’
rnb.section.diffMeth.region: no visible global function definition for
‘%dopar%’
rnb.section.diffMeth.region: no visible global function definition for
‘foreach’
rnb.section.diffMeth.region: no visible binding for global variable ‘k’
rnb.section.diffMeth.region : do.enrichment.table: no visible global
function definition for ‘sigCategories’
rnb.section.diffMeth.site: no visible global function definition for
‘%dopar%’
rnb.section.diffMeth.site: no visible global function definition for
‘foreach’
rnb.section.gender.prediction: no visible global function definition
for ‘muted’
rnb.section.import: no visible global function definition for ‘samples’
rnb.section.import: no visible global function definition for
‘phenoData’
rnb.section.locus.profiles: no visible global function definition for
‘samples’
rnb.section.locus.profiles : do.plots: no visible global function
definition for ‘plotTracks’
rnb.section.locus.profiles: no visible global function definition for
‘%dopar%’
rnb.section.locus.profiles: no visible global function definition for
‘foreach’
rnb.section.normalization: no visible global function definition for
‘samples’
rnb.section.region.description: no visible binding for global variable
‘size’
rnb.section.region.description: no visible binding for global variable
‘n.sites’
rnb.section.region.profiles: no visible global function definition for
‘samples’
rnb.section.region.subsegmentation : get.summary.df.from.list: no
visible global function definition for ‘melt’
rnb.section.region.subsegmentation: no visible binding for global
variable ‘region.size’
rnb.section.region.subsegmentation: no visible binding for global
variable ‘is.subsegmentation’
rnb.section.region.subsegmentation: no visible binding for global
variable ‘num.sites’
rnb.step.betadistribution.internal: no visible global function
definition for ‘%dopar%’
rnb.step.betadistribution.internal: no visible global function
definition for ‘foreach’
rnb.step.betadistribution.internal: no visible binding for global
variable ‘params’
rnb.step.cell.types: no visible global function definition for
‘samples’
rnb.step.clustering.internal: no visible global function definition for
‘samples’
rnb.step.cnv: no visible binding for global variable ‘intensities’
rnb.step.dreduction: no visible global function definition for
‘%dopar%’
rnb.step.dreduction: no visible global function definition for
‘foreach’
rnb.step.dreduction: no visible binding for global variable ‘target’
rnb.step.filter.summary.internal: no visible global function definition
for ‘percent_format’
rnb.step.import: no visible global function definition for ‘samples’
rnb.step.import: no visible global function definition for ‘phenoData’
rnb.step.normalization: no visible global function definition for
‘phenoData’
robustHyperGResultSummary: no visible global function definition for
‘sigCategories’
robustHyperGResultSummary: no visible global function definition for
‘pvalues’
robustHyperGResultSummary: no visible global function definition for
‘oddsRatios’
robustHyperGResultSummary: no visible global function definition for
‘expectedCounts’
robustHyperGResultSummary: no visible global function definition for
‘geneCounts’
robustHyperGResultSummary: no visible global function definition for
‘universeCounts’
robustHyperGResultSummary: no visible binding for global variable
‘Term’
set.covariates.ct: no visible global function definition for ‘samples’
symmetric.melt: no visible global function definition for ‘melt’
addDiffMethTable,RnBDiffMeth : .local: no visible binding for global
variable ‘reg.type’
coerce,RnBeadRawSet-MethyLumiSet: no visible global function definition
for ‘featureData<-’
coerce,RnBeadRawSet-MethyLumiSet: no visible global function definition
for ‘featureNames<-’
combine,RnBSet-RnBSet : .local: no visible global function definition
for ‘samples’
remove.samples,RnBSet: no visible global function definition for
‘samples’
remove.samples,RnBeadRawSet: no visible global function definition for
‘samples’
remove.samples,RnBeadSet: no visible global function definition for
‘samples’
sampleCovgApply,RnBSet : .local: no visible global function definition
for ‘samples’
sampleMethApply,RnBSet : .local: no visible global function definition
for ‘samples’
summarize.regions,RnBSet : .local: no visible global function
definition for ‘samples’
summarize.regions,RnBSet : .local: multiple local function definitions
for ‘aggr.f’ with different formal arguments
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
generic '[' and siglist 'BigFfMat,ANY,ANY,ANY'
generic '[<-' and siglist 'BigFfMat,ANY,ANY,ANY'
generic 'dim' and siglist 'BigFfMat'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'read.single.bed'
‘chr.col’ ‘start.col’ ‘end.col’ ‘strand.col’ ‘c.col’ ‘t.col’
‘is.epp.style’ ‘coord.shift’ ‘ffread’ ‘context’ ‘...’
Undocumented arguments in documentation object 'sampleCovgApply,RnBSet-method'
‘object’ ‘type’ ‘...’
Undocumented arguments in documentation object 'sampleMethApply,RnBSet-method'
‘object’ ‘type’ ‘...’
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [13s/13s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’ [64s/64s]
[64s/64s] OK
* 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, 3 NOTEs
See
‘/home/biocbuild/bbs-3.2-bioc/meat/RnBeads.Rcheck/00check.log’
for details.
RnBeads.Rcheck/00install.out:
* installing *source* package ‘RnBeads’ ... ** R ** inst ** preparing package for lazy loading Warning: replacing previous import ‘gridExtra::combine’ by ‘methylumi::combine’ when loading ‘RnBeads’ Creating a generic function for ‘vmode’ from package ‘ff’ in package ‘RnBeads’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded Warning: replacing previous import ‘gridExtra::combine’ by ‘methylumi::combine’ when loading ‘RnBeads’ * DONE (RnBeads)
RnBeads.Rcheck/RnBeads-Ex.timings:
| name | user | system | elapsed | |
| M-methods | 0.001 | 0.000 | 0.001 | |
| U-methods | 0.001 | 0.000 | 0.000 | |
| addDiffMethTable-RnBDiffMeth-methods | 0 | 0 | 0 | |
| addPheno-RnBSet-methods | 0.000 | 0.000 | 0.001 | |
| addRegionSubsegments | 0.001 | 0.000 | 0.000 | |
| annotation-methods | 0 | 0 | 0 | |
| assembly-methods | 0 | 0 | 0 | |
| combine-methods | 0.000 | 0.000 | 0.001 | |
| combineTestPvalsMeth | 0 | 0 | 0 | |
| computeDiffTab.region | 0 | 0 | 0 | |
| computeDiffTab.site | 0.000 | 0.000 | 0.001 | |
| covg-methods | 0.001 | 0.000 | 0.000 | |
| create.densityScatter | 0 | 0 | 0 | |
| create.scatter.dens.points | 0.000 | 0.000 | 0.001 | |
| createReport | 0.001 | 0.000 | 0.001 | |
| createReportPlot | 0 | 0 | 0 | |
| dpval-methods | 0 | 0 | 0 | |
| exportDMRs2regionFile | 0.000 | 0.000 | 0.001 | |
| get.adjustment.variables | 0 | 0 | 0 | |
| get.comparison.grouplabels-RnBDiffMeth-methods | 0 | 0 | 0 | |
| get.comparison.groupsizes-RnBDiffMeth-methods | 0.000 | 0.000 | 0.001 | |
| get.comparison.info | 0.001 | 0.000 | 0.001 | |
| get.comparisons-RnBDiffMeth-methods | 0 | 0 | 0 | |
| get.covariates.sva | 0 | 0 | 0 | |
| get.covg.thres-RnBDiffMeth-methods | 0.000 | 0.000 | 0.001 | |
| get.files | 0.001 | 0.000 | 0.000 | |
| get.region.types-RnBDiffMeth-methods | 0 | 0 | 0 | |
| get.site.test.method-RnBDiffMeth-methods | 0 | 0 | 0 | |
| get.table-RnBDiffMeth-methods | 0.000 | 0.000 | 0.001 | |
| getSubCmdTokens-ClusterArchitectureSGE-methods | 0.001 | 0.000 | 0.000 | |
| has.covariates.sva | 0 | 0 | 0 | |
| hasCovg-methods | 0.000 | 0.000 | 0.001 | |
| includes.sites-RnBDiffMeth-methods | 0.001 | 0.000 | 0.001 | |
| is.valid-RnBDiffMeth-methods | 0 | 0 | 0 | |
| join.diffMeth-methods | 0 | 0 | 0 | |
| limmaP | 0.000 | 0.000 | 0.001 | |
| logger.argument | 0.001 | 0.000 | 0.000 | |
| logger.getfiles | 0 | 0 | 0 | |
| logger.isinitialized | 0.000 | 0.000 | 0.001 | |
| logger.validate.file | 0.001 | 0.000 | 0.001 | |
| loggerManagement | 0.001 | 0.000 | 0.000 | |
| loggerMessages | 0 | 0 | 0 | |
| mergeSamples-methods | 0.000 | 0.000 | 0.001 | |
| meth-methods | 0.001 | 0.000 | 0.000 | |
| mval-methods | 0 | 0 | 0 | |
| nsites-methods | 0 | 0 | 0 | |
| parallel.getNumWorkers | 0.000 | 0.000 | 0.001 | |
| parallel.isEnabled | 0.001 | 0.000 | 0.000 | |
| parallel.setup | 0 | 0 | 0 | |
| parallel.teardown | 0.000 | 0.000 | 0.001 | |
| performEnrichment.diffMeth | 0.000 | 0.000 | 0.001 | |
| performGOenrichment.diffMeth.entrez | 0 | 0 | 0 | |
| pheno-methods | 0 | 0 | 0 | |
| qc-methods | 0.000 | 0.000 | 0.001 | |
| read.sample.annotation | 0.000 | 0.004 | 0.000 | |
| regionMapping-methods | 0 | 0 | 0 | |
| regions-methods | 0.000 | 0.000 | 0.001 | |
| reload-RnBDiffMeth-methods | 0.001 | 0.000 | 0.001 | |
| remove.regions-methods | 0.001 | 0.000 | 0.000 | |
| remove.samples-methods | 0 | 0 | 0 | |
| remove.sites-methods | 0.000 | 0.000 | 0.001 | |
| rnb.RnBSet.to.GRangesList | 0.001 | 0.000 | 0.000 | |
| rnb.RnBSet.to.bed | 0 | 0 | 0 | |
| rnb.RnBSet.to.bedGraph | 0.000 | 0.000 | 0.001 | |
| rnb.add.list | 0.001 | 0.000 | 0.000 | |
| rnb.add.paragraph | 0 | 0 | 0 | |
| rnb.add.reference | 0 | 0 | 0 | |
| rnb.add.section | 0.000 | 0.000 | 0.001 | |
| rnb.annotation.size | 0.001 | 0.000 | 0.000 | |
| rnb.annotation2data.frame | 0 | 0 | 0 | |
| rnb.beta2mval | 0.000 | 0.000 | 0.001 | |
| rnb.execute.batcheffects | 0.001 | 0.000 | 0.000 | |
| rnb.execute.clustering | 0 | 0 | 0 | |
| rnb.execute.computeDiffMeth | 0.000 | 0.000 | 0.001 | |
| rnb.execute.context.removal | 0 | 0 | 0 | |
| rnb.execute.cross.reactive.removal | 0.000 | 0.004 | 0.000 | |
| rnb.execute.dreduction | 0.000 | 0.000 | 0.001 | |
| rnb.execute.export.csv | 0 | 0 | 0 | |
| rnb.execute.gender.prediction | 0 | 0 | 0 | |
| rnb.execute.greedycut | 0.000 | 0.000 | 0.001 | |
| rnb.execute.import | 0 | 0 | 0 | |
| rnb.execute.na.removal | 0 | 0 | 0 | |
| rnb.execute.normalization | 0 | 0 | 0 | |
| rnb.execute.sex.removal | 0.000 | 0.000 | 0.001 | |
| rnb.execute.snp.removal | 0.000 | 0.004 | 0.000 | |
| rnb.execute.sva | 0 | 0 | 0 | |
| rnb.execute.tnt | 0.000 | 0.000 | 0.001 | |
| rnb.execute.variability.removal | 0.001 | 0.000 | 0.000 | |
| rnb.export.all.annotation | 0 | 0 | 0 | |
| rnb.export.annotation | 0.000 | 0.000 | 0.001 | |
| rnb.export.to.ewasher | 0.001 | 0.000 | 0.000 | |
| rnb.export.to.trackhub | 0.001 | 0.000 | 0.000 | |
| rnb.get.annotation | 0 | 0 | 0 | |
| rnb.get.assemblies | 0.000 | 0.000 | 0.001 | |
| rnb.get.chromosomes | 0.001 | 0.000 | 0.000 | |
| rnb.get.directory | 0 | 0 | 0 | |
| rnb.get.mapping | 0.000 | 0.000 | 0.001 | |
| rnb.get.reference | 0 | 0 | 0 | |
| rnb.get.reliability.matrix | 0.001 | 0.000 | 0.000 | |
| rnb.infinium.control.targets | 0 | 0 | 0 | |
| rnb.initialize.reports | 0.000 | 0.000 | 0.001 | |
| rnb.is.option | 0.001 | 0.000 | 0.000 | |
| rnb.message.plot | 0.001 | 0.000 | 0.000 | |
| rnb.mval2beta | 0 | 0 | 0 | |
| rnb.options | 0.000 | 0.000 | 0.001 | |
| rnb.options2xml | 0.001 | 0.000 | 0.000 | |
| rnb.plot.betadistribution.probeCategories | 0 | 0 | 0 | |
| rnb.plot.betadistribution.sampleGroups | 0.000 | 0.000 | 0.001 | |
| rnb.plot.control.barplot | 0 | 0 | 0 | |
| rnb.plot.control.boxplot | 0.001 | 0.000 | 0.000 | |
| rnb.plot.dreduction | 0 | 0 | 0 | |
| rnb.plot.locus.profile | 0.000 | 0.000 | 0.001 | |
| rnb.plot.negative.boxplot | 0.001 | 0.000 | 0.000 | |
| rnb.plot.region.profile.density | 0 | 0 | 0 | |
| rnb.plot.region.profiles | 0.000 | 0.000 | 0.001 | |
| rnb.plot.region.site.density | 0.000 | 0.000 | 0.001 | |
| rnb.plot.sentrix.distribution | 0.001 | 0.000 | 0.000 | |
| rnb.plot.snp.barplot | 0 | 0 | 0 | |
| rnb.plot.snp.boxplot | 0.000 | 0.000 | 0.001 | |
| rnb.plot.snp.heatmap | 0 | 0 | 0 | |
| rnb.region.types | 0 | 0 | 0 | |
| rnb.region.types.for.analysis | 0 | 0 | 0 | |
| rnb.remove.annotation | 0.000 | 0.000 | 0.001 | |
| rnb.run.example | 0.001 | 0.000 | 0.000 | |
| rnb.runs | 0.001 | 0.000 | 0.000 | |
| rnb.sample.groups | 0.000 | 0.000 | 0.001 | |
| rnb.sample.summary.table | 0 | 0 | 0 | |
| rnb.set.annotation | 0.001 | 0.000 | 0.000 | |
| rnb.write.table | 0 | 0 | 0 | |
| rnb.xml2options | 0.000 | 0.000 | 0.001 | |
| rowOneSampleTP | 0 | 0 | 0 | |
| rowWelchP | 0 | 0 | 0 | |
| run-RnBClusterRun-methods | 0 | 0 | 0 | |
| samples-methods | 0.000 | 0.000 | 0.001 | |
| save.tables-RnBDiffMeth-methods | 0.001 | 0.000 | 0.000 | |
| set.covariates.sva | 0 | 0 | 0 | |
| sites-methods | 0.000 | 0.000 | 0.001 | |
| summarize.regions-methods | 0.001 | 0.000 | 0.000 | |
| summarized.regions-methods | 0.001 | 0.000 | 0.000 | |