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BioC 3.2: CHECK report for methyAnalysis on zin1

This page was generated on 2016-04-23 10:12:37 -0700 (Sat, 23 Apr 2016).

Package 631/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
methyAnalysis 1.12.2
Pan Du
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/methyAnalysis
Last Changed Rev: 116670 / Revision: 116712
Last Changed Date: 2016-04-21 12:59:04 -0700 (Thu, 21 Apr 2016)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (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: 1.12.2
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings methyAnalysis_1.12.2.tar.gz
StartedAt: 2016-04-23 02:45:33 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 02:54:15 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 521.8 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: methyAnalysis.Rcheck
Warnings: 4

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings methyAnalysis_1.12.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/methyAnalysis.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 ‘methyAnalysis/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘methyAnalysis’ version ‘1.12.2’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘methyAnalysis’ can be installed ... [30s/30s] 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
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [142s/228s] 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 31.941  0.096  65.117
MethyLumiM2GenoSet           17.047  0.236  17.364
buildAnnotationTracks        13.802  0.124  50.319
heatmapByChromosome          13.731  0.032  13.833
plotHeatmapByGene            13.511  0.053  30.259
createTranscriptTrack        12.838  0.052  12.885
plotTracksWithDataTrackInfo  12.602  0.016  12.674
* 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: 4 WARNINGs, 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/methyAnalysis.Rcheck/00check.log’
for details.

methyAnalysis.Rcheck/00install.out:

* installing *source* package ‘methyAnalysis’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (methyAnalysis)

methyAnalysis.Rcheck/methyAnalysis-Ex.timings:

nameusersystemelapsed
MethyGenoSet-class0.0860.0000.085
MethyLumiM2GenoSet17.047 0.23617.364
annotateDMRInfo3.7260.0883.844
annotateGRanges1.6800.0121.694
buildAnnotationTracks13.802 0.12450.319
checkChrName0.0910.0000.091
createTranscriptTrack12.838 0.05212.885
detectDMR.slideWin0.4620.0040.465
exampleMethyGenoSet0.1240.0000.124
export.DMRInfo3.1060.0003.104
export.methyGenoSet0.1980.0000.198
getContinuousRegion0.4690.0040.471
heatmapByChromosome13.731 0.03213.833
identifyCpG0.0000.0000.001
identifySigDMR0.6580.0000.659
plotHeatmapByGene13.511 0.05330.259
plotMethylationHeatmapByGene31.941 0.09665.117
plotTracksWithDataTrackInfo12.602 0.01612.674
smoothMethyData0.3140.0000.314