Pan Du
| 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) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:50:30 -0400 (Wed, 16 Oct 2019).
| Package 977/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| methyAnalysis 1.26.0 Pan Du
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | |
| Package: methyAnalysis |
| Version: 1.26.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:methyAnalysis.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings methyAnalysis_1.26.0.tar.gz |
| StartedAt: 2019-10-16 04:30:59 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 04:46:24 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 924.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: methyAnalysis.Rcheck |
| Warnings: 2 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:methyAnalysis.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings methyAnalysis_1.26.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/methyAnalysis.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.26.0’
* 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 for sufficient/correct file permissions ... 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:
‘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
* 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 ... OK
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
plotMethylationHeatmapByGene 54.662 2.907 84.419
buildAnnotationTracks 31.462 1.883 60.601
MethyLumiM2GenoSet 29.633 1.751 31.549
heatmapByChromosome 29.108 1.240 31.496
plotHeatmapByGene 28.931 1.259 44.377
plotTracksWithDataTrackInfo 21.352 1.252 22.965
createTranscriptTrack 19.618 1.109 20.728
annotateDMRInfo 7.446 0.754 8.332
* 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: 2 WARNINGs, 4 NOTEs
See
‘/Users/biocbuild/bbs-3.9-bioc/meat/methyAnalysis.Rcheck/00check.log’
for details.
methyAnalysis.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL methyAnalysis ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * 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 ** 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 * DONE (methyAnalysis)
methyAnalysis.Rcheck/methyAnalysis-Ex.timings
| name | user | system | elapsed | |
| MethyGenoSet-class | 0.149 | 0.014 | 0.163 | |
| MethyLumiM2GenoSet | 29.633 | 1.751 | 31.549 | |
| annotateDMRInfo | 7.446 | 0.754 | 8.332 | |
| annotateGRanges | 4.010 | 0.261 | 4.293 | |
| buildAnnotationTracks | 31.462 | 1.883 | 60.601 | |
| checkChrName | 0.126 | 0.015 | 0.141 | |
| createTranscriptTrack | 19.618 | 1.109 | 20.728 | |
| detectDMR.slideWin | 0.983 | 0.119 | 1.102 | |
| exampleMethyGenoSet | 0.126 | 0.018 | 0.143 | |
| export.DMRInfo | 4.048 | 0.409 | 4.561 | |
| export.methyGenoSet | 0.263 | 0.042 | 0.321 | |
| getContinuousRegion | 1.019 | 0.108 | 1.158 | |
| heatmapByChromosome | 29.108 | 1.240 | 31.496 | |
| identifyCpG | 0 | 0 | 0 | |
| identifySigDMR | 0.870 | 0.025 | 0.895 | |
| plotHeatmapByGene | 28.931 | 1.259 | 44.377 | |
| plotMethylationHeatmapByGene | 54.662 | 2.907 | 84.419 | |
| plotTracksWithDataTrackInfo | 21.352 | 1.252 | 22.965 | |
| smoothMethyData | 0.509 | 0.041 | 0.551 | |