MethylSeekR 1.12.0
Lukas Burger
| Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/MethylSeekR | | Last Changed Rev: 117079 / Revision: 122332 | | Last Changed Date: 2016-05-03 14:20:18 -0700 (Tue, 03 May 2016) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | [ ERROR ] | | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK |  |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | ERROR | skipped | skipped | |
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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings MethylSeekR_1.12.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/MethylSeekR.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MethylSeekR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MethylSeekR’ version ‘1.12.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ‘MethylSeekR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘parallel’
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 ... NOTE
Namespace in Imports field not imported from: ‘geneplotter’
All declared Imports should be used.
Package in Depends field not imported from: ‘rtracklayer’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
PMDviterbiSegmentation : <anonymous>: no visible global function
definition for ‘predict’
PMDviterbiSegmentation : <anonymous>: no visible global function
definition for ‘Rle’
PMDviterbiSegmentation : <anonymous>: no visible global function
definition for ‘runValue’
calculateAlphaDistr : <anonymous>: no visible global function
definition for ‘Rle’
calculateFDRs: no visible global function definition for ‘queryHits’
calculateFDRs : <anonymous>: no visible global function definition for
‘Rle’
calculateFDRs : <anonymous>: no visible global function definition for
‘runValue’
createGRangesObjectPMDSegmentation : <anonymous>: no visible global
function definition for ‘Rle’
createGRangesObjectPMDSegmentation : <anonymous>: no visible global
function definition for ‘nrun’
createGRangesObjectPMDSegmentation : <anonymous>: no visible global
function definition for ‘runValue’
plotFinalSegmentation: no visible global function definition for ‘Rle’
removeSNPs: no visible global function definition for ‘queryHits’
segmentUMRsLMRs : <anonymous>: no visible global function definition
for ‘Rle’
segmentUMRsLMRs : <anonymous>: no visible global function definition
for ‘runValue’
segmentUMRsLMRs: no visible global function definition for ‘queryHits’
segmentUMRsLMRs: no visible global function definition for
‘subjectHits’
segmentUMRsLMRs: no visible global function definition for ‘Rle’
segmentUMRsLMRs: no visible global function definition for ‘DataFrame’
segmentUMRsLMRs: no visible global function definition for
‘colorRampPalette’
Undefined global functions or variables:
DataFrame Rle colorRampPalette nrun predict queryHits runValue
subjectHits
Consider adding
importFrom("grDevices", "colorRampPalette")
importFrom("stats", "predict")
to your NAMESPACE file.
* checking Rd files ... OK
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘MethylSeekR-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: MethylSeekR-package
> ### Title: Segmentation of Bis-seq methylation data
> ### Aliases: MethylSeekR-package MethylSeekR
> ### Keywords: package
>
> ### ** Examples
>
>
> library(MethylSeekR)
>
> # get chromosome lengths
> library("BSgenome.Hsapiens.UCSC.hg18")
Loading required package: BSgenome
Loading required package: Biostrings
Loading required package: XVector
> sLengths=seqlengths(Hsapiens)
>
> # read methylation data
> methFname <- system.file("extdata", "Lister2009_imr90_hg18_chr22.tab",
+ package="MethylSeekR")
> meth.gr <- readMethylome(FileName=methFname, seqLengths=sLengths)
reading methylome data
Read 200000 records
>
> #read SNP data
> snpFname <- system.file("extdata", "SNVs_hg18_chr22.tab",
+ package="MethylSeekR")
> snps.gr <- readSNPTable(FileName=snpFname, seqLengths=sLengths)
reading SNP table
Read 11750 records
>
> # remove SNPs
> meth.gr <- removeSNPs(meth.gr, snps.gr)
removing SNPs
11604 (6.2%) CpGs removed
>
> #calculate alpha distribution for one chromosome
> plotAlphaDistributionOneChr(m=meth.gr, chr.sel="chr22", num.cores=1)
determining alpha distribution for chromosome: chr22
>
> #segment PMDs
> PMDsegments.gr <- segmentPMDs(m=meth.gr, chr.sel="chr22", num.cores=1,
+ seqLengths=sLengths)
training PMD-HMM on chromosome chr22
performing viterbi segmentation
creating GRanges object
>
> #plot PMD segmentation examples
> plotPMDSegmentation(m=meth.gr, segs=PMDsegments.gr, numRegions=1)
>
> #save PMD segments
> savePMDSegments(PMDs=PMDsegments.gr, GRangesFilename="PMDs.gr.rds",
+ TableFilename="PMDs.tab")
>
> #load CpG islands
> library(rtracklayer)
> session <- browserSession()
> genome(session) <- "hg18"
> query <- ucscTableQuery(session, "cpgIslandExt")
Error in normArgTable(value, x) : unknown table name 'chromInfo'
Calls: ucscTableQuery ... tableName<- -> tableName<- -> .local -> normArgTable
Execution halted
* 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: 1 ERROR, 3 NOTEs
See
‘/home/biocbuild/bbs-3.3-bioc/meat/MethylSeekR.Rcheck/00check.log’
for details.