MEDIPS 1.21.4
Lukas Chavez
| Snapshot Date: 2016-04-20 17:20:35 -0700 (Wed, 20 Apr 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MEDIPS | | Last Changed Rev: 116341 / Revision: 116626 | | Last Changed Date: 2016-04-15 02:53:13 -0700 (Fri, 15 Apr 2016) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | ERROR | | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK |  |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | [ ERROR ] | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MEDIPS_1.21.4.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/MEDIPS.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MEDIPS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MEDIPS’ version ‘1.21.4’
* 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 ‘MEDIPS’ can be installed ... [16s/16s] OK
* checking installed package size ... OK
* 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 ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
MEDIPS.CpGenrich: no visible global function definition for ‘seqlevels’
MEDIPS.CpGenrich: no visible global function definition for
‘seqlengths’
MEDIPS.addCNV: no visible global function definition for ‘seqnames’
MEDIPS.correlation: no visible global function definition for ‘png’
MEDIPS.correlation: no visible global function definition for ‘dev.off’
MEDIPS.createROIset: no visible global function definition for
‘seqnames’
MEDIPS.createROIset: no visible global function definition for
‘seqlengths’
MEDIPS.createSet: no visible global function definition for ‘seqnames’
MEDIPS.createSet: no visible global function definition for
‘seqlengths’
MEDIPS.createSet: no visible global function definition for ‘seqlevels’
MEDIPS.diffMeth: no visible global function definition for ‘p.adjust’
MEDIPS.exportWIG: no visible global function definition for ‘seqnames’
MEDIPS.meth: no visible global function definition for ‘seqnames’
MEDIPS.plotCalibrationPlot: no visible global function definition for
‘seqnames’
MEDIPS.plotCalibrationPlot: no visible global function definition for
‘points’
MEDIPS.plotSeqCoverage: no visible global function definition for ‘pie’
MEDIPS.plotSeqCoverage: no visible global function definition for
‘hist’
MEDIPS.saturation: no visible global function definition for
‘seqlevels’
MEDIPS.saturation: no visible global function definition for
‘seqlengths’
MEDIPS.selectROIs: no visible global function definition for
‘elementMetadata<-’
MEDIPS.selectROIs: no visible global function definition for
‘elementMetadata’
MEDIPS.selectROIs: no visible global function definition for
‘findOverlaps’
MEDIPS.selectROIs: no visible global function definition for ‘seqnames’
MEDIPS.seqCoverage: no visible global function definition for
‘seqlevels’
MEDIPS.seqCoverage: no visible global function definition for
‘seqlengths’
MEDIPS.setAnnotation: no visible global function definition for
‘findOverlaps’
getGRange: no visible global function definition for ‘qpois’
getGRange: no visible global function definition for ‘seqlengths’
getGRange: no visible global function definition for ‘countMatches’
getGRange: no visible global function definition for ‘strand<-’
getMObjectFromWIG: no visible global function definition for
‘seqlengths’
getMObjectFromWIG: no visible global function definition for
‘runLength’
getMObjectFromWIG: no visible global function definition for ‘seqnames’
getMObjectFromWIG: no visible global function definition for ‘runValue’
getPairedGRange: no visible global function definition for ‘sd’
getPairedGRange: no visible global function definition for ‘qpois’
getPairedGRange: no visible global function definition for ‘seqlengths’
getPairedGRange: no visible global function definition for
‘countMatches’
getPairedGRange: no visible global function definition for ‘strand<-’
matSd: no visible binding for global variable ‘sd’
matTtest: no visible binding for global variable ‘sd’
matTtest: no visible global function definition for ‘pt’
Undefined global functions or variables:
countMatches dev.off elementMetadata elementMetadata<- findOverlaps
hist p.adjust pie png points pt qpois runLength runValue sd
seqlengths seqlevels seqnames strand<-
Consider adding
importFrom("grDevices", "dev.off", "png")
importFrom("graphics", "hist", "pie", "points")
importFrom("stats", "p.adjust", "pt", "qpois", "sd")
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 ‘MEDIPS-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: MEDIPS.setAnnotation
> ### Title: Funtion to annotate a matrix of genomic coordinates (i.e. a
> ### result table) by a given annotation object.
> ### Aliases: MEDIPS.setAnnotation
>
> ### ** Examples
>
> library(MEDIPSData)
> data(resultTable)
>
> sig = MEDIPS.selectSig(results=resultTable, p.value=0.05, adj=TRUE, ratio=NULL, bg.counts=NULL, CNV=FALSE)
Total number of windows: 513046
Number of windows tested for differential methylation: 220953
Remaining number of windows with adjusted p.value<=0.05: 43
> sig = MEDIPS.mergeFrames(frames=sig, distance=1)
[1] Number of merged frames: 19
> ens_gene = MEDIPS.getAnnotation( annotation="GENE",chr="chr22")
Getting annotation from database Ensembl Genes 84
Selecting dataset Homo sapiens genes (GRCh38.p5)
Extra content at the end of the document
Error: 1: Extra content at the end of the document
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, 1 NOTE
See
‘/Users/biocbuild/bbs-3.3-bioc/meat/MEDIPS.Rcheck/00check.log’
for details.