BioC 3.0: CHECK report for MEDIPS on zin1

Package: MEDIPS

Version: 1.16.0

Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings MEDIPS_1.16.0.tar.gz

StartedAt: 2015-04-10 01:41:46 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 01:48:19 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 393.2 seconds

RetCode: 0

Status:  OK

CheckDir: MEDIPS.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings MEDIPS_1.16.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/MEDIPS.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-linux-gnu (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 ‘1.16.0’
* 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 ‘MEDIPS’ can be installed ... [21s/23s] 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:
  ‘BSgenome’ ‘DNAcopy’
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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
  ‘GenomicFeatures’ ‘GenomicRanges’
  All declared Imports should be used.
* 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.GenomicCoordinates: no visible global function definition for
  ‘GRanges’
MEDIPS.addCNV: no visible global function definition for ‘seqnames’
MEDIPS.couplingVector: no visible global function definition for
  ‘countOverlaps’
MEDIPS.createROIset: no visible global function definition for
  ‘seqlevels’
MEDIPS.createROIset: no visible global function definition for
  ‘seqlengths’
MEDIPS.createROIset: no visible global function definition for
  ‘countOverlaps’
MEDIPS.createSet: no visible global function definition for ‘seqlevels’
MEDIPS.createSet: no visible global function definition for
  ‘seqlengths’
MEDIPS.createSet: no visible global function definition for
  ‘countOverlaps’
MEDIPS.exportWIG: no visible global function definition for ‘seqnames’
MEDIPS.getPositions: no visible global function definition for
  ‘GRanges’
MEDIPS.meth: no visible global function definition for ‘seqnames’
MEDIPS.plotCalibrationPlot: no visible global function definition for
  ‘seqnames’
MEDIPS.saturation: no visible global function definition for
  ‘seqlevels’
MEDIPS.saturation: no visible global function definition for
  ‘seqlengths’
MEDIPS.saturation: no visible global function definition for
  ‘countOverlaps’
MEDIPS.selectROIs: no visible global function definition for ‘GRanges’
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.seqCoverage: no visible global function definition for
  ‘countOverlaps’
MEDIPS.setAnnotation: no visible global function definition for
  ‘GRanges’
MEDIPS.setAnnotation: no visible global function definition for
  ‘findOverlaps’
bin.ROIs: no visible global function definition for ‘GRanges’
getGRange: no visible global function definition for ‘GRanges’
getGRange: no visible global function definition for ‘strand<-’
getMObjectFromWIG: no visible global function definition for ‘GRanges’
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 ‘GRanges’
getPairedGRange: no visible global function definition for ‘strand<-’
scanBamToGRanges: no visible global function definition for ‘GRanges’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [148s/164s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
MEDIPS.meth           52.575  0.028  53.469
MEDIPS.addCNV         33.934  0.196  35.320
MEDIPS.plotSaturation  9.221  0.020   9.412
MEDIPS.saturation      9.121  0.008   9.269
MEDIPS.selectSig       5.472  0.056   5.548
MEDIPS.selectROIs      4.732  0.036   5.322
MEDIPS.setAnnotation   4.433  0.036   8.344
MEDIPS.getAnnotation   0.112  0.004   6.681
* 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

NOTE: There were 3 notes.
See
  ‘/home/biocbuild/bbs-3.0-bioc/meat/MEDIPS.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
COUPLINGset-class	0.004	0.000	0.002
MEDIPS.CpGenrich	0.076	0.016	0.612
MEDIPS.addCNV	33.934	0.196	35.320
MEDIPS.annotate	0.000	0.000	0.001
MEDIPS.correlation	0.388	0.016	1.078
MEDIPS.couplingVector	2.296	0.040	2.583
MEDIPS.coverageAnalysis	0	0	0
MEDIPS.createROIset	0.784	0.012	1.027
MEDIPS.createSet	0.977	0.004	1.017
MEDIPS.exportWIG	1.644	0.004	1.653
MEDIPS.genomeVector	0.004	0.000	0.001
MEDIPS.getAnnotation	0.112	0.004	6.681
MEDIPS.mergeFrames	0.004	0.000	0.006
MEDIPS.mergeSets	0.312	0.000	0.600
MEDIPS.meth	52.575	0.028	53.469
MEDIPS.methylProfiling	0.000	0.000	0.001
MEDIPS.normalize	0.004	0.000	0.000
MEDIPS.plotCalibrationPlot	3.328	0.032	3.477
MEDIPS.plotCoverage	0.004	0.000	0.001
MEDIPS.plotSaturation	9.221	0.020	9.412
MEDIPS.plotSeqCoverage	4.348	0.044	4.636
MEDIPS.readAlignedSequences	0.004	0.000	0.001
MEDIPS.saturation	9.121	0.008	9.269
MEDIPS.saturationAnalysis	0.004	0.000	0.001
MEDIPS.selectROIs	4.732	0.036	5.322
MEDIPS.selectSig	5.472	0.056	5.548
MEDIPS.selectSignificants	0	0	0
MEDIPS.seqCoverage	2.964	0.072	3.044
MEDIPS.setAnnotation	4.433	0.036	8.344
MEDIPSroiSet-class	0.000	0.000	0.001
MEDIPSset-class	0.004	0.000	0.001