BioC 3.2: CHECK report for MEDIPS on linux1.bioconductor.org

Package: MEDIPS

Version: 1.20.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings MEDIPS_1.20.0.tar.gz

StartedAt: 2015-10-27 05:23:29 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 05:28:15 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 286.4 seconds

RetCode: 0

Status:  OK

CheckDir: MEDIPS.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings MEDIPS_1.20.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/MEDIPS.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-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 ‘1.20.0’
* 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 ... [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.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.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.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 ‘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 ‘seqlengths’
getPairedGRange: no visible global function definition for
  ‘countMatches’
getPairedGRange: no visible global function definition for ‘strand<-’
* 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 ... [119s/123s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
MEDIPS.meth           50.594  0.028  50.651
MEDIPS.addCNV         25.525  0.316  25.852
MEDIPS.saturation      6.081  0.004   6.113
MEDIPS.plotSaturation  5.221  0.004   5.233
* 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 NOTE
See
  ‘/home/biocbuild/bbs-3.2-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	0.002	0.000	0.002
MEDIPS.CpGenrich	0.08	0.00	0.08
MEDIPS.addCNV	25.525	0.316	25.852
MEDIPS.correlation	0.435	0.004	0.441
MEDIPS.couplingVector	1.947	0.008	1.962
MEDIPS.createROIset	0.750	0.000	0.751
MEDIPS.createSet	0.874	0.000	0.876
MEDIPS.exportWIG	1.463	0.004	1.467
MEDIPS.getAnnotation	0.115	0.004	3.354
MEDIPS.mergeFrames	0.006	0.000	0.006
MEDIPS.mergeSets	0.404	0.000	0.405
MEDIPS.meth	50.594	0.028	50.651
MEDIPS.plotCalibrationPlot	2.842	0.032	2.877
MEDIPS.plotSaturation	5.221	0.004	5.233
MEDIPS.plotSeqCoverage	2.350	0.020	2.373
MEDIPS.saturation	6.081	0.004	6.113
MEDIPS.selectROIs	3.068	0.012	3.080
MEDIPS.selectSig	3.423	0.020	3.445
MEDIPS.seqCoverage	2.046	0.020	2.069
MEDIPS.setAnnotation	2.889	0.032	3.798
MEDIPSroiSet-class	0.001	0.000	0.001
MEDIPSset-class	0.002	0.000	0.002