BioC 3.5: CHECK report for MEDIPS on veracruz2

Package: MEDIPS

Version: 1.28.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MEDIPS_1.28.0.tar.gz

StartedAt: 2017-08-16 04:57:48 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 05:03:13 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 325.4 seconds

RetCode: 0

Status:  OK

CheckDir: MEDIPS.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MEDIPS_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/MEDIPS.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.28.0’
* 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 ... 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.CpGenrich: no visible global function definition for ‘new’
MEDIPS.addCNV: no visible global function definition for ‘seqnames’
MEDIPS.correlation: no visible global function definition for ‘pdf’
MEDIPS.correlation: no visible global function definition for ‘dev.off’
MEDIPS.couplingVector: no visible global function definition for ‘new’
MEDIPS.createROIset: no visible global function definition for
  ‘seqnames’
MEDIPS.createROIset: no visible global function definition for
  ‘seqlengths’
MEDIPS.createROIset: no visible global function definition for ‘new’
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.createSet: no visible global function definition for ‘new’
MEDIPS.diffMeth: no visible global function definition for ‘p.adjust’
MEDIPS.exportWIG: no visible global function definition for ‘seqnames’
MEDIPS.mergeSets: no visible global function definition for ‘new’
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’
getMObjectFromWIG: no visible global function definition for ‘new’
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 new p.adjust pdf pie points pt qpois runLength runValue sd
  seqlengths seqlevels seqnames strand<-
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "hist", "pie", "points")
  importFrom("methods", "new")
  importFrom("stats", "p.adjust", "pt", "qpois", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
MEDIPS.meth           35.160  2.222  38.482
MEDIPS.addCNV         21.641  0.647  22.982
MEDIPS.plotSaturation  7.115  0.592   7.924
MEDIPS.saturation      6.694  0.538   7.447
* 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
  ‘/Users/biocbuild/bbs-3.5-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	0.001	0.000	0.001
MEDIPS.CpGenrich	0.104	0.013	0.128
MEDIPS.addCNV	21.641	0.647	22.982
MEDIPS.correlation	1.066	0.085	1.207
MEDIPS.couplingVector	2.579	0.153	2.786
MEDIPS.createROIset	0.805	0.086	0.905
MEDIPS.createSet	0.825	0.085	0.930
MEDIPS.exportWIG	1.497	0.102	1.648
MEDIPS.getAnnotation	0.001	0.000	0.001
MEDIPS.mergeFrames	0.004	0.000	0.006
MEDIPS.mergeSets	0.484	0.008	0.520
MEDIPS.meth	35.160	2.222	38.482
MEDIPS.plotCalibrationPlot	2.544	0.223	2.830
MEDIPS.plotSaturation	7.115	0.592	7.924
MEDIPS.plotSeqCoverage	2.748	0.228	3.053
MEDIPS.saturation	6.694	0.538	7.447
MEDIPS.selectROIs	2.434	0.113	2.616
MEDIPS.selectSig	3.082	0.181	3.357
MEDIPS.seqCoverage	2.628	0.241	2.912
MEDIPS.setAnnotation	2.726	0.208	2.981
MEDIPSroiSet-class	0.001	0.000	0.001
MEDIPSset-class	0.001	0.001	0.001