Package: MEDIPS

Version: 1.39.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MEDIPS.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MEDIPS_1.39.0.tar.gz

StartedAt: 2020-01-16 06:11:10 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 06:19:33 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 502.9 seconds

RetCode: 0

Status:  OK

CheckDir: MEDIPS.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MEDIPS.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MEDIPS_1.39.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/MEDIPS.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘1.39.0’
* 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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
MEDIPS.meth           47.771  5.179  52.955
MEDIPS.addCNV         27.273  1.684  28.978
MEDIPS.plotSaturation  8.850  1.600  10.450
MEDIPS.saturation      8.076  1.478   9.553
* 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-3.11-bioc/meat/MEDIPS.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL MEDIPS
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘MEDIPS’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (MEDIPS)

name	user	system	elapsed
COUPLINGset-class	0.003	0.001	0.004
MEDIPS.CpGenrich	0.097	0.009	0.110
MEDIPS.addCNV	27.273	1.684	28.978
MEDIPS.correlation	1.798	0.223	2.023
MEDIPS.couplingVector	4.294	0.346	4.642
MEDIPS.createROIset	1.586	0.212	1.800
MEDIPS.createSet	1.564	0.206	1.769
MEDIPS.exportWIG	2.865	0.242	3.108
MEDIPS.getAnnotation	0.000	0.000	0.001
MEDIPS.mergeFrames	0.008	0.000	0.009
MEDIPS.mergeSets	0.966	0.022	0.992
MEDIPS.meth	47.771	5.179	52.955
MEDIPS.plotCalibrationPlot	4.165	0.514	4.679
MEDIPS.plotSaturation	8.85	1.60	10.45
MEDIPS.plotSeqCoverage	3.790	0.453	4.244
MEDIPS.saturation	8.076	1.478	9.553
MEDIPS.selectROIs	2.141	0.320	2.461
MEDIPS.selectSig	3.452	0.560	4.013
MEDIPS.seqCoverage	3.708	0.480	4.188
MEDIPS.setAnnotation	4.273	0.534	4.807
MEDIPSroiSet-class	0.001	0.001	0.002
MEDIPSset-class	0.002	0.001	0.002