Package: MEDIPS

Version: 1.34.0

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_1.34.0.tar.gz

StartedAt: 2019-04-16 01:05:39 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 01:11:20 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 341.0 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_1.34.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/MEDIPS.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.34.0’
* 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 or elapsed time > 5s
                        user system elapsed
MEDIPS.meth           40.678  2.954  44.070
MEDIPS.addCNV         23.154  0.841  24.306
MEDIPS.plotSaturation  8.053  0.926   9.075
MEDIPS.saturation      7.434  0.824   8.337
* 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-3.8-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/3.5/Resources/library’
* installing *source* package ‘MEDIPS’ ...
** 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
* DONE (MEDIPS)

name	user	system	elapsed
COUPLINGset-class	0.001	0.000	0.002
MEDIPS.CpGenrich	0.054	0.002	0.058
MEDIPS.addCNV	23.154	0.841	24.306
MEDIPS.correlation	1.328	0.086	1.431
MEDIPS.couplingVector	3.697	0.187	3.925
MEDIPS.createROIset	1.206	0.112	1.336
MEDIPS.createSet	1.196	0.110	1.319
MEDIPS.exportWIG	2.146	0.139	2.303
MEDIPS.getAnnotation	0.000	0.000	0.001
MEDIPS.mergeFrames	0.008	0.001	0.008
MEDIPS.mergeSets	0.762	0.010	0.780
MEDIPS.meth	40.678	2.954	44.070
MEDIPS.plotCalibrationPlot	3.449	0.263	3.762
MEDIPS.plotSaturation	8.053	0.926	9.075
MEDIPS.plotSeqCoverage	3.476	0.267	3.787
MEDIPS.saturation	7.434	0.824	8.337
MEDIPS.selectROIs	2.040	0.175	2.246
MEDIPS.selectSig	3.497	0.247	3.794
MEDIPS.seqCoverage	3.385	0.275	3.695
MEDIPS.setAnnotation	3.520	0.286	3.839
MEDIPSroiSet-class	0.001	0.001	0.002
MEDIPSset-class	0.002	0.000	0.001