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CHECK report for MEDIPS on merida2

This page was generated on 2019-04-09 13:25:33 -0400 (Tue, 09 Apr 2019).

Package 929/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MEDIPS 1.35.0
Lukas Chavez
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/MEDIPS
Branch: master
Last Commit: f2465f5
Last Changed Date: 2018-10-30 11:54:29 -0400 (Tue, 30 Oct 2018)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK 

Summary

Package: MEDIPS
Version: 1.35.0
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_1.35.0.tar.gz
StartedAt: 2019-04-09 02:01:59 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 02:07:59 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 359.6 seconds
RetCode: 0
Status:  OK 
CheckDir: MEDIPS.Rcheck
Warnings: 0

Command output

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### Running 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_1.35.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/MEDIPS.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* 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 ‘1.35.0’
* 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           41.559  2.734  44.740
MEDIPS.addCNV         21.980  0.819  22.988
MEDIPS.plotSaturation  7.952  0.879   8.954
MEDIPS.saturation      7.640  0.851   8.590
* 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-3.9-bioc/meat/MEDIPS.Rcheck/00check.log’
for details.



Installation output

MEDIPS.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL MEDIPS
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/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)

Tests output


Example timings

MEDIPS.Rcheck/MEDIPS-Ex.timings

nameusersystemelapsed
COUPLINGset-class0.0010.0000.002
MEDIPS.CpGenrich0.0420.0030.045
MEDIPS.addCNV21.980 0.81922.988
MEDIPS.correlation1.3940.0741.480
MEDIPS.couplingVector3.5110.1833.738
MEDIPS.createROIset1.1040.1111.231
MEDIPS.createSet1.2000.1011.313
MEDIPS.exportWIG2.1030.1292.358
MEDIPS.getAnnotation0.0000.0000.001
MEDIPS.mergeFrames0.0050.0000.005
MEDIPS.mergeSets0.6790.0100.702
MEDIPS.meth41.559 2.73444.740
MEDIPS.plotCalibrationPlot3.2920.3133.695
MEDIPS.plotSaturation7.9520.8798.954
MEDIPS.plotSeqCoverage3.5210.2633.832
MEDIPS.saturation7.6400.8518.590
MEDIPS.selectROIs2.0940.1732.282
MEDIPS.selectSig3.4790.2613.765
MEDIPS.seqCoverage3.3500.2763.670
MEDIPS.setAnnotation2.8260.2763.131
MEDIPSroiSet-class0.0010.0000.001
MEDIPSset-class0.0020.0010.002