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CHECK report for MEDIPS on malbec2

This page was generated on 2020-10-17 11:55:05 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE MEDIPS PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1019/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MEDIPS 1.40.0
Lukas Chavez
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/MEDIPS
Branch: RELEASE_3_11
Last Commit: a95e972
Last Changed Date: 2020-04-27 14:23:35 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 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
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: MEDIPS
Version: 1.40.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:MEDIPS.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings MEDIPS_1.40.0.tar.gz
StartedAt: 2020-10-17 02:54:05 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 03:01:02 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 417.2 seconds
RetCode: 0
Status:  OK 
CheckDir: MEDIPS.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:MEDIPS.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings MEDIPS_1.40.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/MEDIPS.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘1.40.0’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
MEDIPS.meth           40.652  0.028  40.696
MEDIPS.addCNV         22.562  0.339  23.068
MEDIPS.plotSaturation  7.570  0.019   7.591
MEDIPS.saturation      6.908  0.016   6.934
* 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-3.11-bioc/meat/MEDIPS.Rcheck/00check.log’
for details.



Installation output

MEDIPS.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL MEDIPS
###
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/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)

Tests output


Example timings

MEDIPS.Rcheck/MEDIPS-Ex.timings

nameusersystemelapsed
COUPLINGset-class0.0020.0010.002
MEDIPS.CpGenrich0.0790.0000.114
MEDIPS.addCNV22.562 0.33923.068
MEDIPS.correlation1.7530.0002.010
MEDIPS.couplingVector3.8070.0123.818
MEDIPS.createROIset1.4750.0151.511
MEDIPS.createSet1.4990.0011.499
MEDIPS.exportWIG2.7420.0002.741
MEDIPS.getAnnotation0.0000.0000.001
MEDIPS.mergeFrames0.0080.0000.007
MEDIPS.mergeSets0.7690.0040.797
MEDIPS.meth40.652 0.02840.696
MEDIPS.plotCalibrationPlot3.5780.0183.597
MEDIPS.plotSaturation7.5700.0197.591
MEDIPS.plotSeqCoverage2.9150.0432.959
MEDIPS.saturation6.9080.0166.934
MEDIPS.selectROIs2.3070.0402.347
MEDIPS.selectSig2.3390.0322.372
MEDIPS.seqCoverage2.7250.0522.777
MEDIPS.setAnnotation2.8740.0322.906
MEDIPSroiSet-class0.0010.0000.000
MEDIPSset-class000