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CHECK report for wavClusteR on malbec2

This page was generated on 2018-10-17 08:26:16 -0400 (Wed, 17 Oct 2018).

Package 1543/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
wavClusteR 2.14.0
Federico Comoglio
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/wavClusteR
Branch: RELEASE_3_7
Last Commit: 90945d6
Last Changed Date: 2018-04-30 10:35:33 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: wavClusteR
Version: 2.14.0
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:wavClusteR.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings wavClusteR_2.14.0.tar.gz
StartedAt: 2018-10-16 04:27:27 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 04:30:39 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 192.2 seconds
RetCode: 0
Status:  OK 
CheckDir: wavClusteR.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:wavClusteR.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings wavClusteR_2.14.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/wavClusteR.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘wavClusteR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘wavClusteR’ version ‘2.14.0’
* 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 ‘wavClusteR’ 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 ... NOTE
'library' or 'require' call to ‘doMC’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
annotateClusters: no visible binding for global variable ‘Percentage’
annotateClusters: no visible binding for global variable ‘Compartment’
estimateFDR: no visible global function definition for ‘DNAString’
estimateFDR: no visible global function definition for ‘lines’
estimateFDR: no visible global function definition for ‘legend’
estimateFDR: no visible global function definition for ‘axis’
exportGR: no visible global function definition for ‘write.table’
filterClustersCWT: no visible global function definition for
  ‘DNAString’
filterClustersMRN: no visible global function definition for
  ‘txtProgressBar’
filterClustersMRN: no visible global function definition for
  ‘setTxtProgressBar’
getClustersCWT: no visible global function definition for
  ‘registerDoMC’
getClustersCWT: no visible global function definition for ‘seqlevels’
getClustersMRN: no visible global function definition for
  ‘registerDoMC’
getComplSubst: no visible global function definition for ‘DNAStringSet’
getExpInterval: no visible global function definition for ‘par’
getExpInterval: no visible global function definition for ‘lines’
getExpInterval: no visible global function definition for ‘legend’
getExpInterval: no visible global function definition for ‘polygon’
getExpInterval: no visible global function definition for ‘rect’
getExpInterval: no visible global function definition for ‘text’
getLogOdd: no visible global function definition for ‘dbinom’
getMetaCoverage: no visible global function definition for ‘axis’
getMetaGene: no visible global function definition for ‘grid’
getMetaGene: no visible global function definition for ‘axis’
getMetaGene: no visible global function definition for ‘abline’
getMetaTSS: no visible global function definition for ‘grid’
getMetaTSS: no visible global function definition for ‘axis’
plotSizeDistribution: no visible global function definition for ‘hist’
plotStatistics: no visible binding for global variable ‘panel.smooth’
plotStatistics : panelCor: no visible global function definition for
  ‘par’
plotStatistics : panelCor: no visible global function definition for
  ‘strwidth’
plotStatistics : panelCor: no visible global function definition for
  ‘text’
plotStatistics: no visible global function definition for ‘pairs’
plotSubstitutions: no visible global function definition for ‘par’
plotSubstitutions: no visible global function definition for ‘barplot’
processChunk: no visible global function definition for ‘extractAt’
processMD: no visible global function definition for ‘registerDoMC’
readSortedBam: no visible global function definition for ‘scanBamFlag’
readSortedBam : <anonymous>: no visible binding for global variable
  ‘rname’
readSortedBam : <anonymous>: no visible binding for global variable
  ‘qwidth’
Undefined global functions or variables:
  Compartment DNAString DNAStringSet Percentage abline axis barplot
  dbinom extractAt grid hist legend lines pairs panel.smooth par
  polygon qwidth rect registerDoMC rname scanBamFlag seqlevels
  setTxtProgressBar strwidth text txtProgressBar write.table
Consider adding
  importFrom("graphics", "abline", "axis", "barplot", "grid", "hist",
             "legend", "lines", "pairs", "panel.smooth", "par",
             "polygon", "rect", "strwidth", "text")
  importFrom("stats", "dbinom")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar",
             "write.table")
to your NAMESPACE file.
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.7-bioc/meat/wavClusteR.Rcheck/00check.log’
for details.



Installation output

wavClusteR.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL wavClusteR
###
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘wavClusteR’ ...
** R
** data
** 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 (wavClusteR)

Tests output


Example timings

wavClusteR.Rcheck/wavClusteR-Ex.timings

nameusersystemelapsed
FitMixtureModel0.0600.0040.064
annotateClusters3.7880.0323.853
filterClusters2.3680.0162.385
getAllSub1.3040.0321.337
getClusters1.8320.0201.853
getExpInterval0.0360.0000.037
getHighConfSub1.3240.0161.343
getMetaCoverage2.1040.0122.118
getMetaGene2.1840.0242.208
getMetaTSS0.1000.0120.109
plotSizeDistribution2.0960.0282.125
plotStatistics2.1200.0202.144
plotSubstitutions1.3240.0161.344
readSortedBam0.0520.0200.075