BioC 3.3: CHECK report for wavClusteR on linux2.bioconductor.org

Package: wavClusteR

Version: 2.5.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings wavClusteR_2.5.0.tar.gz

StartedAt: 2015-10-27 08:55:07 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 08:58:43 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 215.4 seconds

RetCode: 0

Status:  OK

CheckDir: wavClusteR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings wavClusteR_2.5.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/wavClusteR.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* 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 ‘2.5.0’
* 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 ... [16s/18s] 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 loading without being on the library search path ... 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 global function definition for ‘strand’
annotateClusters: no visible global function definition for ‘strand<-’
annotateClusters: no visible global function definition for
  ‘elementMetadata’
annotateClusters: no visible global function definition for
  ‘elementMetadata<-’
annotateClusters: no visible binding for global variable ‘Percentage’
annotateClusters: no visible binding for global variable ‘Compartment’
computeLogOdds: no visible global function definition for
  ‘elementMetadata’
computeLogOdds: no visible global function definition for
  ‘elementMetadata<-’
estimateFDR : getAllSubstNoStrand: no visible global function
  definition for ‘elementMetadata’
estimateFDR : getAllSubstNoStrand: no visible global function
  definition for ‘GRanges’
estimateFDR : getCountTableRNASeq: no visible global function
  definition for ‘GRanges’
estimateFDR : getCountTableRNASeq: no visible global function
  definition for ‘elementMetadata’
estimateFDR : getCountTableRNASeq: no visible global function
  definition for ‘elementMetadata<-’
estimateFDR : getFDRBounds: no visible global function definition for
  ‘elementMetadata’
estimateFDR: no visible global function definition for
  ‘elementMetadata’
estimateFDR: no visible global function definition for ‘strand<-’
estimateFDR: no visible global function definition for ‘complement’
estimateFDR: no visible global function definition for ‘DNAString’
estimateFDR: no visible global function definition for
  ‘elementMetadata<-’
estimateP: no visible global function definition for ‘elementMetadata’
exportGR: no visible global function definition for ‘seqnames’
exportGR: no visible global function definition for ‘strand’
exportSequences: no visible global function definition for
  ‘elementMetadata’
filterClusters: no visible global function definition for ‘metadata’
filterClustersCWT: no visible global function definition for
  ‘complement’
filterClustersCWT: no visible global function definition for
  ‘DNAString’
filterClustersCWT: no visible global function definition for
  ‘elementMetadata’
filterClustersCWT: no visible global function definition for ‘seqnames’
filterClustersCWT: no visible global function definition for ‘strand’
filterClustersCWT: no visible global function definition for ‘GRanges’
filterClustersMRN: no visible global function definition for ‘seqnames’
filterClustersMRN: no visible global function definition for ‘strand’
filterClustersMRN: no visible global function definition for
  ‘elementMetadata’
filterClustersMRN: no visible global function definition for
  ‘elementMetadata<-’
fitMixtureModel: no visible global function definition for
  ‘elementMetadata’
getAllSub: no visible global function definition for ‘elementMetadata’
getAllSub: no visible global function definition for ‘strand’
getAllSub: no visible global function definition for ‘GRanges’
getClusters: no visible global function definition for ‘metadata<-’
getClustersCWT: no visible global function definition for
  ‘registerDoMC’
getClustersCWT: no visible global function definition for ‘seqnames’
getClustersCWT: no visible global function definition for ‘seqlevels’
getClustersCWT: no visible global function definition for ‘GRanges’
getClustersMRN: no visible global function definition for ‘seqnames’
getClustersMRN: no visible global function definition for
  ‘registerDoMC’
getClustersMRN: no visible global function definition for ‘strand’
getClustersMRN: no visible global function definition for ‘GRanges’
getComplSubst: no visible global function definition for ‘DNAStringSet’
getComplSubst: no visible global function definition for ‘complement’
getCountTable: no visible global function definition for
  ‘elementMetadata’
getCountTable: no visible global function definition for ‘GRanges’
getCountTable: no visible global function definition for
  ‘elementMetadata<-’
getCoverageAtSubst: no visible global function definition for
  ‘seqnames’
getCoverageAtSubst: no visible global function definition for
  ‘elementMetadata’
getCoverageAtSubst: no visible global function definition for
  ‘elementMetadata<-’
getHighConfSub: no visible global function definition for
  ‘elementMetadata’
getHighConfSub: no visible global function definition for
  ‘elementMetadata<-’
getHighConfSub: no visible global function definition for ‘metadata<-’
getMetaCoverage: no visible global function definition for ‘seqnames’
getMetaCoverage: no visible global function definition for ‘strand’
getMetaCoverage: no visible global function definition for ‘GRanges’
getMetaCoverage: no visible global function definition for
  ‘elementMetadata’
getMetaGene: no visible global function definition for ‘seqnames’
getMetaGene: no visible global function definition for ‘strand’
getMetaGene: no visible global function definition for ‘GRanges’
getMetaTSS: no visible global function definition for ‘seqnames’
getMetaTSS: no visible global function definition for ‘strand’
getMetaTSS: no visible global function definition for ‘GRanges’
getSEcoverage: no visible global function definition for ‘strand<-’
learnThreshold: no visible global function definition for ‘seqnames’
plotSizeDistribution: no visible global function definition for
  ‘elementMetadata’
plotStatistics: no visible global function definition for
  ‘elementMetadata’
plotSubstitutions: no visible global function definition for
  ‘elementMetadata’
processChunk: no visible global function definition for ‘strand’
processChunk: no visible global function definition for ‘seqnames’
processChunk: no visible global function definition for ‘extractAt’
processChunk: no visible global function definition for ‘DataFrame’
processMD: no visible global function definition for ‘registerDoMC’
readSortedBam: no visible global function definition for ‘scanBamFlag’
readSortedBam : <anonymous>: no visible global function definition for
  ‘GRanges’
readSortedBam : <anonymous>: no visible binding for global variable
  ‘rname’
readSortedBam : <anonymous>: no visible binding for global variable
  ‘qwidth’
readSortedBam : <anonymous>: no visible binding for global variable
  ‘strand’
readSortedBam: no visible global function definition for ‘GRangesList’
Undefined global functions or variables:
  Compartment DNAString DNAStringSet DataFrame GRanges GRangesList
  Percentage complement elementMetadata elementMetadata<- extractAt
  metadata metadata<- qwidth registerDoMC rname scanBamFlag seqlevels
  seqnames strand strand<-
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [57s/57s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
plotSizeDistribution 6.040  0.016   6.056
annotateClusters     5.562  0.073   5.636
plotStatistics       5.515  0.016   5.541
getMetaGene          5.505  0.012   5.521
getClusters          5.293  0.004   5.298
* 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-3.3-bioc/meat/wavClusteR.Rcheck/00check.log’
for details.

* installing *source* package ‘wavClusteR’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (wavClusteR)

name	user	system	elapsed
FitMixtureModel	0.027	0.000	0.027
annotateClusters	5.562	0.073	5.636
filterClusters	4.911	0.015	4.931
getAllSub	3.374	0.012	3.386
getClusters	5.293	0.004	5.298
getExpInterval	0.034	0.000	0.034
getHighConfSub	4.354	0.008	4.363
getMetaCoverage	4.400	0.020	4.419
getMetaGene	5.505	0.012	5.521
getMetaTSS	0.157	0.012	0.169
plotSizeDistribution	6.040	0.016	6.056
plotStatistics	5.515	0.016	5.541
plotSubstitutions	3.851	0.012	3.865
readSortedBam	0.066	0.000	0.066