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BioC 3.2: CHECK report for wavClusteR on zin1

This page was generated on 2015-08-24 10:49:57 -0700 (Mon, 24 Aug 2015).

Package 1059/1071HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
wavClusteR 2.3.1
Federico Comoglio
Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/wavClusteR
Last Changed Rev: 103420 / Revision: 107696
Last Changed Date: 2015-05-03 12:29:41 -0700 (Sun, 03 May 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: wavClusteR
Version: 2.3.1
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings wavClusteR_2.3.1.tar.gz
StartedAt: 2015-08-24 04:41:18 -0700 (Mon, 24 Aug 2015)
EndedAt: 2015-08-24 04:44:54 -0700 (Mon, 24 Aug 2015)
EllapsedTime: 215.8 seconds
RetCode: 0
Status:  OK 
CheckDir: wavClusteR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings wavClusteR_2.3.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/wavClusteR.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘2.3.1’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘doMC’
* 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/17s] 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’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [54s/54s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
annotateClusters 6.349  0.064   6.408
getMetaCoverage  5.073  0.008   5.082
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/wavClusteR.Rcheck/00check.log’
for details.

wavClusteR.Rcheck/00install.out:

* 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)

wavClusteR.Rcheck/wavClusteR-Ex.timings:

nameusersystemelapsed
FitMixtureModel0.0340.0000.034
annotateClusters6.3490.0646.408
filterClusters4.9520.0164.976
getAllSub3.6350.0003.648
getClusters4.4470.0074.467
getExpInterval0.0380.0000.038
getHighConfSub3.7890.0003.797
getMetaCoverage5.0730.0085.082
getMetaGene4.9600.0124.982
getMetaTSS0.1300.0040.134
plotSizeDistribution4.8140.0164.826
plotStatistics4.7950.0124.804
plotSubstitutions3.4330.0043.435
readSortedBam0.0550.0160.071