Back to the "Multiple platform build/check report" A  B  C  D  E  F  G  H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V [W] X  Y  Z 

BioC 3.2: CHECK report for wavClusteR on oaxaca

This page was generated on 2016-04-23 10:27:55 -0700 (Sat, 23 Apr 2016).

Package 1091/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
wavClusteR 2.4.1
Federico Comoglio
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/wavClusteR
Last Changed Rev: 111848 / Revision: 116712
Last Changed Date: 2015-12-22 13:20:44 -0800 (Tue, 22 Dec 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  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: 2.4.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings wavClusteR_2.4.1.tar.gz
StartedAt: 2016-04-23 05:16:12 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 05:21:32 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 319.6 seconds
RetCode: 0
Status:  OK 
CheckDir: wavClusteR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings wavClusteR_2.4.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/wavClusteR.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘2.4.1’
* 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 ... [24s/26s] 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 ... [71s/73s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
annotateClusters 8.131  0.123   8.336
filterClusters   6.953  0.044   7.011
getClusters      6.642  0.037   6.692
plotStatistics   6.543  0.033   6.617
getMetaCoverage  6.369  0.026   6.405
getMetaGene      5.971  0.027   6.158
* 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
  ‘/Users/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
FitMixtureModel0.0330.0050.039
annotateClusters8.1310.1238.336
filterClusters6.9530.0447.011
getAllSub4.8000.0194.822
getClusters6.6420.0376.692
getExpInterval0.0370.0030.041
getHighConfSub4.6380.0224.664
getMetaCoverage6.3690.0266.405
getMetaGene5.9710.0276.158
getMetaTSS0.1470.0050.151
plotSizeDistribution3.6920.0234.568
plotStatistics6.5430.0336.617
plotSubstitutions4.5240.0164.544
readSortedBam0.0980.0100.108