wavClusteR 2.2.0
Federico Comoglio
| Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/wavClusteR | | Last Changed Rev: 102591 / Revision: 109384 | | Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK | |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | [ OK ] | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings wavClusteR_2.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/wavClusteR.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘2.2.0’
* 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 ... [27s/28s] 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 ... [95s/95s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
annotateClusters 10.829 0.129 10.962
plotStatistics 9.721 0.041 9.786
getMetaCoverage 8.980 0.047 9.033
filterClusters 8.331 0.060 8.392
plotSizeDistribution 8.198 0.043 8.359
getMetaGene 8.144 0.038 8.184
getClusters 8.056 0.072 8.135
plotSubstitutions 6.501 0.029 6.541
getHighConfSub 6.211 0.025 6.240
getAllSub 5.234 0.022 5.256
* 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
‘/Users/biocbuild/bbs-3.1-bioc/meat/wavClusteR.Rcheck/00check.log’
for details.
* installing *source* package ‘wavClusteR’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (wavClusteR)