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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### rm -rf wavClusteR.buildbin-libdir wavClusteR.Rcheck && mkdir wavClusteR.buildbin-libdir wavClusteR.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=wavClusteR.buildbin-libdir wavClusteR_2.2.0.tar.gz >wavClusteR.Rcheck\00install.out 2>&1 && cp wavClusteR.Rcheck\00install.out wavClusteR-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=wavClusteR.buildbin-libdir --install="check:wavClusteR-install.out" --force-multiarch --no-vignettes --timings wavClusteR_2.2.0.tar.gz
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* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/wavClusteR.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [64s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
getMetaCoverage 6.85 0.02 6.86
annotateClusters 6.77 0.05 6.82
filterClusters 5.63 0.01 5.64
plotSizeDistribution 5.43 0.03 5.46
plotStatistics 5.41 0.02 5.42
getMetaGene 5.28 0.05 5.32
getClusters 5.20 0.02 5.21
** running examples for arch 'x64' ... [71s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
annotateClusters 7.55 0.08 7.63
getClusters 7.12 0.01 7.13
plotSizeDistribution 6.90 0.03 6.96
getMetaCoverage 6.85 0.05 6.89
getMetaGene 6.12 0.00 6.11
filterClusters 5.96 0.03 5.99
plotStatistics 5.97 0.01 6.01
getHighConfSub 5.51 0.00 5.51
plotSubstitutions 5.26 0.02 5.27
* 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
'E:/biocbld/bbs-3.1-bioc/meat/wavClusteR.Rcheck/00check.log'
for details.
install for i386
* 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'
install for x64
* installing *source* package 'wavClusteR' ...
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
* MD5 sums
packaged installation of 'wavClusteR' as wavClusteR_2.2.0.zip
* DONE (wavClusteR)