BioC 3.3: CHECK report for wavClusteR on windows2.bioconductor.org
This page was generated on 2015-10-27 12:15:38 -0400 (Tue, 27 Oct 2015).
wavClusteR 2.5.0
Federico Comoglio
| Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/wavClusteR | | Last Changed Rev: 109592 / Revision: 109948 | | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | [ OK ] | OK | |
Summary
| Package: wavClusteR
|
| Version: 2.5.0
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| Command: rm -rf wavClusteR.buildbin-libdir wavClusteR.Rcheck && mkdir wavClusteR.buildbin-libdir wavClusteR.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=wavClusteR.buildbin-libdir wavClusteR_2.5.0.tar.gz >wavClusteR.Rcheck\00install.out 2>&1 && cp wavClusteR.Rcheck\00install.out wavClusteR-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=wavClusteR.buildbin-libdir --install="check:wavClusteR-install.out" --force-multiarch --no-vignettes --timings wavClusteR_2.5.0.tar.gz
|
| StartedAt: 2015-10-27 06:50:52 -0400 (Tue, 27 Oct 2015)
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| EndedAt: 2015-10-27 06:55:43 -0400 (Tue, 27 Oct 2015)
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| EllapsedTime: 290.6 seconds
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| RetCode: 0
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| Status: OK
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| CheckDir: wavClusteR.Rcheck
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| Warnings: 0
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Command output
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### Running command:
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### rm -rf wavClusteR.buildbin-libdir wavClusteR.Rcheck && mkdir wavClusteR.buildbin-libdir wavClusteR.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=wavClusteR.buildbin-libdir wavClusteR_2.5.0.tar.gz >wavClusteR.Rcheck\00install.out 2>&1 && cp wavClusteR.Rcheck\00install.out wavClusteR-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=wavClusteR.buildbin-libdir --install="check:wavClusteR-install.out" --force-multiarch --no-vignettes --timings wavClusteR_2.5.0.tar.gz
###
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* using log directory 'c:/biocbld/bbs-3.3-bioc/meat/wavClusteR.Rcheck'
* using R Under development (unstable) (2015-09-22 r69418)
* 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 '2.5.0'
* 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'
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 ...
** running examples for arch 'i386' ... [40s] OK
** running examples for arch 'x64' ... [53s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
getMetaCoverage 5.87 0.02 5.90
annotateClusters 5.77 0.03 5.79
plotSizeDistribution 5.71 0.02 5.74
* 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
'c:/biocbld/bbs-3.3-bioc/meat/wavClusteR.Rcheck/00check.log'
for details.
wavClusteR.Rcheck/00install.out:
install for i386
* 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
install for x64
* installing *source* package 'wavClusteR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'wavClusteR' as wavClusteR_2.5.0.zip
* DONE (wavClusteR)
wavClusteR.Rcheck/examples_i386/wavClusteR-Ex.timings:
| name | user | system | elapsed
|
| FitMixtureModel | 0.02 | 0.04 | 0.05 |
|
| annotateClusters | 4.68 | 0.12 | 4.81 |
|
| filterClusters | 3.63 | 0.03 | 3.66 |
|
| getAllSub | 2.65 | 0.00 | 2.66 |
|
| getClusters | 3.54 | 0.02 | 3.54 |
|
| getExpInterval | 0.04 | 0.00 | 0.05 |
|
| getHighConfSub | 2.62 | 0.00 | 2.63 |
|
| getMetaCoverage | 3.94 | 0.01 | 3.95 |
|
| getMetaGene | 3.48 | 0.00 | 3.49 |
|
| getMetaTSS | 0.1 | 0.0 | 0.1 |
|
| plotSizeDistribution | 3.73 | 0.00 | 3.73 |
|
| plotStatistics | 3.58 | 0.06 | 3.64 |
|
| plotSubstitutions | 2.59 | 0.00 | 2.60 |
|
| readSortedBam | 0.08 | 0.00 | 0.07 |
|
wavClusteR.Rcheck/examples_x64/wavClusteR-Ex.timings:
| name | user | system | elapsed
|
| FitMixtureModel | 0.03 | 0.00 | 0.03 |
|
| annotateClusters | 5.77 | 0.03 | 5.79 |
|
| filterClusters | 4.59 | 0.00 | 4.60 |
|
| getAllSub | 3.27 | 0.00 | 3.26 |
|
| getClusters | 4.21 | 0.02 | 4.24 |
|
| getExpInterval | 0.05 | 0.00 | 0.05 |
|
| getHighConfSub | 4.08 | 0.03 | 4.10 |
|
| getMetaCoverage | 5.87 | 0.02 | 5.90 |
|
| getMetaGene | 4.63 | 0.01 | 4.64 |
|
| getMetaTSS | 0.16 | 0.01 | 0.17 |
|
| plotSizeDistribution | 5.71 | 0.02 | 5.74 |
|
| plotStatistics | 4.72 | 0.01 | 4.73 |
|
| plotSubstitutions | 3.50 | 0.02 | 3.52 |
|
| readSortedBam | 0.08 | 0.01 | 0.09 |
|