Package: R453Plus1Toolbox

Version: 1.1.2

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch R453Plus1Toolbox_1.1.2.tar.gz

StartedAt: 2011-02-24 20:55:44 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 21:00:13 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 268.9 seconds

RetCode: 0

Status:  OK

CheckDir: R453Plus1Toolbox.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.8-bioc/meat/R453Plus1Toolbox.Rcheck’
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘R453Plus1Toolbox/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘R453Plus1Toolbox’ version ‘1.1.2’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘R453Plus1Toolbox’ can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.getMutations: no visible binding for global variable ‘PatternStart’
.getMutations: no visible binding for global variable ‘PatternEnd’
.htmlReport: no visible binding for global variable ‘VarFreqForward’
.htmlReport: no visible binding for global variable ‘VarFreqReverse’
* 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 data for non-ASCII characters ... OK
* checking examples ... OK
* checking package vignettes in ‘inst/doc’ ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package ‘R453Plus1Toolbox’ ...
** R
** data
** inst
** preparing package for lazy loading

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: IRanges

Attaching package: 'IRanges'

The following object(s) are masked from 'package:Biobase':

    updateObject

The following object(s) are masked from 'package:base':

    Map, cbind, eval, intersect, mapply, order, paste, pmax, pmax.int,
    pmin, pmin.int, rbind, rep.int, setdiff, table, union

Loading required package: BSgenome
Loading required package: GenomicRanges
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (R453Plus1Toolbox)

name	user	system	elapsed
AVASet-class	0.14	0.01	0.15
AVASet	0.040	0.001	0.042
AnnotatedVariants-class	0.005	0.001	0.005
MapperSet-class	0.065	0.013	0.080
MapperSet	0.014	0.001	0.015
alignShortReads	1.200	0.008	1.225
annotateVariants	0.004	0.000	0.005
assayDataAmp	0.010	0.001	0.011
avaSetExample	0.034	0.004	0.040
avaSetFiltered	0.069	0.008	0.077
avaSetFiltered_annot	0.004	0.001	0.004
breakpoints	0.006	0.001	0.008
calculateTiTv	0.030	0.005	0.035
captureArray	0.003	0.001	0.004
coverageOnTarget	0.563	0.018	0.589
demultiplexReads	0.358	0.004	0.362
detectBreakpoints	0.858	0.018	0.896
fDataAmp	0.039	0.002	0.041
featureDataAmp	0.034	0.001	0.035
filterChimericReads	2.769	0.018	2.796
genomeSequencerMIDs	0.078	0.001	0.079
getAlignedReads	0.265	0.005	0.270
getVariantPercentages	0.084	0.002	0.086
htmlReport	8.218	0.345	8.919
mapperSetExample	0.014	0.002	0.015
mergeBreakpoints	12.547	1.431	14.099
plotAmpliconCoverage	0	0	0
plotChimericReads	7.961	0.014	7.974
plotVariants	0.003	0.000	0.004
plotVariationFrequency	0.000	0.001	0.000
readsOnTarget	0.915	0.011	0.928
referenceSequences	0.015	0.001	0.017
removeLinker	0.052	0.001	0.053
sequenceCaptureLinkers	0.012	0.001	0.012
setVariantFilter	0.146	0.003	0.150
transcriptdf	0.003	0.001	0.003