Package: R453Plus1Toolbox

Version: 1.3.1

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch R453Plus1Toolbox_1.3.1.tar.gz

StartedAt: 2011-06-16 04:40:21 -0700 (Thu, 16 Jun 2011)

EndedAt: 2011-06-16 04:45:44 -0700 (Thu, 16 Jun 2011)

EllapsedTime: 323.5 seconds

RetCode: 0

Status:  OK

CheckDir: R453Plus1Toolbox.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.9-bioc/meat/R453Plus1Toolbox.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-06-03 r56037)
* 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 ‘1.3.1’
* 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 installed package size ... 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 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 examples ... OK
* 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 vignettes ... 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 ...
*** tangling vignette sources ...
   ‘vignette.Rnw’ 
** testing if installed package can be loaded

* DONE (R453Plus1Toolbox)

name	user	system	elapsed
AVASet-class	0.138	0.008	0.147
AVASet	0.038	0.004	0.042
AnnotatedVariants-class	0.005	0.001	0.005
MapperSet-class	0.064	0.013	0.078
MapperSet	0.013	0.001	0.014
alignShortReads	1.044	0.006	1.082
annotateVariants	0.004	0.001	0.004
assayDataAmp	0.010	0.002	0.012
avaSetExample	0.034	0.005	0.039
avaSetFiltered	0.067	0.009	0.075
avaSetFiltered_annot	0.004	0.001	0.005
breakpoints	0.006	0.001	0.007
calculateTiTv	0.030	0.005	0.042
captureArray	0.004	0.001	0.005
coverageOnTarget	0.587	0.024	0.617
demultiplexReads	0.354	0.004	0.361
detectBreakpoints	0.768	0.010	0.797
fDataAmp	0.035	0.001	0.037
featureDataAmp	0.033	0.001	0.035
filterChimericReads	2.818	0.018	2.841
genomeSequencerMIDs	0.069	0.001	0.070
getAlignedReads	0.246	0.005	0.251
getVariantPercentages	0.088	0.004	0.092
htmlReport	8.187	0.380	9.180
mapperSetExample	0.014	0.001	0.015
mergeBreakpoints	12.361	1.549	14.039
plotAmpliconCoverage	0.000	0.000	0.001
plotChimericReads	7.608	0.020	7.680
plotVariants	0.004	0.000	0.004
plotVariationFrequency	0	0	0
readsOnTarget	0.899	0.010	0.913
referenceSequences	0.015	0.002	0.017
removeLinker	0.043	0.001	0.045
sequenceCaptureLinkers	0.012	0.001	0.012
setVariantFilter	0.145	0.007	0.156
transcriptdf	0.003	0.001	0.003