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: 2011-03-17 17:12:57 -0700 (Thu, 17 Mar 2011)

EndedAt: 2011-03-17 17:16:48 -0700 (Thu, 17 Mar 2011)

EllapsedTime: 230.5 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) (2011-03-06 r54683)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* 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 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 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	0.246	0.004	0.251
AVASet	0.024	0.001	0.025
AnnotatedVariants-class	0.003	0.001	0.003
MapperSet-class	0.042	0.010	0.053
MapperSet	0.010	0.000	0.011
alignShortReads	0.809	0.002	0.827
annotateVariants	0.002	0.001	0.002
assayDataAmp	0.007	0.001	0.008
avaSetExample	0.025	0.003	0.028
avaSetFiltered	0.052	0.005	0.056
avaSetFiltered_annot	0.002	0.000	0.003
breakpoints	0.004	0.000	0.005
calculateTiTv	0.022	0.003	0.024
captureArray	0.003	0.001	0.003
coverageOnTarget	0.427	0.013	0.452
demultiplexReads	0.122	0.001	0.123
detectBreakpoints	0.782	0.004	0.807
fDataAmp	0.028	0.001	0.029
featureDataAmp	0.026	0.001	0.027
filterChimericReads	1.995	0.004	2.000
genomeSequencerMIDs	0.057	0.000	0.058
getAlignedReads	0.195	0.002	0.198
getVariantPercentages	0.066	0.002	0.067
htmlReport	6.468	0.332	7.243
mapperSetExample	0.010	0.001	0.011
mergeBreakpoints	9.505	0.677	10.236
plotAmpliconCoverage	0	0	0
plotChimericReads	5.916	0.006	5.922
plotVariants	0.002	0.001	0.002
plotVariationFrequency	0	0	0
readsOnTarget	0.692	0.004	0.696
referenceSequences	0.010	0.001	0.011
removeLinker	0.039	0.000	0.039
sequenceCaptureLinkers	0.009	0.000	0.008
setVariantFilter	0.108	0.002	0.109
transcriptdf	0.002	0.000	0.002