Package: R453Plus1Toolbox

Version: 1.3.0

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch R453Plus1Toolbox_1.3.0.tar.gz

StartedAt: 2011-05-09 16:28:53 -0700 (Mon, 09 May 2011)

EndedAt: 2011-05-09 16:34:14 -0700 (Mon, 09 May 2011)

EllapsedTime: 320.7 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) (2011-04-24 r55634)
* 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 ‘1.3.0’
* 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’ ... NOTE
  ‘qpdf’ made some significant size reductions:
     compacted ‘vignette.pdf’ from 317Kb to 178Kb
  consider running tools::compactPDF() on these files
* 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	0.328	0.008	0.336
AVASet	0.034	0.004	0.038
AnnotatedVariants-class	0.009	0.000	0.010
MapperSet-class	0.065	0.013	0.078
MapperSet	0.013	0.001	0.014
alignShortReads	1.046	0.006	1.071
annotateVariants	0.004	0.000	0.005
assayDataAmp	0.010	0.001	0.011
avaSetExample	0.034	0.005	0.040
avaSetFiltered	0.068	0.010	0.077
avaSetFiltered_annot	0.004	0.001	0.005
breakpoints	0.006	0.001	0.007
calculateTiTv	0.031	0.005	0.036
captureArray	0.003	0.002	0.004
coverageOnTarget	0.575	0.025	0.618
demultiplexReads	0.380	0.004	0.385
detectBreakpoints	0.818	0.010	0.842
fDataAmp	0.036	0.002	0.038
featureDataAmp	0.034	0.002	0.036
filterChimericReads	2.687	0.018	2.714
genomeSequencerMIDs	0.070	0.001	0.072
getAlignedReads	0.252	0.005	0.258
getVariantPercentages	0.081	0.003	0.084
htmlReport	8.244	0.368	9.257
mapperSetExample	0.013	0.001	0.014
mergeBreakpoints	12.393	1.517	14.216
plotAmpliconCoverage	0	0	0
plotChimericReads	7.950	0.019	8.045
plotVariants	0.005	0.000	0.009
plotVariationFrequency	0	0	0
readsOnTarget	0.932	0.013	0.973
referenceSequences	0.015	0.001	0.016
removeLinker	0.053	0.001	0.055
sequenceCaptureLinkers	0.012	0.000	0.012
setVariantFilter	0.145	0.005	0.159
transcriptdf	0.003	0.001	0.004