Package: R453Plus1Toolbox

Version: 1.2.2

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch R453Plus1Toolbox_1.2.2.tar.gz

StartedAt: 2011-10-20 16:46:37 -0700 (Thu, 20 Oct 2011)

EndedAt: 2011-10-20 16:51:53 -0700 (Thu, 20 Oct 2011)

EllapsedTime: 316.7 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 2.13.2 (2011-09-30)
* 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 '1.2.2'
* checking package namespace 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 namespace can be loaded with stated dependencies ... OK
* checking whether the namespace 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 343Kb to 235Kb
  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
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (R453Plus1Toolbox)

name	user	system	elapsed
AVASet-class	0.141	0.013	0.156
AVASet	0.030	0.002	0.032
AnnotatedVariants-class	0.004	0.001	0.004
MapperSet-class	0.051	0.014	0.068
MapperSet	0.014	0.001	0.015
alignShortReads	0.985	0.006	1.019
annotateVariants	0.003	0.000	0.003
assayDataAmp	0.009	0.002	0.010
avaSetExample	0.033	0.005	0.038
avaSetFiltered	0.071	0.011	0.086
avaSetFiltered_annot	0.003	0.001	0.005
breakpoints	0.006	0.001	0.009
calculateTiTv	0.032	0.006	0.041
captureArray	0.004	0.001	0.004
coverageOnTarget	0.754	0.019	0.805
demultiplexReads	0.161	0.002	0.164
detectBreakpoints	0.846	0.020	1.022
fDataAmp	0.034	0.002	0.036
featureDataAmp	0.033	0.002	0.034
filterChimericReads	2.767	0.021	2.941
genomeSequencerMIDs	0.073	0.001	0.074
getAlignedReads	0.240	0.005	0.246
getVariantPercentages	0.086	0.003	0.095
htmlReport	8.079	0.349	9.382
mapperSetExample	0.013	0.001	0.015
mergeBreakpoints	12.321	1.454	13.922
plotAmpliconCoverage	0	0	0
plotChimericReads	7.771	0.020	7.838
plotVariants	0.002	0.000	0.002
plotVariationFrequency	0	0	0
readsOnTarget	0.917	0.010	0.933
referenceSequences	0.015	0.001	0.016
removeLinker	0.053	0.001	0.054
sequenceCaptureLinkers	0.012	0.001	0.012
setVariantFilter	0.150	0.004	0.153
transcriptdf	0.002	0.001	0.003