Package: R453Plus1Toolbox

Version: 1.2.2

Command: /home/biocbuild/bbs-2.8-bioc/R/bin/R CMD check --no-vignettes --timings R453Plus1Toolbox_1.2.2.tar.gz

StartedAt: 2011-10-20 14:04:47 -0700 (Thu, 20 Oct 2011)

EndedAt: 2011-10-20 14:08:43 -0700 (Thu, 20 Oct 2011)

EllapsedTime: 236.2 seconds

RetCode: 0

Status:  OK

CheckDir: R453Plus1Toolbox.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.8-bioc/meat/R453Plus1Toolbox.Rcheck’
* using R version 2.13.2 (2011-09-30)
* using platform: x86_64-unknown-linux-gnu (64-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 ‘1.2.2’
* 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 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	0.356	0.004	0.370
AVASet	0.020	0.000	0.022
AnnotatedVariants-class	0.004	0.000	0.003
MapperSet-class	0.040	0.008	0.045
MapperSet	0.008	0.000	0.010
alignShortReads	1.272	0.008	1.308
annotateVariants	0.000	0.000	0.002
assayDataAmp	0.000	0.004	0.014
avaSetExample	0.024	0.000	0.025
avaSetFiltered	0.044	0.004	0.048
avaSetFiltered_annot	0.004	0.000	0.003
breakpoints	0.004	0.000	0.004
calculateTiTv	0.016	0.004	0.021
captureArray	0.000	0.000	0.003
coverageOnTarget	0.676	0.008	0.686
demultiplexReads	0.112	0.000	0.111
detectBreakpoints	0.572	0.012	0.600
fDataAmp	0.024	0.000	0.032
featureDataAmp	0.024	0.000	0.024
filterChimericReads	2.012	0.000	2.013
genomeSequencerMIDs	0.060	0.000	0.059
getAlignedReads	0.188	0.004	0.191
getVariantPercentages	0.064	0.000	0.068
htmlReport	5.205	0.080	5.340
mapperSetExample	0.012	0.000	0.010
mergeBreakpoints	8.472	0.180	8.979
plotAmpliconCoverage	0	0	0
plotChimericReads	5.601	0.008	5.695
plotVariants	0.000	0.000	0.002
plotVariationFrequency	0.000	0.000	0.001
readsOnTarget	0.636	0.000	0.649
referenceSequences	0.012	0.000	0.010
removeLinker	0.036	0.000	0.036
sequenceCaptureLinkers	0.008	0.000	0.008
setVariantFilter	0.112	0.000	0.111
transcriptdf	0.004	0.000	0.002