Package: R453Plus1Toolbox

Version: 1.3.1

Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings R453Plus1Toolbox_1.3.1.tar.gz

StartedAt: 2011-07-07 01:57:47 -0700 (Thu, 07 Jul 2011)

EndedAt: 2011-07-07 02:01:53 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 246.2 seconds

RetCode: 0

Status:  OK

CheckDir: R453Plus1Toolbox.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/R453Plus1Toolbox.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-06-15 r56138)
* 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 ‘1.3.1’
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... 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’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c readSFF.c -o readSFF.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o R453Plus1Toolbox.so readSFF.o -L/home/biocbuild/bbs-2.9-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.9-bioc/meat/R453Plus1Toolbox.Rcheck/R453Plus1Toolbox/libs
** 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
Creating a new generic function for “name” in package “R453Plus1Toolbox”
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘vignette.Rnw’ 
** testing if installed package can be loaded
Warning message:
multiple methods tables found for ‘name’ 

* DONE (R453Plus1Toolbox)

name	user	system	elapsed
AVASet-class	0.084	0.004	0.090
AVASet	0.024	0.000	0.025
AnnotatedVariants-class	0.004	0.000	0.003
MapperSet-class	0.040	0.008	0.047
MapperSet	0.012	0.000	0.010
SFFContainer-class	0.000	0.000	0.001
SFFRead-class	0.004	0.000	0.001
alignShortReads	1.372	0.004	1.395
annotateVariants	0.000	0.000	0.002
assayDataAmp	0.004	0.000	0.007
avaSetExample	0.024	0.004	0.025
avaSetFiltered	0.036	0.016	0.051
avaSetFiltered_annot	0.004	0.000	0.003
breakpoints	0.000	0.004	0.005
calculateTiTv	0.012	0.012	0.022
captureArray	0.004	0.000	0.003
coverageOnTarget	0.680	0.076	0.756
demultiplexReads	0.104	0.000	0.105
detectBreakpoints	0.540	0.004	0.555
fDataAmp	0.024	0.000	0.024
featureDataAmp	0.024	0.000	0.023
filterChimericReads	1.928	0.032	1.968
genomeSequencerMIDs	0.048	0.000	0.051
getAlignedReads	0.168	0.004	0.170
getVariantPercentages	0.064	0.000	0.064
htmlReport	4.981	0.084	5.153
mapperSetExample	0.012	0.000	0.010
mergeBreakpoints	8.252	0.136	8.392
plotAmpliconCoverage	0	0	0
plotChimericReads	5.961	0.004	5.998
plotVariants	0.000	0.000	0.002
plotVariationFrequency	0	0	0
readSFF	0	0	0
readsOnTarget	0.676	0.052	0.729
referenceSequences	0.008	0.000	0.010
removeLinker	0.032	0.000	0.034
sequenceCaptureLinkers	0.012	0.000	0.009
setVariantFilter	0.116	0.000	0.118
transcriptdf	0.000	0.000	0.002