Package: htSeqTools

Version: 0.99.1

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch htSeqTools_0.99.1.tar.gz

StartedAt: 2011-07-07 03:50:21 -0700 (Thu, 07 Jul 2011)

EndedAt: 2011-07-07 03:53:31 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 189.8 seconds

RetCode: 0

Status:  OK

CheckDir: htSeqTools.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/htSeqTools.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-22 r56208)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'htSeqTools/DESCRIPTION' ... OK
* this is package 'htSeqTools' version '0.99.1'
* checking package name space information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: multicore
* checking if this is a source package ... OK
* checking whether package 'htSeqTools' 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 ... OK
* 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' ... 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 'htSeqTools' ...
** 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")'.


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: GenomicRanges
Loading required package: Biostrings
Creating a generic function for "plot" from package "graphics" in package "htSeqTools"
Creating a generic function for "lines" from package "graphics" in package "htSeqTools"
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'htSeqTools.Rnw' 
** testing if installed package can be loaded

* DONE (htSeqTools)

name	user	system	elapsed
alignPeaks	0.269	0.006	0.277
cmds	5.158	0.660	6.129
cmdsFit-class	0.001	0.000	0.001
cmdsFit	0.003	0.000	0.003
countHitsWindow	0.099	0.004	0.102
coverageDiff	0.203	0.015	0.219
enrichedChrRegions	2.780	0.011	2.827
enrichedPeaks	1.004	0.007	1.076
enrichedRegions	0.363	0.003	0.370
extendRanges	0.439	0.006	0.448
fdrEnrichedCounts	0.318	0.067	0.389
filterDuplReads	0.660	0.064	0.736
giniCoverage	0.623	0.011	0.643
gridCover-class	0	0	0
htSample	0.688	0.022	0.718
islandCounts	0.430	0.004	0.439
listOverlap	0.01	0.00	0.01
mergeRegions	0.093	0.001	0.096
plot-methods	0.004	0.000	0.005
plotChrRegions	0.029	0.001	0.029
regionsCoverage	0	0	0
rowLogRegLRT	0.004	0.001	0.004
ssdCoverage	0.517	0.003	0.527
stdPeakLocation	0.140	0.002	0.143