Package: leeBamViews

Version: 0.99.11

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch leeBamViews_0.99.11.tar.gz

StartedAt: 2011-10-02 01:32:34 -0700 (Sun, 02 Oct 2011)

EndedAt: 2011-10-02 01:35:56 -0700 (Sun, 02 Oct 2011)

EllapsedTime: 201.7 seconds

RetCode: 0

Status:  OK

CheckDir: leeBamViews.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.8-data-experiment/meat/leeBamViews.Rcheck'
* using R version 2.13.1 (2011-07-08)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'leeBamViews/DESCRIPTION' ... OK
* this is package 'leeBamViews' version '0.99.11'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'leeBamViews' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 11.7Mb
  sub-directories of 1Mb or more:
    bam   10.1Mb
    data   1.0Mb
* 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 ... NOTE
  'qpdf' made some significant size reductions:
     compacted 'leeViews.pdf' from 365Kb to 183Kb
  consider running tools::compactPDF() on these files
* checking examples ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'lbvtest.R'
 OK
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: IRanges
* 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 'leeBamViews' ...
** 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: GenomicRanges
Loading required package: Biostrings
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (leeBamViews)

name	user	system	elapsed
bs1	2.427	0.106	3.790
leeRPKM	0.085	0.007	0.122
leeUnn	0.312	0.009	0.360
tabulateReads	15.143	0.335	16.638
totalReadCounts	3.046	0.145	3.309