Package: leeBamViews

Version: 0.99.13

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch leeBamViews_0.99.13.tar.gz

StartedAt: 2012-03-02 14:17:58 -0800 (Fri, 02 Mar 2012)

EndedAt: 2012-03-02 14:21:57 -0800 (Fri, 02 Mar 2012)

EllapsedTime: 239.4 seconds

RetCode: 0

Status:  OK

CheckDir: leeBamViews.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.9-data-experiment/meat/leeBamViews.Rcheck'
* using R version 2.14.2 (2012-02-29)
* 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 '0.99.13'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package 'leeBamViews' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 11.6Mb
  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 ... NOTE
Non-standard license specification:
  Artistic 2.0
Standardizable: TRUE
Standardized license specification:
  Artistic-2.0
* 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 ... 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 ... NOTE
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
              old_size new_size compress
  leeRPKM.rda    275Kb    180Kb       xz
  leeUnn.rda     752Kb    506Kb       xz
* checking sizes of PDF files under 'inst/doc' ... OK
* 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
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'leeViews.Rnw' 
** testing if installed package can be loaded

* DONE (leeBamViews)

name	user	system	elapsed
bs1	1.837	0.101	2.044
leeRPKM	0.064	0.004	0.078
leeUnn	0.387	0.007	0.399
tabulateReads	11.523	0.302	11.915
totalReadCounts	2.007	0.112	2.234