Package: leeBamViews

Version: 0.99.20

Command: /home/biocbuild/bbs-2.11-bioc/R/bin/R CMD check --no-vignettes --timings leeBamViews_0.99.20.tar.gz

StartedAt: 2013-01-10 12:51:21 -0800 (Thu, 10 Jan 2013)

EndedAt: 2013-01-10 12:54:13 -0800 (Thu, 10 Jan 2013)

EllapsedTime: 171.7 seconds

RetCode: 0

Status:  OK

CheckDir: leeBamViews.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.11-data-experiment/meat/leeBamViews.Rcheck’
* using R version 2.15.2 (2012-10-26)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘leeBamViews/DESCRIPTION’ ... OK
* this is package ‘leeBamViews’ version ‘0.99.20’
* 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 11.3Mb
  sub-directories of 1Mb or more:
    bam  10.1Mb
* 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 for left-over 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
tabulateReads,BamViews-characterORNULL-missing-missing: no visible
  binding for global variable ‘mclapply’
tabulateReads,BamViews-missing-missing-missing: no visible binding for
  global variable ‘mclapply’
* 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 installed files from ‘inst/doc’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
tabulateReads 9.161  0.176   9.356* 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

NOTE: There were 4 notes.
See
  ‘/loc/home/biocbuild/bbs-2.11-data-experiment/meat/leeBamViews.Rcheck/00check.log’
for details.

* installing *source* package ‘leeBamViews’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘leeViews.Rnw’ 
** testing if installed package can be loaded

* DONE (leeBamViews)

name	user	system	elapsed
bs1	1.464	0.136	1.742
leeRPKM	0.052	0.000	0.055
leeUnn	0.068	0.004	0.069
tabulateReads	9.161	0.176	9.356
totalReadCounts	1.732	0.036	1.885