Package: Rcade

Version: 1.1.1

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings Rcade_1.1.1.tar.gz

StartedAt: 2013-01-16 05:43:22 -0800 (Wed, 16 Jan 2013)

EndedAt: 2013-01-16 05:46:31 -0800 (Wed, 16 Jan 2013)

EllapsedTime: 188.5 seconds

RetCode: 0

Status:  OK

CheckDir: Rcade.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/Rcade.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rcade/DESCRIPTION’ ... OK
* this is package ‘Rcade’ version ‘1.1.1’
* 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 for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Rcade’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.7Mb
  sub-directories of 1Mb or more:
    extdata   5.2Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 ... OK
* checking Rd files ... NOTE
prepare_Rd: constructRcadeTable.Rd:43-45: Dropping empty section \details
prepare_Rd: constructRcadeTable.Rd:46-52: Dropping empty section \value
prepare_Rd: constructRcadeTable.Rd:59-61: Dropping empty section \note
prepare_Rd: constructRcadeTable.Rd:56-58: Dropping empty section \author
prepare_Rd: constructRcadeTable.Rd:53-55: Dropping empty section \references
prepare_Rd: diffCountsBaySeq.Rd:58-60: Dropping empty section \note
prepare_Rd: diffCountsBaySeq.Rd:54-56: Dropping empty section \references
* 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
diffCountsBaySeq 14.637  0.020  14.658
RcadeAnalysis    14.093  0.072  15.225
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’
 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

NOTE: There were 3 notes.
See
  ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/Rcade.Rcheck/00check.log’
for details.

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

* DONE (Rcade)

name	user	system	elapsed
Rcade-class	0.176	0.040	0.694
RcadeAnalysis	14.093	0.072	15.225
RcadeSTAT1	0.016	0.000	0.017
constructRcadeTable	0.028	0.004	0.034
countReads	4.860	0.012	4.875
defineBins	0.048	0.000	0.046
diffCountsBaySeq	14.637	0.020	14.658
exportRcade-methods	0.008	0.000	0.009