Package: siggenes

Version: 1.33.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings siggenes_1.33.0.tar.gz

StartedAt: 2013-01-16 06:20:52 -0800 (Wed, 16 Jan 2013)

EndedAt: 2013-01-16 06:22:04 -0800 (Wed, 16 Jan 2013)

EllapsedTime: 71.9 seconds

RetCode: 0

Status:  OK

CheckDir: siggenes.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/siggenes.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 ‘siggenes/DESCRIPTION’ ... OK
* this is package ‘siggenes’ version ‘1.33.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘siggenes’ can be installed ... OK
* checking installed package size ... OK
* 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 ... NOTE
Foreign function call with ‘PACKAGE’ argument in a different package:
  .C("get_stat_num_denum", ..., PACKAGE = "multtest")
See the chapter ‘System and foreign language interfaces’ of the
‘Writing R Extensions’ manual.
* 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 installed files from ‘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

NOTE: There was 1 note.
See
  ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/siggenes.Rcheck/00check.log’
for details.

* installing *source* package ‘siggenes’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘print’ from package ‘base’ in package ‘siggenes’
Creating a generic function for ‘identify’ from package ‘graphics’ in package ‘siggenes’
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘siggenes.Rnw’ 
** testing if installed package can be loaded

* DONE (siggenes)

name	user	system	elapsed
EBAM-class	0.016	0.008	0.022
SAM-class	0.028	0.004	0.029
chisq.ebam	0.020	0.004	0.024
chisq.stat	0.112	0.012	0.123
delta.plot	0.004	0.008	0.013
denspr	0.012	0.000	0.011
ebam	0.036	0.000	0.036
find.a0	0.020	0.000	0.019
help.ebam	0.000	0.008	0.009
help.finda0	0.008	0.000	0.009
help.sam	0.008	0.000	0.008
list.siggenes	0.012	0.000	0.012
md.plot	0.008	0.004	0.013
pi0.est	0.012	0.000	0.011
qvalue.cal	0.004	0.008	0.013
sam	0.028	0.008	0.038
sam.plot2	0.012	0.004	0.014
trend.ebam	0.012	0.012	0.024
trend.stat	0.012	0.012	0.022