BioC 2.14: CHECK report for siggenes on petty

Package: siggenes

Version: 1.38.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch siggenes_1.38.0.tar.gz

StartedAt: 2014-10-08 00:08:16 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 00:10:30 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 134.5 seconds

RetCode: 0

Status:  OK

CheckDir: siggenes.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch siggenes_1.38.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/siggenes.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘siggenes/DESCRIPTION’ ... OK
* this is package ‘siggenes’ version ‘1.38.0’
* 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 ... [8s/11s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 dependencies in R code ... NOTE
'library' or 'require' call to ‘splines’ which was already attached by Depends.
  Please remove these calls from your code.
Unexported object imported by a ':::' call: ‘annotate:::getTDRows’
  See the note in ?`:::` about the use of this operator.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call to 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [3s/3s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-2.14-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
** testing if installed package can be loaded
* DONE (siggenes)

name	user	system	elapsed
EBAM-class	0.002	0.001	0.071
SAM-class	0.004	0.000	0.004
chisq.ebam	0.003	0.000	0.018
chisq.stat	0.003	0.000	0.003
delta.plot	0.001	0.000	0.002
denspr	0.001	0.000	0.002
ebam	0.005	0.001	0.005
find.a0	0.002	0.000	0.002
help.ebam	0.001	0.000	0.001
help.finda0	0.001	0.001	0.001
help.sam	0.001	0.000	0.001
list.siggenes	0.001	0.000	0.001
md.plot	0.001	0.000	0.002
pi0.est	0.002	0.000	0.002
qvalue.cal	0.002	0.001	0.002
sam	0.004	0.001	0.005
sam.plot2	0.002	0.000	0.002
trend.ebam	0.003	0.000	0.003
trend.stat	0.003	0.000	0.003