Package: bumphunter

Version: 0.99.25

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings bumphunter_0.99.25.tar.gz

StartedAt: 2013-01-16 01:09:55 -0800 (Wed, 16 Jan 2013)

EndedAt: 2013-01-16 01:12:56 -0800 (Wed, 16 Jan 2013)

EllapsedTime: 180.8 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: bumphunter.Rcheck

Warnings: 3

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/bumphunter.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 ‘bumphunter/DESCRIPTION’ ... OK
* this is package ‘bumphunter’ version ‘0.99.25’
* 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 ‘bumphunter’ 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 ... OK
* checking R code for possible problems ... OK
* checking Rd files ... NOTE
prepare_Rd: matchGenes.Rd:19-20: Dropping empty section \details
prepare_Rd: matchGenes.Rd:38-39: Dropping empty section \examples
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Data with usage in documentation object 'TT' but not in code:
  TT

Codoc mismatches from documentation object 'matchGenes':
matchGenes
  Code: function(object, promoterDist = 2500, verbose = TRUE, all =
                 FALSE, genes = NULL, nexons = NULL, EXONS = NULL, job
                 = 0, mc.cores = 1)
  Docs: function(x, subject, annotate = TRUE, ...)
  Argument names in code not in docs:
    object promoterDist verbose all genes nexons EXONS job mc.cores
  Argument names in docs not in code:
    x subject annotate ...
  Mismatches in argument names (first 3):
    Position: 1 Code: object Docs: x
    Position: 2 Code: promoterDist Docs: subject
    Position: 3 Code: verbose Docs: annotate

* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'matchGenes'
  ‘x’ ‘subject’ ‘annotate’ ‘...’
Documented arguments not in \usage in documentation object 'matchGenes':
  ‘object’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See the chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... WARNING
Argument items with no description in Rd object 'matchGenes':
  ‘object’

* checking for unstated dependencies in examples ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
bumphunter 9.904  0.888   8.073
* 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

WARNING: There were 3 warnings.
NOTE: There was 1 note.
See
  ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/bumphunter.Rcheck/00check.log’
for details.

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

* DONE (bumphunter)

name	user	system	elapsed
annotateNearest	0.152	0.016	0.167
bumphunter	9.904	0.888	8.073
clusterMaker	0.036	0.000	0.033
dummyData	0.016	0.000	0.015
getSegments	0.020	0.000	0.021
loessByCluster	0.560	0.012	0.576
pointMatch	0.412	0.004	0.416
regionFinder	0.056	0.000	0.057
runmedByCluster	0.276	0.008	0.286
smoother	0.912	0.128	0.284