BioC 2.12: CHECK report for SplicingGraphs on petty

Package: SplicingGraphs

Version: 1.0.4

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch SplicingGraphs_1.0.4.tar.gz

StartedAt: 2013-10-09 00:00:07 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 00:13:49 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 822.3 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: SplicingGraphs.Rcheck

Warnings: 2

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/SplicingGraphs.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'SplicingGraphs/DESCRIPTION' ... OK
* this is package 'SplicingGraphs' version '1.0.4'
* 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 'SplicingGraphs' can be installed ... [38s/39s] OK
* checking installed package size ... NOTE
  installed size is 19.6Mb
  sub-directories of 1Mb or more:
    doc      15.5Mb
    extdata   3.7Mb
* 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 ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'reportReads'
Undocumented S4 methods:
  generic 'reportReads' and siglist 'SplicingGraphs'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Objects in \usage without \alias in documentation object 'countReads-methods':
  'reportReads'

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 ... 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 examples ... [427s/435s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
plotTranscripts-methods 54.791  0.198  55.126
toy_data                23.107  0.065  23.652
countReads-methods      16.917  0.076  17.160
sgedges-methods         10.035  0.040  10.081
bubbles-methods          8.659  0.030   8.747
assignReads              8.391  0.076   8.481
sgedgesByGene-methods    7.496  0.050   7.554
rsgedgesByGene-methods   7.246  0.033   7.291
SplicingGraphs-class     5.898  0.244  11.256
txpath-methods           5.335  0.063   5.415
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'run_unitTests.R' [19s/19s]
 [19s/19s] 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 2 warnings.
NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/SplicingGraphs.Rcheck/00check.log'
for details.

* installing *source* package 'SplicingGraphs' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (SplicingGraphs)

name	user	system	elapsed
SplicingGraphs-class	5.898	0.244	11.256
SplicingGraphs-package	0.016	0.003	0.019
assignReads	8.391	0.076	8.481
bubbles-methods	8.659	0.030	8.747
countReads-methods	16.917	0.076	17.160
plotTranscripts-methods	54.791	0.198	55.126
rsgedgesByGene-methods	7.246	0.033	7.291
sgedges-methods	10.035	0.040	10.081
sgedgesByGene-methods	7.496	0.050	7.554
sgraph-methods	3.750	0.031	3.783
toy_data	23.107	0.065	23.652
txpath-methods	5.335	0.063	5.415