BioC 2.12: CHECK report for SplicingGraphs on george2

Package: SplicingGraphs

Version: 1.0.4

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings SplicingGraphs_1.0.4.tar.gz

StartedAt: 2013-10-09 05:08:21 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 05:24:43 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 981.8 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: SplicingGraphs.Rcheck

Warnings: 2

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/SplicingGraphs.Rcheck’
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 ... [37s/47s] 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 installed files from ‘inst/doc’ ... OK
* checking examples ... [541s/566s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
plotTranscripts-methods 59.708  0.096  62.882
toy_data                30.350  0.028  31.455
countReads-methods      17.553  0.028  18.508
sgedges-methods         11.229  0.012  11.449
rsgedgesByGene-methods   8.800  0.012   8.980
bubbles-methods          8.636  0.004   9.327
assignReads              7.973  0.004   8.129
txpath-methods           6.816  0.028   6.929
sgedgesByGene-methods    6.737  0.020   7.059
SplicingGraphs-class     5.288  0.084   6.011
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘run_unitTests.R’ [25s/25s]
 [25s/26s] 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
  ‘/home/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	5.288	0.084	6.011
SplicingGraphs-package	0.028	0.000	0.027
assignReads	7.973	0.004	8.129
bubbles-methods	8.636	0.004	9.327
countReads-methods	17.553	0.028	18.508
plotTranscripts-methods	59.708	0.096	62.882
rsgedgesByGene-methods	8.800	0.012	8.980
sgedges-methods	11.229	0.012	11.449
sgedgesByGene-methods	6.737	0.020	7.059
sgraph-methods	3.984	0.008	4.377
toy_data	30.350	0.028	31.455
txpath-methods	6.816	0.028	6.929