BioC 2.13: CHECK report for SplicingGraphs on perceval

Package: SplicingGraphs

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch SplicingGraphs_1.2.0.tar.gz

StartedAt: 2014-04-05 04:34:53 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 04:45:01 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 608.0 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: SplicingGraphs.Rcheck

Warnings: 2

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/SplicingGraphs.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SplicingGraphs/DESCRIPTION’ ... OK
* this is package ‘SplicingGraphs’ version ‘1.2.0’
* 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 ‘SplicingGraphs’ can be installed ... [34s/34s] OK
* checking installed package size ... NOTE
  installed size is 19.7Mb
  sub-directories of 1Mb or more:
    doc      15.6Mb
    extdata   3.7Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘BiocGenerics’ ‘IRanges’ ‘GenomicRanges’ ‘GenomicFeatures’ ‘Rgraphviz’ ‘igraph’
A package should be listed in only one of these fields.
* 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
Unexported objects imported by ‘:::’ calls:
  ‘BiocGenerics:::testPackage’ ‘GenomicRanges:::fillGaps’
  ‘IRanges:::decodeRle’ ‘IRanges:::matchIntegerPairs’
  ‘IRanges:::newCompressedList0’ ‘IRanges:::orderIntegerPairs’
  ‘IRanges:::selfmatchIntegerPairs’ ‘IRanges:::setPrototypeFromObject’
  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 ... 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘SplicingGraphs.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [250s/256s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
plotTranscripts-methods 44.714  0.227  45.447
toy_data                28.689  0.175  29.614
countReads-methods      10.552  0.080  10.818
sgedges-methods          8.535  0.083   8.753
bubbles-methods          7.158  0.080   7.481
assignReads              6.516  0.066   6.706
sgedgesByGene-methods    6.096  0.063   6.248
rsgedgesByGene-methods   5.599  0.057   5.779
txpath-methods           5.557  0.093   5.697
SplicingGraphs-class     4.095  0.252   5.730
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘run_unitTests.R’ [23s/23s]
 [23s/23s] 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

WARNING: There were 2 warnings.
NOTE: There were 4 notes.
See
  ‘/Users/biocbuild/bbs-2.13-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	4.095	0.252	5.730
SplicingGraphs-package	0.015	0.002	0.019
assignReads	6.516	0.066	6.706
bubbles-methods	7.158	0.080	7.481
countReads-methods	10.552	0.080	10.818
plotTranscripts-methods	44.714	0.227	45.447
rsgedgesByGene-methods	5.599	0.057	5.779
sgedges-methods	8.535	0.083	8.753
sgedgesByGene-methods	6.096	0.063	6.248
sgraph-methods	3.499	0.038	3.848
toy_data	28.689	0.175	29.614
txpath-methods	5.557	0.093	5.697