BioC 2.13: CHECK report for RpsiXML on perceval

Package: RpsiXML

Version: 2.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch RpsiXML_2.4.0.tar.gz

StartedAt: 2014-04-05 04:07:30 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 04:12:22 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 292.5 seconds

RetCode: 0

Status:  OK

CheckDir: RpsiXML.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/RpsiXML.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 ‘RpsiXML/DESCRIPTION’ ... OK
* this is package ‘RpsiXML’ version ‘2.4.0’
* 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 ‘RpsiXML’ can be installed ... [17s/19s] OK
* checking installed package size ... NOTE
  installed size is 33.8Mb
  sub-directories of 1Mb or more:
    extdata  32.7Mb
* 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
Packages in Depends field not imported from:
  ‘annotate’ ‘AnnotationDbi’ ‘RBGL’ ‘XML’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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 ... 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’ ... NOTE
The following files should probably not be installed:
  ‘underscore.sty’

Consider the use of a .Rinstignore file: see ‘Writing R Extensions’,
or move the vignette sources from ‘inst/doc’ to ‘vignettes’.
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘RpsiXML.Rnw’, ‘RpsiXMLApp.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [52s/53s] OK
Examples with CPU or elapsed time > 5s
             user system elapsed
translateID 9.478  0.119   9.695
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘psimi25Source_test.R’ [46s/47s]
 [47s/47s] 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 4 notes.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/RpsiXML.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
availableXrefs	0.117	0.011	0.129
bait	0.106	0.007	0.112
buildPCHypergraph	3.275	0.050	3.342
complexName	3.298	0.050	3.385
complexes	3.528	0.063	3.620
eListHandler	0.028	0.002	0.031
getAbstractByPMID	0.721	0.022	1.237
graphSpeciesConverter	4.552	0.088	4.744
interactionType	0.517	0.025	0.543
interactions	0.093	0.008	0.101
interactorInfo	0.094	0.005	0.101
interactors	3.118	0.095	3.327
null2na	0.009	0.003	0.012
parsePsimi25Interaction	4.111	0.068	4.259
psimi25Complex-class	0.011	0.004	0.024
psimi25ComplexEntry-class	0.011	0.003	0.016
psimi25Experiment-class	0.011	0.002	0.014
psimi25Graph-class	0.038	0.003	0.052
psimi25Hypergraph-class	3.038	0.023	3.090
psimi25Hypergraph2GraphNEL	0.010	0.002	0.011
psimi25Interaction-class	0.045	0.012	0.057
psimi25InteractionEntry-class	0.020	0.007	0.027
psimi25Interactor-class	0.011	0.004	0.015
psimi25Source-class	0.011	0.003	0.014
psimi25XML2Graph	4.444	0.045	4.527
separateXMLDataByExpt	0.870	0.031	0.909
translateID	9.478	0.119	9.695
uniprot	0.012	0.002	0.013
validatePSIMI25	0.081	0.038	0.171