Package: RpsiXML

Version: 2.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch RpsiXML_2.0.0.tar.gz

StartedAt: 2013-03-20 09:58:21 -0700 (Wed, 20 Mar 2013)

EndedAt: 2013-03-20 10:03:24 -0700 (Wed, 20 Mar 2013)

EllapsedTime: 302.6 seconds

RetCode: 0

Status:  OK

CheckDir: RpsiXML.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/RpsiXML.Rcheck'
* using R version 3.0.0 alpha (2013-03-16 r62280)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'RpsiXML/DESCRIPTION' ... OK
* this is package 'RpsiXML' version '2.0.0'
* 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 ... [19s/29s] 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 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 ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... 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 examples ... [55s/57s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
translateID           9.565  0.158   9.849
graphSpeciesConverter 4.951  0.182   5.235
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'psimi25Source_test.R' [45s/45s]
 [46s/46s] 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

NOTE: There were 2 notes.
See
  '/Users/biocbuild/bbs-2.12-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
   'RpsiXML.Rnw' 
   'RpsiXMLApp.Rnw' 
** testing if installed package can be loaded
* DONE (RpsiXML)

name	user	system	elapsed
availableXrefs	0.140	0.008	0.149
bait	0.097	0.007	0.123
buildPCHypergraph	3.722	0.069	3.858
complexName	3.333	0.070	3.470
complexes	4.265	0.149	4.516
eListHandler	0.029	0.004	0.033
getAbstractByPMID	0.786	0.039	1.989
graphSpeciesConverter	4.951	0.182	5.235
interactionType	0.448	0.024	0.478
interactions	0.123	0.011	0.152
interactorInfo	0.104	0.007	0.112
interactors	3.455	0.131	3.674
null2na	0.009	0.003	0.012
parsePsimi25Interaction	4.444	0.076	4.536
psimi25Complex-class	0.009	0.004	0.014
psimi25ComplexEntry-class	0.010	0.004	0.014
psimi25Experiment-class	0.009	0.003	0.012
psimi25Graph-class	0.010	0.004	0.014
psimi25Hypergraph-class	3.419	0.027	3.467
psimi25Hypergraph2GraphNEL	0.009	0.003	0.011
psimi25Interaction-class	0.017	0.004	0.020
psimi25InteractionEntry-class	0.015	0.003	0.019
psimi25Interactor-class	0.011	0.004	0.016
psimi25Source-class	0.011	0.003	0.014
psimi25XML2Graph	4.421	0.062	4.511
separateXMLDataByExpt	0.879	0.032	0.912
translateID	9.565	0.158	9.849
uniprot	0.010	0.004	0.014
validatePSIMI25	0.112	0.034	0.187