Package: RpsiXML

Version: 1.18.1

Command: /home/biocbuild/bbs-2.11-bioc/R/bin/R CMD check --no-vignettes --timings RpsiXML_1.18.1.tar.gz

StartedAt: 2013-03-25 04:37:35 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 04:41:55 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 259.2 seconds

RetCode: 0

Status:  OK

CheckDir: RpsiXML.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/RpsiXML.Rcheck’
* using R version 2.15.3 (2013-03-01)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RpsiXML/DESCRIPTION’ ... OK
* this is package ‘RpsiXML’ version ‘1.18.1’
* 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 whether package ‘RpsiXML’ can be installed ... 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 for portable file names ... OK
* checking for sufficient/correct file permissions ... 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 ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
translateID           6.984  0.068   7.195
graphSpeciesConverter 3.932  0.076   5.687
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘psimi25Source_test.R’
 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
  ‘/loc/home/biocbuild/bbs-2.11-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	0.120	0.004	0.441
bait	0.336	0.012	0.433
buildPCHypergraph	3.080	0.040	3.613
complexName	2.900	0.032	3.135
complexes	2.620	0.044	2.796
eListHandler	0.016	0.000	0.027
getAbstractByPMID	0.733	0.024	2.082
graphSpeciesConverter	3.932	0.076	5.687
interactionType	0.068	0.004	0.071
interactions	0.072	0.000	0.073
interactorInfo	0.080	0.000	0.083
interactors	2.996	0.036	3.450
null2na	0	0	0
parsePsimi25Interaction	3.188	0.016	3.425
psimi25Complex-class	0.000	0.000	0.001
psimi25ComplexEntry-class	0	0	0
psimi25Experiment-class	0.000	0.000	0.001
psimi25Graph-class	0.000	0.000	0.001
psimi25Hypergraph-class	3.140	0.024	3.537
psimi25Hypergraph2GraphNEL	0	0	0
psimi25Interaction-class	0.004	0.000	0.000
psimi25InteractionEntry-class	0.000	0.000	0.001
psimi25Interactor-class	0	0	0
psimi25Source-class	0.004	0.000	0.001
psimi25XML2Graph	3.381	0.012	3.722
separateXMLDataByExpt	0.600	0.004	0.705
translateID	6.984	0.068	7.195
uniprot	0	0	0
validatePSIMI25	0.048	0.044	0.286