Package: RpsiXML

Version: 1.17.0

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch RpsiXML_1.17.0.tar.gz

StartedAt: 2012-06-21 03:23:47 -0700 (Thu, 21 Jun 2012)

EndedAt: 2012-06-21 03:28:36 -0700 (Thu, 21 Jun 2012)

EllapsedTime: 289.0 seconds

RetCode: 0

Status:  OK

CheckDir: RpsiXML.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/RpsiXML.Rcheck'
* using R version 2.15.0 Patched (2012-04-26 r59216)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'RpsiXML/DESCRIPTION' ... OK
* this is package 'RpsiXML' version '1.17.0'
* 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 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 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 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 examples ... OK
* 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
  '/Users/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	0.124	0.008	0.133
bait	0.098	0.003	0.121
buildPCHypergraph	3.756	0.039	3.868
complexName	3.207	0.033	3.280
complexes	3.777	0.067	3.953
eListHandler	0.025	0.002	0.027
getAbstractByPMID	0.742	0.014	1.470
graphSpeciesConverter	4.827	0.091	4.979
interactionType	0.101	0.003	0.105
interactions	0.104	0.004	0.108
interactorInfo	0.119	0.004	0.123
interactors	3.595	0.096	3.796
null2na	0.001	0.000	0.001
parsePsimi25Interaction	4.110	0.034	4.256
psimi25Complex-class	0.002	0.000	0.002
psimi25ComplexEntry-class	0.001	0.000	0.003
psimi25Experiment-class	0.001	0.001	0.002
psimi25Graph-class	0.001	0.000	0.001
psimi25Hypergraph-class	3.757	0.034	4.007
psimi25Hypergraph2GraphNEL	0	0	0
psimi25Interaction-class	0.001	0.000	0.001
psimi25InteractionEntry-class	0.001	0.000	0.001
psimi25Interactor-class	0.001	0.001	0.001
psimi25Source-class	0.001	0.000	0.001
psimi25XML2Graph	4.089	0.036	4.332
separateXMLDataByExpt	0.871	0.011	0.895
translateID	8.566	0.069	8.820
uniprot	0.000	0.001	0.000
validatePSIMI25	0.101	0.033	0.195