BioC 2.12: CHECK report for RpsiXML on petty

Package: RpsiXML

Version: 2.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch RpsiXML_2.2.0.tar.gz

StartedAt: 2013-10-08 23:47:08 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 23:53:18 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 370.4 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 3.0.1 (2013-05-16)
* 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 '2.2.0'
* 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 'RpsiXML' can be installed ... [22s/28s] 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 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 ... [67s/77s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
translateID             10.768  0.084  10.993
graphSpeciesConverter    6.747  0.125   8.126
psimi25XML2Graph         5.516  0.039   5.753
parsePsimi25Interaction  5.364  0.043   5.562
complexes                4.925  0.070   7.947
buildPCHypergraph        4.744  0.053   5.106
interactors              4.537  0.105   5.603
complexName              4.550  0.037   7.114
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'psimi25Source_test.R' [55s/55s]
 [55s/56s] 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
** testing if installed package can be loaded
* DONE (RpsiXML)

name	user	system	elapsed
availableXrefs	0.383	0.011	0.396
bait	0.120	0.004	0.124
buildPCHypergraph	4.744	0.053	5.106
complexName	4.550	0.037	7.114
complexes	4.925	0.070	7.947
eListHandler	0.041	0.004	0.079
getAbstractByPMID	1.107	0.025	2.069
graphSpeciesConverter	6.747	0.125	8.126
interactionType	0.501	0.018	0.750
interactions	0.156	0.008	0.264
interactorInfo	0.157	0.008	0.257
interactors	4.537	0.105	5.603
null2na	0.007	0.002	0.009
parsePsimi25Interaction	5.364	0.043	5.562
psimi25Complex-class	0.010	0.004	0.015
psimi25ComplexEntry-class	0.009	0.003	0.012
psimi25Experiment-class	0.008	0.002	0.010
psimi25Graph-class	0.009	0.002	0.011
psimi25Hypergraph-class	4.601	0.040	4.765
psimi25Hypergraph2GraphNEL	0.007	0.002	0.011
psimi25Interaction-class	0.017	0.003	0.025
psimi25InteractionEntry-class	0.008	0.004	0.014
psimi25Interactor-class	0.008	0.003	0.014
psimi25Source-class	0.006	0.003	0.009
psimi25XML2Graph	5.516	0.039	5.753
separateXMLDataByExpt	1.036	0.018	1.074
translateID	10.768	0.084	10.993
uniprot	0.009	0.002	0.010
validatePSIMI25	0.128	0.031	0.236