BioC 2.12: CHECK report for RpsiXML on george2

Package: RpsiXML

Version: 2.2.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings RpsiXML_2.2.0.tar.gz

StartedAt: 2013-10-09 04:43:56 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 04:49:12 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 315.4 seconds

RetCode: 0

Status:  OK

CheckDir: RpsiXML.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/RpsiXML.Rcheck’
* using R version 3.0.1 (2013-05-16)
* 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 ‘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 ... [20s/20s] 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 ... [59s/60s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
translateID           10.753  0.064  10.912
graphSpeciesConverter  5.288  0.052   5.480
psimi25XML2Graph       4.976  0.024   5.111
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘psimi25Source_test.R’ [49s/50s]
 [50s/50s] 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
  ‘/home/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	0.504	0.008	0.510
bait	0.116	0.004	0.122
buildPCHypergraph	4.048	0.024	4.074
complexName	3.229	0.040	3.269
complexes	4.332	0.028	4.361
eListHandler	0.028	0.004	0.031
getAbstractByPMID	0.768	0.004	1.401
graphSpeciesConverter	5.288	0.052	5.480
interactionType	0.136	0.000	0.135
interactions	0.140	0.004	0.144
interactorInfo	0.152	0.000	0.150
interactors	3.544	0.060	3.606
null2na	0.012	0.004	0.016
parsePsimi25Interaction	4.501	0.040	4.555
psimi25Complex-class	0.116	0.004	0.120
psimi25ComplexEntry-class	0.016	0.000	0.018
psimi25Experiment-class	0.016	0.000	0.017
psimi25Graph-class	0.024	0.000	0.021
psimi25Hypergraph-class	4.004	0.012	4.019
psimi25Hypergraph2GraphNEL	0.004	0.000	0.003
psimi25Interaction-class	0.024	0.000	0.024
psimi25InteractionEntry-class	0.024	0.000	0.025
psimi25Interactor-class	0.012	0.000	0.012
psimi25Source-class	0.012	0.000	0.012
psimi25XML2Graph	4.976	0.024	5.111
separateXMLDataByExpt	0.992	0.008	1.002
translateID	10.753	0.064	10.912
uniprot	0.024	0.000	0.025
validatePSIMI25	0.188	0.064	0.342