Package: RpsiXML

Version: 1.10.0

Command: /home/biocbuild/bbs-2.7-bioc/R/bin/R CMD check --no-vignettes --timings RpsiXML_1.10.0.tar.gz

StartedAt: 2011-04-07 08:48:18 -0700 (Thu, 07 Apr 2011)

EndedAt: 2011-04-07 08:50:12 -0700 (Thu, 07 Apr 2011)

EllapsedTime: 114.7 seconds

RetCode: 0

Status:  OK

CheckDir: RpsiXML.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.7-bioc/meat/RpsiXML.Rcheck’
* using R version 2.12.2 (2011-02-25)
* 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 ‘1.10.0’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘RpsiXML’ can be installed ... OK
* 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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 ... NOTE
Error: parse error in file 'RpsiXML-Ex.R':
0: unexpected end of input
722: ### End: ***
723: quit('no')
    ^
Execution halted
* checking examples ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘psimi25Source_test.R’
 OK
* checking package vignettes in ‘inst/doc’ ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package ‘RpsiXML’ ...
** R
** inst
** preparing package for lazy loading
Loading required package: AnnotationDbi
Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.


Attaching package: 'XML'

The following object(s) are masked from 'package:graph':

    addNode


Attaching package: 'hypergraph'

The following object(s) are masked from 'package:AnnotationDbi':

    head, tail

The following object(s) are masked from 'package:utils':

    head, tail

** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (RpsiXML)

name	user	system	elapsed
availableXrefs	0.076	0.008	0.087
bait	0.060	0.004	0.063
buildPCHypergraph	2.528	0.076	2.603
complexName	2.188	0.016	2.206
complexes	2.728	0.076	2.805
eListHandler	0.016	0.000	0.016
getAbstractByPMID	0.472	0.012	0.984