Package: ppiStats

Version: 1.19.0

Command: D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings ppiStats_1.19.0.tar.gz

StartedAt: 2011-05-09 19:09:19 -0700 (Mon, 09 May 2011)

EndedAt: 2011-05-09 19:12:02 -0700 (Mon, 09 May 2011)

EllapsedTime: 163.4 seconds

RetCode: 0

Status:  OK

CheckDir: ppiStats.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/ppiStats.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-04-17 r55484)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ppiStats/DESCRIPTION' ... OK
* this is package 'ppiStats' version '1.19.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'ppiStats' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... 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 ... NOTE
prepare_Rd: findAdjacent.Rd:27-29: Dropping empty section \examples
prepare_Rd: hgParams.Rd:39: Dropping empty section \references
prepare_Rd: hgParams.Rd:42-44: Dropping empty section \examples
prepare_Rd: hgTests.Rd:40: Dropping empty section \references
prepare_Rd: hgTests.Rd:43-45: Dropping empty section \examples
* 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 examples ... 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

* installing *source* package 'ppiStats' ...
** R
** inst
** preparing package for lazy loading
Loading required package: GO.db
Loading required package: AnnotationDbi
Loading required package: Biobase

Welcome to Bioconductor

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

Loading required package: DBI

Loading required package: RpsiXML
Loading required package: annotate
Loading required package: graph
Loading required package: RBGL
Loading required package: XML

Attaching package: 'XML'

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

    addNode

Loading required package: hypergraph

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

Loading required package: apComplex

Warning in fun(...) :
  Rgraphviz built with Graphviz version 2.20.3.
Found installed Graphviz version 2.25.20090912.445. This _may_ cause problems.
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'ppiStats.Rnw' 
** testing if installed package can be loaded
Warning message:
In fun(...) : Rgraphviz built with Graphviz version 2.20.3.
Found installed Graphviz version 2.25.20090912.445. This _may_ cause problems.

* DONE (ppiStats)

name	user	system	elapsed
assessSymmetry	3.12	0.56	3.71
bpMatrix	0.75	0.17	0.92
calcInOutDegStats	0	0	0
createSummaryTables	0.25	0.00	0.25
degreeEstimates	0.01	0.00	0.02
estErrProbMethodOfMoments	0	0	0
estimateCCMErrorRates	2.21	0.33	2.53
estimatePPIErrorRates	9.31	0.28	9.60
genBPGraph	0.05	0.00	0.04
idProteinErrorType	2.15	0.42	2.58
idProteinType	0.19	0.10	0.28
inOutScatterCharts	0	0	0
nullDistDoublyTestedEdges	0.50	0.04	0.54
twPERM	0	0	0
viabilityCharts	0.39	0.00	0.39