Package: ppiStats

Version: 1.25.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ppiStats_1.25.0.tar.gz

StartedAt: 2013-03-25 04:06:43 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 04:10:36 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 233.8 seconds

RetCode: 0

Status:  OK

CheckDir: ppiStats.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/ppiStats.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'ppiStats/DESCRIPTION' ... OK
* this is package 'ppiStats' version '1.25.0'
* 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 'ppiStats' can be installed ... [19s/20s] OK
* checking installed package size ... OK
* 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 ... NOTE
createSummaryTables: warning in round(numVBP/numVB, digit = 2): partial
  argument match of 'digit' to 'digits'
createSummaryTables: warning in round(numVP/numVB, digit = 2): partial
  argument match of 'digit' to 'digits'
createSummaryTables: warning in round(numInteractions/numVB, digit =
  2): partial argument match of 'digit' to 'digits'
* 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [37s/37s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
estimatePPIErrorRates 6.346  0.940   7.322
assessSymmetry        4.305  1.174   5.508
* 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/ppiStats.Rcheck/00check.log'
for details.

* installing *source* package 'ppiStats' ...
** R
** inst
** preparing package for lazy loading

*** Deprecation warning ***:
The package 'ppiData' is deprecated and will not be supported after Bioconductor release 2.11


** help
*** installing help indices
** building package indices
** installing vignettes
   'ppiStats.Rnw' 
** testing if installed package can be loaded

*** Deprecation warning ***:
The package 'ppiData' is deprecated and will not be supported after Bioconductor release 2.11


* DONE (ppiStats)

name	user	system	elapsed
assessSymmetry	4.305	1.174	5.508
bpMatrix	0.951	0.730	1.698
calcInOutDegStats	0.006	0.006	0.012
createSummaryTables	0.304	0.051	0.355
degreeEstimates	0.004	0.005	0.010
estErrProbMethodOfMoments	0.004	0.006	0.010
estimateCCMErrorRates	3.237	0.908	4.186
estimatePPIErrorRates	6.346	0.940	7.322
genBPGraph	0.070	0.012	0.083
idProteinErrorType	3.115	1.292	4.453
idProteinType	0.064	0.034	0.099
inOutScatterCharts	0.015	0.006	0.020
nullDistDoublyTestedEdges	0.999	0.243	1.249
twPERM	0.004	0.005	0.009
viabilityCharts	0.455	0.032	0.486