Package: ppiStats

Version: 1.24.0

Command: /home/biocbuild/bbs-2.11-bioc/R/bin/R CMD check --no-vignettes --timings ppiStats_1.24.0.tar.gz

StartedAt: 2013-03-25 03:54:42 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 03:59:08 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 266.1 seconds

RetCode: 0

Status:  OK

CheckDir: ppiStats.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/ppiStats.Rcheck’
* using R version 2.15.3 (2013-03-01)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ppiStats/DESCRIPTION’ ... OK
* this is package ‘ppiStats’ version ‘1.24.0’
* 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 whether package ‘ppiStats’ can be installed ... OK
* checking installed package size ... 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 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 installed files from ‘inst/doc’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
assessSymmetry        5.052  4.372  16.467
estimatePPIErrorRates 5.780  2.648  12.551
idProteinErrorType    2.440  3.660  11.650
estimateCCMErrorRates 2.945  0.780   5.994
* 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
  ‘/loc/home/biocbuild/bbs-2.11-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	5.052	4.372	16.467
bpMatrix	1.004	0.328	1.518
calcInOutDegStats	0.004	0.000	0.018
createSummaryTables	0.228	0.036	0.300
degreeEstimates	0.004	0.000	0.002
estErrProbMethodOfMoments	0.000	0.004	0.001
estimateCCMErrorRates	2.945	0.780	5.994
estimatePPIErrorRates	5.780	2.648	12.551
genBPGraph	0.064	0.000	0.066
idProteinErrorType	2.44	3.66	11.65
idProteinType	0.064	0.004	0.108
inOutScatterCharts	0.012	0.000	0.011
nullDistDoublyTestedEdges	0.492	0.028	0.576
twPERM	0	0	0
viabilityCharts	0.428	0.004	0.432