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Package 480/653HostnameOS / ArchBUILDCHECKBUILD BIN
ppiStats 1.25.0
Tony Chiang
Snapshot Date: 2013-03-19 17:01:12 -0700 (Tue, 19 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ppiStats
Last Changed Rev: 70052 / Revision: 74585
Last Changed Date: 2012-10-01 15:43:56 -0700 (Mon, 01 Oct 2012)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 
pelham Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

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: 2013-03-20 09:01:53 -0700 (Wed, 20 Mar 2013)
EndedAt: 2013-03-20 09:06:23 -0700 (Wed, 20 Mar 2013)
EllapsedTime: 270.3 seconds
RetCode: 0
Status:  OK 
CheckDir: ppiStats.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/ppiStats.Rcheck'
* using R version 3.0.0 alpha (2013-03-16 r62280)
* using platform: x86_64-apple-darwin10.8.0 (64-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 ... [24s/24s] 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 installed files from 'inst/doc' ... OK
* checking examples ... [42s/44s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
estimatePPIErrorRates 7.365  1.020   8.603
assessSymmetry        6.743  0.810   7.852
idProteinErrorType    4.274  1.123   5.554
estimateCCMErrorRates 4.081  0.800   5.004
* 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.

ppiStats.Rcheck/00install.out:

* 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)

ppiStats.Rcheck/ppiStats-Ex.timings:

nameusersystemelapsed
assessSymmetry6.7430.8107.852
bpMatrix1.1090.7491.989
calcInOutDegStats0.0070.0060.015
createSummaryTables0.3740.1070.534
degreeEstimates0.0060.0060.012
estErrProbMethodOfMoments0.0050.0070.017
estimateCCMErrorRates4.0810.8005.004
estimatePPIErrorRates7.3651.0208.603
genBPGraph0.0910.0130.108
idProteinErrorType4.2741.1235.554
idProteinType0.0830.0290.112
inOutScatterCharts0.0110.0070.018
nullDistDoublyTestedEdges0.8560.3641.309
twPERM0.0030.0050.008
viabilityCharts0.5420.0420.667