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Package 465/631HostnameOS / ArchBUILDCHECKBUILD BIN
ppiStats 1.25.0
Tony Chiang
Snapshot Date: 2013-01-15 17:01:14 -0800 (Tue, 15 Jan 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ppiStats
Last Changed Rev: 70052 / Revision: 72575
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 
lamb2 Linux (openSUSE 11.4) / 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 

Summary

Package: ppiStats
Version: 1.25.0
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings ppiStats_1.25.0.tar.gz
StartedAt: 2013-01-16 05:23:17 -0800 (Wed, 16 Jan 2013)
EndedAt: 2013-01-16 05:26:50 -0800 (Wed, 16 Jan 2013)
EllapsedTime: 213.3 seconds
RetCode: 0
Status:  OK 
CheckDir: ppiStats.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/ppiStats.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* 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 ‘1.25.0’
* 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 ... 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 ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
assessSymmetry        6.168  0.892   7.062
estimatePPIErrorRates 6.488  0.424   6.913
* 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-2.12-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
assessSymmetry6.1680.8927.062
bpMatrix0.9210.4201.342
calcInOutDegStats0.0080.0000.008
createSummaryTables0.3000.0240.321
degreeEstimates0.0040.0040.008
estErrProbMethodOfMoments0.0080.0000.006
estimateCCMErrorRates3.4720.0763.546
estimatePPIErrorRates6.4880.4246.913
genBPGraph0.0720.0040.074
idProteinErrorType3.3920.5963.989
idProteinType0.0680.0040.072
inOutScatterCharts0.0120.0000.014
nullDistDoublyTestedEdges0.6320.0160.645
twPERM0.0040.0000.004
viabilityCharts0.4560.0000.454