BioC 3.1: CHECK report for ppiStats on petty

Package: ppiStats

Version: 1.34.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ppiStats_1.34.0.tar.gz

StartedAt: 2015-10-09 01:10:35 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 01:14:55 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 259.3 seconds

RetCode: 0

Status:  OK

CheckDir: ppiStats.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ppiStats_1.34.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/ppiStats.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ppiStats/DESCRIPTION’ ... OK
* this is package ‘ppiStats’ version ‘1.34.0’
* 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 ... [23s/23s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘lattice’
A package should be listed in only one of these fields.
* 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 dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘ppiData’ ‘ScISI’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* 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 ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... [36s/39s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
estimatePPIErrorRates 5.537  0.678   6.220
assessSymmetry        5.395  0.645   6.225
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/ppiStats.Rcheck/00check.log’
for details.

* installing *source* package ‘ppiStats’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
No methods found in "Biobase" for requests: listlen
No methods found in "annotate" for requests: pubmed, buildPubMedAbst
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
No methods found in "Biobase" for requests: listlen
No methods found in "annotate" for requests: pubmed, buildPubMedAbst
* DONE (ppiStats)

name	user	system	elapsed
assessSymmetry	5.395	0.645	6.225
bpMatrix	0.774	0.633	4.381
calcInOutDegStats	0.005	0.000	0.005
createSummaryTables	0.419	0.008	0.427
degreeEstimates	0.004	0.000	0.004
estErrProbMethodOfMoments	0.003	0.000	0.003
estimateCCMErrorRates	3.137	0.878	4.018
estimatePPIErrorRates	5.537	0.678	6.220
genBPGraph	0.160	0.008	0.168
idProteinErrorType	3.588	0.968	4.563
idProteinType	0.074	0.014	0.089
inOutScatterCharts	0.001	0.000	0.002
nullDistDoublyTestedEdges	0.579	0.037	0.617
twPERM	0.000	0.001	0.001
viabilityCharts	0.425	0.059	0.483