BioC 2.14: CHECK report for ppiStats on moscato2

Package: ppiStats

Version: 1.30.0

Command: rm -rf ppiStats.buildbin-libdir && mkdir ppiStats.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ppiStats.buildbin-libdir ppiStats_1.30.0.tar.gz >ppiStats-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=ppiStats.buildbin-libdir --install="check:ppiStats-install.out" --force-multiarch --no-vignettes --timings ppiStats_1.30.0.tar.gz

StartedAt: 2014-10-08 03:58:38 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 04:03:21 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 283.3 seconds

RetCode: 0

Status:  OK

CheckDir: ppiStats.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf ppiStats.buildbin-libdir && mkdir ppiStats.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ppiStats.buildbin-libdir ppiStats_1.30.0.tar.gz >ppiStats-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=ppiStats.buildbin-libdir --install="check:ppiStats-install.out" --force-multiarch --no-vignettes --timings ppiStats_1.30.0.tar.gz
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* using log directory 'E:/biocbld/bbs-2.14-bioc/meat/ppiStats.Rcheck'
* using R version 3.1.1 (2014-07-10)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ppiStats/DESCRIPTION' ... OK
* this is package 'ppiStats' version '1.30.0'
* 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 whether package 'ppiStats' can be installed ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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:
  'ScISI' 'ppiData'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [25s] OK
** running examples for arch 'x64' ... [29s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
estimatePPIErrorRates 5.06    0.2    5.26
* 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

NOTE: There were 2 notes.
See
  'E:/biocbld/bbs-2.14-bioc/meat/ppiStats.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'ppiStats' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'ppiStats' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ppiStats' as ppiStats_1.30.0.zip
* DONE (ppiStats)

name	user	system	elapsed
assessSymmetry	3.79	0.25	4.04
bpMatrix	0.52	0.17	0.69
calcInOutDegStats	0	0	0
createSummaryTables	0.23	0.00	0.23
degreeEstimates	0	0	0
estErrProbMethodOfMoments	0.02	0.00	0.02
estimateCCMErrorRates	2.55	0.19	2.75
estimatePPIErrorRates	4.70	0.19	4.88
genBPGraph	0.09	0.01	0.11
idProteinErrorType	2.13	0.22	2.34
idProteinType	0.03	0.00	0.03
inOutScatterCharts	0	0	0
nullDistDoublyTestedEdges	0.42	0.05	0.47
twPERM	0	0	0
viabilityCharts	0.32	0.00	0.31

name	user	system	elapsed
assessSymmetry	4.57	0.25	4.82
bpMatrix	0.50	0.12	0.62
calcInOutDegStats	0	0	0
createSummaryTables	0.47	0.02	0.48
degreeEstimates	0	0	0
estErrProbMethodOfMoments	0	0	0
estimateCCMErrorRates	2.67	0.15	2.82
estimatePPIErrorRates	5.06	0.20	5.26
genBPGraph	0.11	0.00	0.11
idProteinErrorType	2.62	0.21	2.82
idProteinType	0.04	0.00	0.05
inOutScatterCharts	0	0	0
nullDistDoublyTestedEdges	0.44	0.01	0.45
twPERM	0	0	0
viabilityCharts	0.39	0.00	0.42