BioC 2.12: CHECK report for ddgraph on george2

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/ddgraph.Rcheck’
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ddgraph/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ddgraph’ version ‘1.4.0’
* 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 ‘ddgraph’ can be installed ... [15s/16s] 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 ... 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... [47s/47s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
plotPCalg      26.141  0.008  26.226
calcDependence 10.632  0.056  10.770
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘test-all.R’ [182s/186s]
 [183s/187s] OK
* 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

* installing *source* package ‘ddgraph’ ...
** libs
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c mcX2cloop.cpp -o mcX2cloop.o
mcX2cloop.cpp: In function ‘SEXPREC* mcX2CLoopC(SEXP, SEXP, SEXP, SEXP)’:
mcX2cloop.cpp:14:2: warning: label ‘Rcpp’ defined but not used [-Wunused-label]
g++ -shared -L/usr/local/lib -o ddgraph.so mcX2cloop.o -L/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/lib -lRcpp -Wl,-rpath,/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/lib -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.12-bioc/meat/ddgraph.Rcheck/ddgraph/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ddgraph)

name	user	system	elapsed
biased-dot-bn-dot-fit	0.048	0.000	0.050
biased-dot-graph	0.012	0.000	0.014
calcDependence	10.632	0.056	10.770
ciTest-comma-DDDataSet-dash-method	0.088	0.000	0.090
combinationsTest	0.064	0.000	0.062
convertPvalueToColorIndex	0.016	0.000	0.015
convertToFactor	0.044	0.000	0.044
estimateNetworkDistribution	0.204	0.000	0.204
formulaFalseNeg	0.024	0.000	0.024
independent-dot-contributions-dot-formula-dot-mul	0.040	0.000	0.041
independent-dot-contributions-dot-formula	0.016	0.000	0.019
is-dot-binary	0.02	0.00	0.02
logseq	0.008	0.000	0.008
makeDDDataSet	0.020	0.000	0.021
mapEnrichmentToColorsDual	0.016	0.000	0.014
mcMITest	0.032	0.000	0.034
mcX2Test	0.276	0.000	0.278
mcX2TestB50k	1.048	0.008	1.059
mesoBin	0.016	0.000	0.015
mesoCont	0.016	0.000	0.015
ncpc	3.629	0.016	3.654
ncpcResampling	0.012	0.000	0.012
plot-comma-DDGraph-comma-missing-dash-method	0.012	0.000	0.012
plotBNLearn	0.676	0.008	0.684
plotPCalg	26.141	0.008	26.226
prob-dot-distr-dot-norm	0.020	0.004	0.025
prob-dot-distr-dot-unif	0.008	0.000	0.008
random-dot-bn-dot-fit	0.016	0.000	0.018
readFurlongData	0.044	0.008	0.054
recalculateSVMparams	0.008	0.000	0.008
toDDDataSet-comma-FurlongDataSet-dash-method	0.180	0.004	0.187
toyExample	0.116	0.000	0.119

BioC 2.12: CHECK report for ddgraph on george2

Summary

Command output