BioC 2.12: CHECK report for ddgraph on petty

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/ddgraph.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [47s/48s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
plotPCalg      24.254  0.162  24.559
calcDependence 12.289  0.107  12.756
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'test-all.R' [140s/142s]
 [141s/143s] 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
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2  -c mcX2cloop.cpp -o mcX2cloop.o
llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o ddgraph.so mcX2cloop.o /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/lib/libRcpp.a -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/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	0.034	0.003	0.037
biased-dot-graph	0.015	0.000	0.015
calcDependence	12.289	0.107	12.756
ciTest-comma-DDDataSet-dash-method	0.080	0.001	0.082
combinationsTest	0.049	0.002	0.052
convertPvalueToColorIndex	0.009	0.000	0.010
convertToFactor	0.022	0.000	0.023
estimateNetworkDistribution	0.243	0.004	0.249
formulaFalseNeg	0.016	0.000	0.016
independent-dot-contributions-dot-formula-dot-mul	0.016	0.000	0.017
independent-dot-contributions-dot-formula	0.014	0.000	0.014
is-dot-binary	0.008	0.001	0.010
logseq	0.006	0.001	0.006
makeDDDataSet	0.010	0.001	0.011
mapEnrichmentToColorsDual	0.005	0.001	0.005
mcMITest	0.019	0.001	0.019
mcX2Test	0.032	0.001	0.032
mcX2TestB50k	0.708	0.010	0.719
mesoBin	0.010	0.002	0.013
mesoCont	0.011	0.002	0.014
ncpc	4.193	0.039	4.241
ncpcResampling	0.008	0.001	0.010
plot-comma-DDGraph-comma-missing-dash-method	0.008	0.002	0.011
plotBNLearn	0.809	0.012	0.823
plotPCalg	24.254	0.162	24.559
prob-dot-distr-dot-norm	0.005	0.001	0.006
prob-dot-distr-dot-unif	0.011	0.001	0.011
random-dot-bn-dot-fit	0.015	0.002	0.017
readFurlongData	0.057	0.025	0.082
recalculateSVMparams	0.007	0.000	0.008
toDDDataSet-comma-FurlongDataSet-dash-method	0.219	0.005	0.224
toyExample	0.140	0.009	0.149

BioC 2.12: CHECK report for ddgraph on petty

Summary

Command output