BioC 3.2: CHECK report for ddgraph on oaxaca

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ddgraph_1.13.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/ddgraph.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.13.0’
* 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 ... [10s/11s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to ‘Rgraphviz’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in 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 ... NOTE
customPlotPCAlgo: no visible global function definition for
  ‘layoutGraph’
customPlotPCAlgo: no visible global function definition for
  ‘renderGraph’
plotSVMPerformance: no visible global function definition for
  ‘prediction’
plotSVMPerformance: no visible global function definition for
  ‘performance’
recalculateSVMparams: no visible global function definition for ‘svm’
recalculateSVMparams : <anonymous>: no visible global function
  definition for ‘svm’
recalculateSVMparams: no visible global function definition for
  ‘prediction’
recalculateSVMparams: no visible global function definition for
  ‘performance’
svmFeatureSelectionLOOCV: no visible global function definition for
  ‘svm’
plot,DDGraph-missing : .local: no visible global function definition
  for ‘layoutGraph’
plot,DDGraph-missing : .local: no visible global function definition
  for ‘renderGraph’
* 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 compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... 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 files in ‘vignettes’ ... OK
* checking examples ... [30s/31s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
plotPCalg      17.301  0.092  17.608
calcDependence  7.149  0.067   7.313
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’ [68s/69s]
 [68s/69s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/ddgraph.Rcheck/00check.log’
for details.

* installing *source* package ‘ddgraph’ ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c mcX2cloop.cpp -o mcX2cloop.o
mcX2cloop.cpp:14:2: warning: unused label 'Rcpp' [-Wunused-label]
        Rcpp:NumericVector res(iB);
        ^˜˜˜˜
1 warning generated.
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o ddgraph.so mcX2cloop.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.2-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	0.017	0.003	0.043
biased-dot-graph	0.006	0.001	0.006
calcDependence	7.149	0.067	7.313
ciTest-comma-DDDataSet-dash-method	0.029	0.000	0.030
combinationsTest	0.030	0.001	0.031
convertPvalueToColorIndex	0.001	0.001	0.001
convertToFactor	0.007	0.000	0.007
estimateNetworkDistribution	0.102	0.001	0.106
formulaFalseNeg	0.002	0.000	0.001
independent-dot-contributions-dot-formula-dot-mul	0.002	0.000	0.002
independent-dot-contributions-dot-formula	0.002	0.000	0.002
is-dot-binary	0.002	0.001	0.002
logseq	0.001	0.000	0.000
makeDDDataSet	0.002	0.000	0.002
mapEnrichmentToColorsDual	0	0	0
mcMITest	0.008	0.000	0.008
mcX2Test	0.015	0.000	0.015
mcX2TestB50k	0.319	0.006	0.325
mesoBin	0.004	0.001	0.004
mesoCont	0.003	0.000	0.004
ncpc	2.121	0.023	2.174
ncpcResampling	0.001	0.000	0.001
plot-comma-DDGraph-comma-missing-dash-method	0.001	0.000	0.000
plotBNLearn	0.325	0.003	0.339
plotPCalg	17.301	0.092	17.608
prob-dot-distr-dot-norm	0.000	0.001	0.001
prob-dot-distr-dot-unif	0.001	0.000	0.001
random-dot-bn-dot-fit	0.004	0.000	0.005
readFurlongData	0.031	0.014	0.048
recalculateSVMparams	0.001	0.000	0.000
toDDDataSet-comma-FurlongDataSet-dash-method	0.121	0.005	0.126
toyExample	0.079	0.001	0.079

BioC 3.2: CHECK report for ddgraph on oaxaca

Summary

Command output