BioC 3.0: CHECK report for ddgraph on oaxaca

Package: ddgraph

Version: 1.10.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ddgraph_1.10.1.tar.gz

StartedAt: 2015-04-09 22:49:50 -0700 (Thu, 09 Apr 2015)

EndedAt: 2015-04-09 22:52:49 -0700 (Thu, 09 Apr 2015)

EllapsedTime: 179.3 seconds

RetCode: 0

Status:  OK

CheckDir: ddgraph.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 --no-multiarch ddgraph_1.10.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/ddgraph.Rcheck’
* using R version 3.1.3 (2015-03-09)
* 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 ‘1.10.1’
* 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’
* 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 ... [28s/29s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
plotPCalg      16.290  0.055  16.427
calcDependence  7.027  0.058   7.258
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘test-all.R’ [70s/71s]
 [70s/71s] 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

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-3.0-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/3.1/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-3.0-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	0.014	0.001	0.041
biased-dot-graph	0.003	0.000	0.004
calcDependence	7.027	0.058	7.258
ciTest-comma-DDDataSet-dash-method	0.019	0.000	0.020
combinationsTest	0.025	0.002	0.026
convertPvalueToColorIndex	0.000	0.000	0.001
convertToFactor	0.005	0.000	0.005
estimateNetworkDistribution	0.073	0.001	0.075
formulaFalseNeg	0.001	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	0.001
is-dot-binary	0.002	0.000	0.001
logseq	0	0	0
makeDDDataSet	0.005	0.000	0.006
mapEnrichmentToColorsDual	0.001	0.000	0.000
mcMITest	0.006	0.000	0.007
mcX2Test	0.013	0.000	0.013
mcX2TestB50k	0.198	0.006	0.204
mesoBin	0.003	0.000	0.003
mesoCont	0.009	0.001	0.009
ncpc	1.861	0.012	1.875
ncpcResampling	0	0	0
plot-comma-DDGraph-comma-missing-dash-method	0	0	0
plotBNLearn	0.278	0.002	0.280
plotPCalg	16.290	0.055	16.427
prob-dot-distr-dot-norm	0.001	0.000	0.001
prob-dot-distr-dot-unif	0.001	0.000	0.001
random-dot-bn-dot-fit	0.005	0.001	0.005
readFurlongData	0.032	0.012	0.044
recalculateSVMparams	0.001	0.000	0.000
toDDDataSet-comma-FurlongDataSet-dash-method	0.112	0.005	0.117
toyExample	0.078	0.000	0.080