BioC 2.13: CHECK report for ddgraph on perceval

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/ddgraph.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.6.3’
* 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 ... [13s/13s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘Rcpp’ ‘testthat’
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
* 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 ... 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 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘ddgraph.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [41s/41s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
plotPCalg      23.349  0.079  23.525
calcDependence  9.205  0.078   9.293
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘test-all.R’ [107s/108s]
 [108s/108s] 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

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/ddgraph.Rcheck/00check.log’
for details.

* 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 -Wall  -c mcX2cloop.cpp -o mcX2cloop.o
mcX2cloop.cpp: In function ‘SEXPREC* mcX2CLoopC(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)’:
mcX2cloop.cpp:14: warning: label ‘Rcpp’ defined but not used
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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.13-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	0.146	0.003	0.149
biased-dot-graph	0.008	0.000	0.009
calcDependence	9.205	0.078	9.293
ciTest-comma-DDDataSet-dash-method	0.049	0.003	0.053
combinationsTest	0.039	0.003	0.042
convertPvalueToColorIndex	0.008	0.000	0.009
convertToFactor	0.017	0.001	0.018
estimateNetworkDistribution	0.140	0.003	0.145
formulaFalseNeg	0.023	0.001	0.023
independent-dot-contributions-dot-formula-dot-mul	0.013	0.001	0.014
independent-dot-contributions-dot-formula	0.011	0.001	0.011
is-dot-binary	0.012	0.000	0.013
logseq	0.009	0.000	0.009
makeDDDataSet	0.013	0.001	0.014
mapEnrichmentToColorsDual	0.009	0.001	0.010
mcMITest	0.025	0.001	0.026
mcX2Test	0.033	0.000	0.034
mcX2TestB50k	0.423	0.009	0.441
mesoBin	0.013	0.003	0.015
mesoCont	0.014	0.002	0.016
ncpc	3.368	0.036	3.445
ncpcResampling	0.010	0.002	0.012
plot-comma-DDGraph-comma-missing-dash-method	0.011	0.002	0.017
plotBNLearn	0.561	0.014	0.591
plotPCalg	23.349	0.079	23.525
prob-dot-distr-dot-norm	0.009	0.003	0.012
prob-dot-distr-dot-unif	0.008	0.001	0.009
random-dot-bn-dot-fit	0.027	0.003	0.031
readFurlongData	0.040	0.022	0.062
recalculateSVMparams	0.007	0.000	0.007
toDDDataSet-comma-FurlongDataSet-dash-method	0.160	0.003	0.164
toyExample	0.105	0.005	0.110

BioC 2.13: CHECK report for ddgraph on perceval

Summary

Command output