Package: ddgraph

Version: 1.3.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ddgraph_1.3.1.tar.gz

StartedAt: 2013-03-24 04:13:18 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 04:17:43 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 265.0 seconds

RetCode: 0

Status:  OK

CheckDir: ddgraph.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/ddgraph.Rcheck'
* using R version 3.0.0 beta (2013-03-21 r62346)
* 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 '1.3.1'
* 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 ... [14s/15s] 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 ... NOTE
File '/Users/biocbuild/bbs-2.12-bioc/meat/ddgraph.Rcheck/ddgraph/libs/ddgraph.so':
  Found non-API calls to R: 'Rf_EncodeComplex', 'Rf_EncodeReal',
    'Rf_formatComplex', 'Rf_formatReal'

Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking examples ... [42s/42s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
plotPCalg      22.695  0.248  23.085
calcDependence  9.854  0.114  10.043
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'test-all.R' [127s/131s]
 [128s/131s] 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

NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.12-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  -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 -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
   'ddgraph.Rnw' 
** testing if installed package can be loaded
* DONE (ddgraph)

name	user	system	elapsed
biased-dot-bn-dot-fit	0.143	0.003	0.153
biased-dot-graph	0.012	0.000	0.012
calcDependence	9.854	0.114	10.043
ciTest-comma-DDDataSet-dash-method	0.053	0.003	0.057
combinationsTest	0.047	0.004	0.051
convertPvalueToColorIndex	0.011	0.000	0.012
convertToFactor	0.020	0.001	0.021
estimateNetworkDistribution	0.192	0.005	0.197
formulaFalseNeg	0.013	0.000	0.013
independent-dot-contributions-dot-formula-dot-mul	0.025	0.001	0.026
independent-dot-contributions-dot-formula	0.016	0.001	0.015
is-dot-binary	0.020	0.001	0.021
logseq	0.008	0.001	0.009
makeDDDataSet	0.017	0.001	0.018
mapEnrichmentToColorsDual	0.140	0.001	0.142
mcMITest	0.019	0.001	0.022
mcX2Test	0.035	0.001	0.036
mcX2TestB50k	0.585	0.019	0.603
mesoBin	0.023	0.005	0.028
mesoCont	0.012	0.004	0.016
ncpc	3.461	0.049	3.524
ncpcResampling	0.013	0.003	0.016
plot-comma-DDGraph-comma-missing-dash-method	0.008	0.004	0.012
plotBNLearn	0.679	0.019	0.703
plotPCalg	22.695	0.248	23.085
prob-dot-distr-dot-norm	0.009	0.002	0.011
prob-dot-distr-dot-unif	0.005	0.001	0.006
random-dot-bn-dot-fit	0.014	0.002	0.015
readFurlongData	0.073	0.034	0.107
recalculateSVMparams	0.013	0.001	0.013
toDDDataSet-comma-FurlongDataSet-dash-method	0.220	0.004	0.225
toyExample	0.148	0.004	0.151