Package: ddgraph

Version: 1.3.1

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings ddgraph_1.3.1.tar.gz

StartedAt: 2013-01-16 01:56:39 -0800 (Wed, 16 Jan 2013)

EndedAt: 2013-01-16 02:00:11 -0800 (Wed, 16 Jan 2013)

EllapsedTime: 212.1 seconds

RetCode: 0

Status:  OK

CheckDir: ddgraph.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/ddgraph.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* using platform: x86_64-unknown-linux-gnu (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 ‘1.3.1’
* 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 ... 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 installed files from ‘inst/doc’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
plotPCalg      20.973  0.016  21.004
calcDependence  8.928  0.048   9.002
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘test-all.R’
 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
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c mcX2cloop.cpp -o mcX2cloop.o
g++ -shared -L/usr/local/lib64 -o ddgraph.so mcX2cloop.o -L/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/lib -lRcpp -Wl,-rpath,/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/lib -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /loc/home/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	0.028	0.000	0.029
biased-dot-graph	0.012	0.000	0.012
calcDependence	8.928	0.048	9.002
ciTest-comma-DDDataSet-dash-method	0.052	0.000	0.052
combinationsTest	0.044	0.000	0.044
convertPvalueToColorIndex	0.008	0.000	0.008
convertToFactor	0.02	0.00	0.02
estimateNetworkDistribution	0.172	0.004	0.175
formulaFalseNeg	0.016	0.000	0.018
independent-dot-contributions-dot-formula-dot-mul	0.016	0.000	0.017
independent-dot-contributions-dot-formula	0.016	0.000	0.017
is-dot-binary	0.016	0.004	0.022
logseq	0.008	0.000	0.008
makeDDDataSet	0.016	0.000	0.017
mapEnrichmentToColorsDual	0.016	0.000	0.017
mcMITest	0.024	0.000	0.024
mcX2Test	0.192	0.000	0.194
mcX2TestB50k	0.420	0.000	0.421
mesoBin	0.02	0.00	0.02
mesoCont	0.008	0.000	0.012
ncpc	3.328	0.012	3.344
ncpcResampling	0.012	0.000	0.010
plot-comma-DDGraph-comma-missing-dash-method	0.016	0.000	0.016
plotBNLearn	0.601	0.004	0.601
plotPCalg	20.973	0.016	21.004
prob-dot-distr-dot-norm	0.004	0.000	0.005
prob-dot-distr-dot-unif	0.016	0.000	0.015
random-dot-bn-dot-fit	0.012	0.000	0.011
readFurlongData	0.036	0.012	0.047
recalculateSVMparams	0.008	0.000	0.008
toDDDataSet-comma-FurlongDataSet-dash-method	0.148	0.000	0.150
toyExample	0.136	0.000	0.142