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: 2013-03-25 01:04:50 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 01:10:30 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 340.2 seconds

RetCode: 0

Status:  OK

CheckDir: ddgraph.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/ddgraph.Rcheck’
* using R version 3.0.0 beta (2013-03-19 r62328)
* 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 ... [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 ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... [49s/50s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
plotPCalg      27.630  0.004  28.352
calcDependence 11.252  0.048  11.339
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘test-all.R’ [185s/188s]
 [186s/188s] 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"/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c mcX2cloop.cpp -o mcX2cloop.o
mcX2cloop.cpp: In function ‘SEXPREC* mcX2CLoopC(SEXP, SEXP, SEXP, SEXP)’:
mcX2cloop.cpp:14:2: warning: label ‘Rcpp’ defined but not used [-Wunused-label]
g++ -shared -L/usr/local/lib -o ddgraph.so mcX2cloop.o -L/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/lib -lRcpp -Wl,-rpath,/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/lib -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /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	0.036	0.004	0.040
biased-dot-graph	0.008	0.004	0.011
calcDependence	11.252	0.048	11.339
ciTest-comma-DDDataSet-dash-method	0.088	0.004	0.092
combinationsTest	0.06	0.00	0.06
convertPvalueToColorIndex	0.016	0.000	0.015
convertToFactor	0.032	0.000	0.029
estimateNetworkDistribution	0.208	0.000	0.205
formulaFalseNeg	0.024	0.000	0.024
independent-dot-contributions-dot-formula-dot-mul	0.036	0.000	0.039
independent-dot-contributions-dot-formula	0.028	0.000	0.028
is-dot-binary	0.036	0.000	0.036
logseq	0.020	0.000	0.019
makeDDDataSet	0.040	0.000	0.043
mapEnrichmentToColorsDual	0.016	0.000	0.015
mcMITest	0.024	0.000	0.026
mcX2Test	0.048	0.000	0.048
mcX2TestB50k	0.917	0.004	0.920
mesoBin	0.020	0.000	0.018
mesoCont	0.016	0.000	0.018
ncpc	3.888	0.008	3.922
ncpcResampling	0.020	0.000	0.019
plot-comma-DDGraph-comma-missing-dash-method	0.02	0.00	0.02
plotBNLearn	0.676	0.000	0.689
plotPCalg	27.630	0.004	28.352
prob-dot-distr-dot-norm	0.008	0.000	0.007
prob-dot-distr-dot-unif	0.008	0.000	0.009
random-dot-bn-dot-fit	0.028	0.000	0.030
readFurlongData	0.048	0.004	0.054
recalculateSVMparams	0.016	0.000	0.015
toDDDataSet-comma-FurlongDataSet-dash-method	0.208	0.004	0.211
toyExample	0.148	0.000	0.148