BioC 3.2: CHECK report for ddgraph on linux1.bioconductor.org

Package: ddgraph

Version: 1.14.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings ddgraph_1.14.0.tar.gz

StartedAt: 2015-10-27 02:48:22 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 02:50:39 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 137.1 seconds

RetCode: 0

Status:  OK

CheckDir: ddgraph.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings ddgraph_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/ddgraph.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-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 ‘1.14.0’
* 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 ... [8s/8s] 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’
plot,DDGraph-missing : .local: no visible global function definition
  for ‘layoutGraph’
plot,DDGraph-missing : .local: no visible global function definition
  for ‘renderGraph’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [26s/26s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
plotPCalg      15.347  0.007  15.374
calcDependence  6.339  0.016   6.356
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’ [56s/56s]
 [56s/56s] 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

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/ddgraph.Rcheck/00check.log’
for details.

* installing *source* package ‘ddgraph’ ...
** libs
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-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]
  Rcpp:NumericVector res(iB);
  ^
g++ -shared -L/home/biocbuild/bbs-3.2-bioc/R/lib -L/usr/local/lib -o ddgraph.so mcX2cloop.o -L/home/biocbuild/bbs-3.2-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.2-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	0.007	0.003	0.011
biased-dot-graph	0.003	0.000	0.003
calcDependence	6.339	0.016	6.356
ciTest-comma-DDDataSet-dash-method	0.028	0.000	0.028
combinationsTest	0.030	0.000	0.031
convertPvalueToColorIndex	0.000	0.000	0.001
convertToFactor	0.006	0.000	0.006
estimateNetworkDistribution	0.099	0.000	0.099
formulaFalseNeg	0.001	0.000	0.001
independent-dot-contributions-dot-formula-dot-mul	0.003	0.000	0.002
independent-dot-contributions-dot-formula	0.001	0.000	0.002
is-dot-binary	0.002	0.000	0.002
logseq	0.001	0.000	0.001
makeDDDataSet	0.002	0.000	0.002
mapEnrichmentToColorsDual	0.000	0.000	0.001
mcMITest	0.009	0.000	0.010
mcX2Test	0.017	0.000	0.016
mcX2TestB50k	0.393	0.003	0.397
mesoBin	0.004	0.001	0.004
mesoCont	0.004	0.000	0.004
ncpc	1.591	0.015	1.608
ncpcResampling	0	0	0
plot-comma-DDGraph-comma-missing-dash-method	0.001	0.001	0.000
plotBNLearn	0.190	0.003	0.194
plotPCalg	15.347	0.007	15.374
prob-dot-distr-dot-norm	0.001	0.000	0.000
prob-dot-distr-dot-unif	0.000	0.000	0.001
random-dot-bn-dot-fit	0.004	0.000	0.004
readFurlongData	0.024	0.012	0.035
recalculateSVMparams	0.001	0.000	0.000
toDDDataSet-comma-FurlongDataSet-dash-method	0.117	0.000	0.121
toyExample	0.086	0.000	0.086