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BioC 3.5: CHECK report for ddgraph on oaxaca

This page was generated on 2017-03-04 16:43:46 -0500 (Sat, 04 Mar 2017).

Package 307/1339HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ddgraph 1.19.0
Robert Stojnic
Snapshot Date: 2017-03-03 17:15:47 -0500 (Fri, 03 Mar 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ddgraph
Last Changed Rev: 122712 / Revision: 127142
Last Changed Date: 2016-10-17 15:10:43 -0400 (Mon, 17 Oct 2016)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  ERROR  skipped 
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 

Summary

Package: ddgraph
Version: 1.19.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ddgraph_1.19.0.tar.gz
StartedAt: 2017-03-04 01:36:05 -0800 (Sat, 04 Mar 2017)
EndedAt: 2017-03-04 01:38:24 -0800 (Sat, 04 Mar 2017)
EllapsedTime: 139.5 seconds
RetCode: 0
Status:  OK 
CheckDir: ddgraph.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ddgraph_1.19.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/ddgraph.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.19.0’
* 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 ... 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
biased.bn.fit: no visible global function definition for ‘rbeta’
color.legend.DDGraph: no visible global function definition for ‘par’
color.legend.DDGraph: no visible global function definition for
  ‘strheight’
color.legend.DDGraph: no visible global function definition for
  ‘strwidth’
color.legend.DDGraph: no visible global function definition for ‘text’
combinationsTest: no visible global function definition for
  ‘fisher.test’
combinationsTest: no visible global function definition for ‘p.adjust’
customPlotPCAlgo: no visible global function definition for
  ‘layoutGraph’
customPlotPCAlgo: no visible global function definition for
  ‘renderGraph’
formulaFalseNeg: no visible global function definition for ‘runif’
independent.contributions.formula: no visible global function
  definition for ‘runif’
independent.contributions.formula.mul: no visible global function
  definition for ‘runif’
makeDDDataSet: no visible binding for global variable ‘var’
ncpc: no visible global function definition for ‘p.adjust’
ncpc : <anonymous>: no visible global function definition for
  ‘p.adjust’
pValueAfterMultipleTesting: no visible global function definition for
  ‘p.adjust’
plotSVMPerformance: no visible global function definition for
  ‘prediction’
plotSVMPerformance: no visible global function definition for
  ‘performance’
plotSVMPerformance: no visible global function definition for ‘pdf’
plotSVMPerformance: no visible global function definition for ‘par’
plotSVMPerformance: no visible global function definition for ‘abline’
plotSVMPerformance: no visible global function definition for ‘barplot’
plotSVMPerformance: no visible global function definition for ‘hist’
plotSVMPerformance: no visible global function definition for ‘dev.off’
predSVM: no visible global function definition for ‘predict’
prob.distr.norm: no visible global function definition for ‘rnorm’
prob.distr.unif: no visible global function definition for ‘runif’
readFurlongData: no visible global function definition for ‘glob2rx’
readFurlongData: no visible global function definition for ‘read.delim’
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’
ciTest,DDDataSet: no visible global function definition for
  ‘fisher.test’
plot,DDGraph-missing: no visible global function definition for ‘par’
plot,DDGraph-missing: no visible global function definition for
  ‘layoutGraph’
plot,DDGraph-missing: no visible global function definition for
  ‘renderGraph’
Undefined global functions or variables:
  abline barplot dev.off fisher.test glob2rx hist layoutGraph p.adjust
  par pdf performance predict prediction rbeta read.delim renderGraph
  rnorm runif strheight strwidth svm text var
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "abline", "barplot", "hist", "par", "strheight",
             "strwidth", "text")
  importFrom("stats", "fisher.test", "p.adjust", "predict", "rbeta",
             "rnorm", "runif", "var")
  importFrom("utils", "glob2rx", "read.delim")
to your NAMESPACE file.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
plotPCalg      12.048  0.057  12.110
calcDependence  7.672  0.069   7.777
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/ddgraph.Rcheck/00check.log’
for details.


ddgraph.Rcheck/00install.out:

* installing *source* package ‘ddgraph’ ...
** libs
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c mcX2cloop.cpp -o mcX2cloop.o
mcX2cloop.cpp:14:2: warning: unused label 'Rcpp' [-Wunused-label]
        Rcpp:NumericVector res(iB);
        ^˜˜˜˜
1 warning generated.
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/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-3.5-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)

ddgraph.Rcheck/ddgraph-Ex.timings:

nameusersystemelapsed
biased-dot-bn-dot-fit0.0880.0070.121
biased-dot-graph0.2950.0060.304
calcDependence7.6720.0697.777
ciTest-comma-DDDataSet-dash-method0.0180.0000.018
combinationsTest0.0260.0030.028
convertPvalueToColorIndex0.0010.0000.001
convertToFactor0.0060.0000.006
estimateNetworkDistribution0.3820.0020.385
formulaFalseNeg0.0040.0000.004
independent-dot-contributions-dot-formula-dot-mul0.0030.0010.002
independent-dot-contributions-dot-formula0.0020.0000.002
is-dot-binary0.0020.0000.002
logseq000
makeDDDataSet0.0040.0010.004
mapEnrichmentToColorsDual0.0000.0000.001
mcMITest0.0080.0000.008
mcX2Test0.0130.0000.013
mcX2TestB50k0.1720.0030.175
mesoBin0.0020.0000.003
mesoCont0.0020.0000.002
ncpc1.4760.0231.499
ncpcResampling0.0000.0000.001
plot-comma-DDGraph-comma-missing-dash-method0.0010.0000.001
plotBNLearn0.4040.0050.409
plotPCalg12.048 0.05712.110
prob-dot-distr-dot-norm0.0010.0000.001
prob-dot-distr-dot-unif0.0010.0000.000
random-dot-bn-dot-fit0.0140.0010.014
readFurlongData0.0320.0150.047
recalculateSVMparams0.0010.0000.000
toDDDataSet-comma-FurlongDataSet-dash-method0.2290.0040.232
toyExample0.0810.0030.083