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BioC 3.4: CHECK report for ddgraph on morelia

This page was generated on 2016-09-21 03:51:39 -0700 (Wed, 21 Sep 2016).

Package 294/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ddgraph 1.17.0
Robert Stojnic
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ddgraph
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: ddgraph
Version: 1.17.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ddgraph_1.17.0.tar.gz
StartedAt: 2016-09-20 05:23:48 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 05:25:51 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 123.3 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_1.17.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/ddgraph.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.17.0’
* 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 12.513   0.09  12.611
* 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-3.4-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/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/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-3.4-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-fit0.0140.0030.142
biased-dot-graph0.0060.0010.006
calcDependence4.4590.0514.513
ciTest-comma-DDDataSet-dash-method0.0230.0010.024
combinationsTest0.0270.0030.030
convertPvalueToColorIndex0.0010.0000.000
convertToFactor0.0060.0000.006
estimateNetworkDistribution0.0840.0030.086
formulaFalseNeg0.0020.0000.002
independent-dot-contributions-dot-formula-dot-mul0.0020.0000.002
independent-dot-contributions-dot-formula0.0010.0000.002
is-dot-binary0.0010.0000.002
logseq0.0010.0000.001
makeDDDataSet0.0020.0000.001
mapEnrichmentToColorsDual0.0000.0000.001
mcMITest0.0060.0000.006
mcX2Test0.0070.0000.007
mcX2TestB50k0.1510.0030.154
mesoBin0.0020.0010.003
mesoCont0.0020.0010.003
ncpc1.2460.0101.256
ncpcResampling0.0010.0000.000
plot-comma-DDGraph-comma-missing-dash-method0.0000.0000.001
plotBNLearn0.1970.0030.201
plotPCalg12.513 0.09012.611
prob-dot-distr-dot-norm0.0000.0000.001
prob-dot-distr-dot-unif000
random-dot-bn-dot-fit0.0040.0010.004
readFurlongData0.0290.0140.043
recalculateSVMparams0.0010.0000.000
toDDDataSet-comma-FurlongDataSet-dash-method0.2120.0010.213
toyExample0.0410.0010.042