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BioC 3.5: CHECK report for ddgraph on veracruz2

This page was generated on 2017-08-16 13:30:17 -0400 (Wed, 16 Aug 2017).

Package 321/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ddgraph 1.20.0
Robert Stojnic
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/ddgraph
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  ERROR 
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  ERROR  OK 
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ ERROR ] OK 

Summary

Package: ddgraph
Version: 1.20.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ddgraph_1.20.0.tar.gz
StartedAt: 2017-08-16 01:47:45 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 01:49:50 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 125.6 seconds
RetCode: 1
Status:  ERROR 
CheckDir: ddgraph.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ddgraph_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/ddgraph.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.20.0’
* 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 ... ERROR
Running examples in ‘ddgraph-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: calcDependence
> ### Title: Dependence with target variable
> ### Aliases: calcDependence
> 
> ### ** Examples
> # load in the data for fly mesoderm
> data(mesoBin)
> 
> # increase alpha to 0.1, suppress progress output
> calcDependence(mesoBin$VM, "ncpc", alpha=0.05)
$obj
DDGraph produced with ncpc algorithm
Direct:  
Joint: Bin 6-8h Bin 8-10h 
Indirect: Tin 6-8h Bin 10-12h Twi 2-4h Twi 4-6h Bap 6-8h 
Using P-value alpha cutoff = 0.05 with conditional independence test = "mc-x2-c"

$nbr
[1] "Bin 6-8h"  "Bin 8-10h"

$labels
$labels$direct
NULL

$labels$joint
[1] "Bin 6-8h"  "Bin 8-10h"

$labels$indirect
[1] "Tin 6-8h"   "Bin 10-12h" "Twi 2-4h"   "Twi 4-6h"   "Bap 6-8h"  


$table
          name          type explained.by explained.pval marginal.pval
5    Bin 8-10h         joint     Bin 6-8h         0.0614        0.0004
4     Bin 6-8h         joint    Bin 8-10h         0.0810        0.0006
10    Bap 6-8h weak indirect     Bin 6-8h         0.0580        0.0058
6   Bin 10-12h weak indirect    Bin 8-10h         1.0000        0.0138
7     Twi 2-4h weak indirect     Bin 6-8h         0.1504        0.0216
8     Twi 4-6h weak indirect    Bin 8-10h         0.1412        0.0268
3     Tin 6-8h weak indirect     Bin 6-8h         0.6406        0.0318
2     Tin 4-6h no dependence                          NA        0.3974
9     Twi 6-8h no dependence                          NA        0.4272
15 Mef2 10-12h no dependence                          NA        0.4934
13   Mef2 6-8h no dependence                          NA        0.5844
12   Mef2 4-6h no dependence                          NA        0.5906
14  Mef2 8-10h no dependence                          NA        0.7392
1     Tin 2-4h no dependence                          NA        1.0000
11   Mef2 2-4h no dependence                          NA        1.0000
       log2FC
5   2.6147098
4   1.9517448
10  1.6147098
6   1.8211607
7  -1.7776076
8  -2.4441838
3   1.1243842
2   0.4627068
9  -0.6416299
15 -1.2921808
13 -0.5729172
12 -0.4002405
14 -0.5816874
1   0.1996723
11 -0.5007674

> 
> # run ncpc* with mutual information with shrinkage and minimal numbers of 
> # samples per conditioning set of 15
> calcDependence(mesoBin$VM, "ncpc*", test.type="mi-sh", min.table.size=15)
$obj
DDGraph produced with ncpc* algorithm
Direct:  
Joint: Bin 6-8h Bin 8-10h 
Conditional:  
Conditional joint:  
Indirect: Tin 6-8h Bin 10-12h Twi 2-4h Twi 4-6h Bap 6-8h 
Using P-value alpha cutoff = 0.05 with conditional independence test = "mi-sh"

$nbr
[1] "Bin 6-8h"  "Bin 8-10h"

$mb
[1] "Bin 6-8h"  "Bin 8-10h"

$labels
$labels$direct
NULL

$labels$joint
[1] "Bin 6-8h"  "Bin 8-10h"

$labels$indirect
[1] "Tin 6-8h"   "Bin 10-12h" "Twi 2-4h"   "Twi 4-6h"   "Bap 6-8h"  

$labels$conditional
NULL

$labels$conditionalJoint
NULL


$table
          name          type explained.by explained.pval conditional.type
5    Bin 8-10h         joint     Bin 6-8h      0.1129735                 
4     Bin 6-8h         joint    Bin 8-10h      0.1543618                 
10    Bap 6-8h weak indirect     Bin 6-8h      0.1077358                 
6   Bin 10-12h weak indirect    Bin 8-10h      0.8052702                 
7     Twi 2-4h weak indirect     Bin 6-8h      0.1527278                 
8     Twi 4-6h weak indirect    Bin 8-10h      0.1125118                 
3     Tin 6-8h weak indirect     Bin 6-8h      0.6210417                 
15 Mef2 10-12h no dependence                          NA                 
2     Tin 4-6h no dependence                          NA                 
9     Twi 6-8h no dependence                          NA                 
13   Mef2 6-8h no dependence                          NA                 
12   Mef2 4-6h no dependence                          NA                 
14  Mef2 8-10h no dependence                          NA                 
1     Tin 2-4h no dependence                          NA                 
11   Mef2 2-4h no dependence                          NA                 
   conditional.on conditional.explained conditional.pval marginal.pval
5                                                         0.0004145264
4                                                         0.0005420886
10                                                        0.0055307127
6                                                         0.0135478039
7                                                         0.0165514158
8                                                         0.0172271300
3                                                         0.0345167513
15                                                        0.3338481472
2                                                         0.3520964001
9                                                         0.4145694525
13                                                        0.4794555793
12                                                        0.5676072714
14                                                        0.5885109046
1                                                         0.7031989752
11                                                        0.7769814858
       log2FC
5   2.6147098
4   1.9517448
10  1.6147098
6   1.8211607
7  -1.7776076
8  -2.4441838
3   1.1243842
15 -1.2921808
2   0.4627068
9  -0.6416299
13 -0.5729172
12 -0.4002405
14 -0.5816874
1   0.1996723
11 -0.5007674

> 
> # run PC algorithm using the G^2 test from pcalg package
> calcDependence(mesoBin$VM, "pc", indepTest=pcalg::binCItest)
$obj
Object of class 'pcAlgo', from Call:
pc(suffStat = suffStat, indepTest = indepTest, alpha = alpha, 
    p = p, verbose = verbose)
Number of undirected edges:  2 
Number of directed edges:    12 
Total number of edges:       14 

$nbr
character(0)

$mb
character(0)

> 
> # run hill-climbing with BIC penalization and plot the resulting Bayesian Network
> # NOTE: plotting requires the Rgraphviz package
> if(require("Rgraphviz"))
+ calcDependence(mesoBin$VM, "hc-bic", make.plot=TRUE)
Loading required package: Rgraphviz
Loading required package: grid
Error in check.colour(highlight$col) : 
  highlight$col must be a single colour.
Calls: calcDependence ... plotBNLearn -> graphviz.plot -> graphviz.backend -> check.colour
Execution halted
* 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: 1 ERROR, 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   -fPIC  -Wall -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-fit0.0850.0040.096
biased-dot-graph0.2480.0090.266