ddgraph 1.21.0
Robert Stojnic
| Snapshot Date: 2017-09-07 17:17:05 -0400 (Thu, 07 Sep 2017) | | URL: https://git.bioconductor.org/packages/ddgraph | | Last Commit: dcb2883 | | Last Changed Date: 2017-04-24 15:50:57 -0400 (Mon, 24 Apr 2017) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | ERROR | | |
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | ERROR | OK | |
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | [ ERROR ] | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ddgraph_1.21.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.6-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 ‘1.21.0’
* 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-3.6-bioc/meat/ddgraph.Rcheck/00check.log’
for details.
* 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-3.6-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)