Package suggested but not available for checking: ‘r2cytoscape’
Missing or unexported objects:
  ‘gRbase::M2graphNEL’ ‘gRbase::graphNEL2M’
Running examples in ‘SourceSet-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ripAllRootsClique
> ### Title: All possible RIP orderings
> ### Aliases: ripAllRootsClique
> 
> ### ** Examples
> 
> if(require(gRbase)){
+ 
+   ## decomposable graph
+   ug.graph<-ug(~1:2:3+3:4+4:5:6:7)
+   ug.rip.all<-ripAllRootsClique(ug.graph)
+   # 7 variables
+   length(ug.rip.all$elements$variables)
+   # 3 max.cliques
+   length(ug.rip.all$elements$cliques)
+   # 7 unique components
+   nrow(ug.rip.all$elements$components)
+   # all rip orderings:
+   ug.rip.all$indices$ordering
+ 
+   ## directed graph
+   dag.graph<-dag(~3:1+3:2+4:3)
+   dag.rip.all<-ripAllRootsClique(dag.graph)
+   # triangulated and morliazed graph
+   dag.rip.all$graph
+   # all rip orderings
+   dag.rip.all$indices$ordering
+ }
Loading required package: gRbase
Error in ripAllRootsClique(ug.graph) : 
  graph argument is not a graphNEL object
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘SourceSet.Rmd’ using rmarkdown

Quitting from lines 151-158 [unnamed-chunk-5] (SourceSet.Rmd)
Error: processing vignette 'SourceSet.Rmd' failed with diagnostics:
Input must be a matrix or a dgCMatrix

--- failed re-building ‘SourceSet.Rmd’

SUMMARY: processing the following file failed:
  ‘SourceSet.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘r2cytoscape’
Missing or unexported objects:
  ‘gRbase::M2graphNEL’ ‘gRbase::graphNEL2M’
Running examples in ‘SourceSet-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ripAllRootsClique
> ### Title: All possible RIP orderings
> ### Aliases: ripAllRootsClique
> 
> ### ** Examples
> 
> if(require(gRbase)){
+ 
+   ## decomposable graph
+   ug.graph<-ug(~1:2:3+3:4+4:5:6:7)
+   ug.rip.all<-ripAllRootsClique(ug.graph)
+   # 7 variables
+   length(ug.rip.all$elements$variables)
+   # 3 max.cliques
+   length(ug.rip.all$elements$cliques)
+   # 7 unique components
+   nrow(ug.rip.all$elements$components)
+   # all rip orderings:
+   ug.rip.all$indices$ordering
+ 
+   ## directed graph
+   dag.graph<-dag(~3:1+3:2+4:3)
+   dag.rip.all<-ripAllRootsClique(dag.graph)
+   # triangulated and morliazed graph
+   dag.rip.all$graph
+   # all rip orderings
+   dag.rip.all$indices$ordering
+ }
Loading required package: gRbase
Error in ripAllRootsClique(ug.graph) : 
  graph argument is not a graphNEL object
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘SourceSet.Rmd’ using rmarkdown

Quitting from lines 151-158 [unnamed-chunk-5] (SourceSet.Rmd)
Error: processing vignette 'SourceSet.Rmd' failed with diagnostics:
Input must be a matrix or a dgCMatrix

--- failed re-building ‘SourceSet.Rmd’

SUMMARY: processing the following file failed:
  ‘SourceSet.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘r2cytoscape’
Missing or unexported objects:
  ‘gRbase::M2graphNEL’ ‘gRbase::graphNEL2M’
Running examples in ‘SourceSet-Ex.R’ failed
The error most likely occurred in:

> ### Name: ripAllRootsClique
> ### Title: All possible RIP orderings
> ### Aliases: ripAllRootsClique
> 
> ### ** Examples
> 
> if(require(gRbase)){
+ 
+   ## decomposable graph
+   ug.graph<-ug(~1:2:3+3:4+4:5:6:7)
+   ug.rip.all<-ripAllRootsClique(ug.graph)
+   # 7 variables
+   length(ug.rip.all$elements$variables)
+   # 3 max.cliques
+   length(ug.rip.all$elements$cliques)
+   # 7 unique components
+   nrow(ug.rip.all$elements$components)
+   # all rip orderings:
+   ug.rip.all$indices$ordering
+ 
+   ## directed graph
+   dag.graph<-dag(~3:1+3:2+4:3)
+   dag.rip.all<-ripAllRootsClique(dag.graph)
+   # triangulated and morliazed graph
+   dag.rip.all$graph
+   # all rip orderings
+   dag.rip.all$indices$ordering
+ }
Loading required package: gRbase
Error in ripAllRootsClique(ug.graph) : 
  graph argument is not a graphNEL object
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘SourceSet.Rmd’ using rmarkdown

Quitting from lines 151-158 [unnamed-chunk-5] (SourceSet.Rmd)
Error: processing vignette 'SourceSet.Rmd' failed with diagnostics:
Input must be a matrix or a dgCMatrix

--- failed re-building ‘SourceSet.Rmd’

SUMMARY: processing the following file failed:
  ‘SourceSet.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘r2cytoscape’
Missing or unexported objects:
  ‘gRbase::M2graphNEL’ ‘gRbase::graphNEL2M’
Running examples in ‘SourceSet-Ex.R’ failed
The error most likely occurred in:

> ### Name: ripAllRootsClique
> ### Title: All possible RIP orderings
> ### Aliases: ripAllRootsClique
> 
> ### ** Examples
> 
> if(require(gRbase)){
+ 
+   ## decomposable graph
+   ug.graph<-ug(~1:2:3+3:4+4:5:6:7)
+   ug.rip.all<-ripAllRootsClique(ug.graph)
+   # 7 variables
+   length(ug.rip.all$elements$variables)
+   # 3 max.cliques
+   length(ug.rip.all$elements$cliques)
+   # 7 unique components
+   nrow(ug.rip.all$elements$components)
+   # all rip orderings:
+   ug.rip.all$indices$ordering
+ 
+   ## directed graph
+   dag.graph<-dag(~3:1+3:2+4:3)
+   dag.rip.all<-ripAllRootsClique(dag.graph)
+   # triangulated and morliazed graph
+   dag.rip.all$graph
+   # all rip orderings
+   dag.rip.all$indices$ordering
+ }
Loading required package: gRbase
Error in ripAllRootsClique(ug.graph) : 
  graph argument is not a graphNEL object
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘SourceSet.Rmd’ using rmarkdown

Quitting from lines 151-158 [unnamed-chunk-5] (SourceSet.Rmd)
Error: processing vignette 'SourceSet.Rmd' failed with diagnostics:
Input must be a matrix or a dgCMatrix

--- failed re-building ‘SourceSet.Rmd’

SUMMARY: processing the following file failed:
  ‘SourceSet.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'r2cytoscape'
Missing or unexported objects:
  'gRbase::M2graphNEL' 'gRbase::graphNEL2M'
Running examples in 'SourceSet-Ex.R' failed
The error most likely occurred in:

> ### Name: ripAllRootsClique
> ### Title: All possible RIP orderings
> ### Aliases: ripAllRootsClique
> 
> ### ** Examples
> 
> if(require(gRbase)){
+ 
+   ## decomposable graph
+   ug.graph<-ug(~1:2:3+3:4+4:5:6:7)
+   ug.rip.all<-ripAllRootsClique(ug.graph)
+   # 7 variables
+   length(ug.rip.all$elements$variables)
+   # 3 max.cliques
+   length(ug.rip.all$elements$cliques)
+   # 7 unique components
+   nrow(ug.rip.all$elements$components)
+   # all rip orderings:
+   ug.rip.all$indices$ordering
+ 
+   ## directed graph
+   dag.graph<-dag(~3:1+3:2+4:3)
+   dag.rip.all<-ripAllRootsClique(dag.graph)
+   # triangulated and morliazed graph
+   dag.rip.all$graph
+   # all rip orderings
+   dag.rip.all$indices$ordering
+ }
Loading required package: gRbase
Error in ripAllRootsClique(ug.graph) : 
  graph argument is not a graphNEL object
Execution halted
Error(s) in re-building vignettes:
--- re-building 'SourceSet.Rmd' using rmarkdown

Quitting from lines 151-158 [unnamed-chunk-5] (SourceSet.Rmd)
Error: processing vignette 'SourceSet.Rmd' failed with diagnostics:
Input must be a matrix or a dgCMatrix

--- failed re-building 'SourceSet.Rmd'

SUMMARY: processing the following file failed:
  'SourceSet.Rmd'

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘r2cytoscape’
Missing or unexported objects:
  ‘gRbase::M2graphNEL’ ‘gRbase::graphNEL2M’
Running examples in ‘SourceSet-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ripAllRootsClique
> ### Title: All possible RIP orderings
> ### Aliases: ripAllRootsClique
> 
> ### ** Examples
> 
> if(require(gRbase)){
+ 
+   ## decomposable graph
+   ug.graph<-ug(~1:2:3+3:4+4:5:6:7)
+   ug.rip.all<-ripAllRootsClique(ug.graph)
+   # 7 variables
+   length(ug.rip.all$elements$variables)
+   # 3 max.cliques
+   length(ug.rip.all$elements$cliques)
+   # 7 unique components
+   nrow(ug.rip.all$elements$components)
+   # all rip orderings:
+   ug.rip.all$indices$ordering
+ 
+   ## directed graph
+   dag.graph<-dag(~3:1+3:2+4:3)
+   dag.rip.all<-ripAllRootsClique(dag.graph)
+   # triangulated and morliazed graph
+   dag.rip.all$graph
+   # all rip orderings
+   dag.rip.all$indices$ordering
+ }
Loading required package: gRbase
Error in ripAllRootsClique(ug.graph) : 
  graph argument is not a graphNEL object
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘SourceSet.Rmd’ using rmarkdown

Quitting from lines 151-158 [unnamed-chunk-5] (SourceSet.Rmd)
Error: processing vignette 'SourceSet.Rmd' failed with diagnostics:
Input must be a matrix or a dgCMatrix

--- failed re-building ‘SourceSet.Rmd’

SUMMARY: processing the following file failed:
  ‘SourceSet.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘r2cytoscape’
Missing or unexported objects:
  ‘gRbase::M2graphNEL’ ‘gRbase::graphNEL2M’
Running examples in ‘SourceSet-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ripAllRootsClique
> ### Title: All possible RIP orderings
> ### Aliases: ripAllRootsClique
> 
> ### ** Examples
> 
> if(require(gRbase)){
+ 
+   ## decomposable graph
+   ug.graph<-ug(~1:2:3+3:4+4:5:6:7)
+   ug.rip.all<-ripAllRootsClique(ug.graph)
+   # 7 variables
+   length(ug.rip.all$elements$variables)
+   # 3 max.cliques
+   length(ug.rip.all$elements$cliques)
+   # 7 unique components
+   nrow(ug.rip.all$elements$components)
+   # all rip orderings:
+   ug.rip.all$indices$ordering
+ 
+   ## directed graph
+   dag.graph<-dag(~3:1+3:2+4:3)
+   dag.rip.all<-ripAllRootsClique(dag.graph)
+   # triangulated and morliazed graph
+   dag.rip.all$graph
+   # all rip orderings
+   dag.rip.all$indices$ordering
+ }
Loading required package: gRbase
Error in ripAllRootsClique(ug.graph) : 
  graph argument is not a graphNEL object
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘SourceSet.Rmd’ using rmarkdown

Quitting from lines 151-158 [unnamed-chunk-5] (SourceSet.Rmd)
Error: processing vignette 'SourceSet.Rmd' failed with diagnostics:
Input must be a matrix or a dgCMatrix

--- failed re-building ‘SourceSet.Rmd’

SUMMARY: processing the following file failed:
  ‘SourceSet.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'r2cytoscape', 'hgu95av2.db'
Error(s) in re-building vignettes:
  ...
--- re-building ‘SourceSet.Rmd’ using rmarkdown
Failed with error:  'there is no package called 'hgu95av2.db''
Quitting from lines 512-527 (SourceSet.Rmd) 
Error: processing vignette 'SourceSet.Rmd' failed with diagnostics:
error in evaluating the argument 'x' in selecting a method for function 'as.list': object 'org.Hs.egSYMBOL' not found
--- failed re-building ‘SourceSet.Rmd’

SUMMARY: processing the following file failed:
  ‘SourceSet.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'r2cytoscape', 'hgu95av2.db'
Error(s) in re-building vignettes:
  ...
--- re-building ‘SourceSet.Rmd’ using rmarkdown
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.
Failed with error:  'there is no package called 'hgu95av2.db''
Quitting from lines 512-527 (SourceSet.Rmd) 
Error: processing vignette 'SourceSet.Rmd' failed with diagnostics:
error in evaluating the argument 'x' in selecting a method for function 'as.list': object 'org.Hs.egSYMBOL' not found
--- failed re-building ‘SourceSet.Rmd’

SUMMARY: processing the following file failed:
  ‘SourceSet.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'r2cytoscape'
Missing or unexported objects:
  'gRbase::M2graphNEL' 'gRbase::graphNEL2M'
Running examples in 'SourceSet-Ex.R' failed
The error most likely occurred in:

> ### Name: ripAllRootsClique
> ### Title: All possible RIP orderings
> ### Aliases: ripAllRootsClique
> 
> ### ** Examples
> 
> if(require(gRbase)){
+ 
+   ## decomposable graph
+   ug.graph<-ug(~1:2:3+3:4+4:5:6:7)
+   ug.rip.all<-ripAllRootsClique(ug.graph)
+   # 7 variables
+   length(ug.rip.all$elements$variables)
+   # 3 max.cliques
+   length(ug.rip.all$elements$cliques)
+   # 7 unique components
+   nrow(ug.rip.all$elements$components)
+   # all rip orderings:
+   ug.rip.all$indices$ordering
+ 
+   ## directed graph
+   dag.graph<-dag(~3:1+3:2+4:3)
+   dag.rip.all<-ripAllRootsClique(dag.graph)
+   # triangulated and morliazed graph
+   dag.rip.all$graph
+   # all rip orderings
+   dag.rip.all$indices$ordering
+ }
Loading required package: gRbase
Error in ripAllRootsClique(ug.graph) : 
  graph argument is not a graphNEL object
Execution halted
Error(s) in re-building vignettes:
--- re-building 'SourceSet.Rmd' using rmarkdown

Quitting from lines 151-158 [unnamed-chunk-5] (SourceSet.Rmd)
Error: processing vignette 'SourceSet.Rmd' failed with diagnostics:
Input must be a matrix or a dgCMatrix

--- failed re-building 'SourceSet.Rmd'

SUMMARY: processing the following file failed:
  'SourceSet.Rmd'

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'r2cytoscape', 'hgu95av2.db'
Error(s) in re-building vignettes:
  ...
--- re-building ‘SourceSet.Rmd’ using rmarkdown
Failed with error:  'there is no package called 'hgu95av2.db''

Quitting from lines 512-527 [unnamed-chunk-25] (SourceSet.Rmd)
Error: processing vignette 'SourceSet.Rmd' failed with diagnostics:
error in evaluating the argument 'x' in selecting a method for function 'as.list': object 'org.Hs.egSYMBOL' not found
--- failed re-building ‘SourceSet.Rmd’

SUMMARY: processing the following file failed:
  ‘SourceSet.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘r2cytoscape’
Package suggested but not available for checking: 'r2cytoscape'
Missing or unexported objects:
  'gRbase::M2graphNEL' 'gRbase::graphNEL2M'
Running examples in 'SourceSet-Ex.R' failed
The error most likely occurred in:

> ### Name: ripAllRootsClique
> ### Title: All possible RIP orderings
> ### Aliases: ripAllRootsClique
> 
> ### ** Examples
> 
> if(require(gRbase)){
+ 
+   ## decomposable graph
+   ug.graph<-ug(~1:2:3+3:4+4:5:6:7)
+   ug.rip.all<-ripAllRootsClique(ug.graph)
+   # 7 variables
+   length(ug.rip.all$elements$variables)
+   # 3 max.cliques
+   length(ug.rip.all$elements$cliques)
+   # 7 unique components
+   nrow(ug.rip.all$elements$components)
+   # all rip orderings:
+   ug.rip.all$indices$ordering
+ 
+   ## directed graph
+   dag.graph<-dag(~3:1+3:2+4:3)
+   dag.rip.all<-ripAllRootsClique(dag.graph)
+   # triangulated and morliazed graph
+   dag.rip.all$graph
+   # all rip orderings
+   dag.rip.all$indices$ordering
+ }
Loading required package: gRbase
Error in ripAllRootsClique(ug.graph) : 
  graph argument is not a graphNEL object
Execution halted
Error(s) in re-building vignettes:
--- re-building 'SourceSet.Rmd' using rmarkdown

Quitting from lines 151-158 [unnamed-chunk-5] (SourceSet.Rmd)
Error: processing vignette 'SourceSet.Rmd' failed with diagnostics:
Input must be a matrix or a dgCMatrix

--- failed re-building 'SourceSet.Rmd'

SUMMARY: processing the following file failed:
  'SourceSet.Rmd'

Error: Vignette re-building failed.
Execution halted