Last updated on 2023-10-06 07:57:12 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.6 | 4.24 | 59.87 | 64.11 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 0.6 | 3.81 | 46.47 | 50.28 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.6 | 82.15 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 0.6 | 88.83 | ERROR | |||
| r-devel-windows-x86_64 | 0.6 | 6.00 | 68.00 | 74.00 | ERROR | |
| r-patched-linux-x86_64 | 0.6 | 5.20 | 58.29 | 63.49 | ERROR | |
| r-release-linux-x86_64 | 0.6 | 3.49 | 57.93 | 61.42 | ERROR | |
| r-release-macos-arm64 | 0.6 | 44.00 | NOTE | |||
| r-release-macos-x86_64 | 0.6 | 72.00 | NOTE | |||
| r-release-windows-x86_64 | 0.6 | 8.00 | 77.00 | 85.00 | ERROR | |
| r-oldrel-macos-arm64 | 0.6 | 36.00 | NOTE | |||
| r-oldrel-macos-x86_64 | 0.6 | 14.00 | ERROR | |||
| r-oldrel-windows-x86_64 | 0.6 | 9.00 | 77.00 | 86.00 | ERROR |
Version: 0.6
Check: examples
Result: ERROR
Running examples in ‘simPATHy-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotCorGraph
> ### Title: Plot correlation or partial correlation matrix
> ### Aliases: plotCorGraph
>
> ### ** Examples
>
> if( require(gRbase) & require(graph)){
+ graph <- gRbase::ug(~a:b, ~a:c, ~c:d, ~b:d, ~b:c)
+
+ S <- matrix(c(2, 0.8,0.5,-0.3,
+ 0.8,1.5,0.6,-0.7,
+ 0.5,0.6,1, 0.7,
+ -0.3,-0.7,0.7,3), ncol=4,nrow=4)
+ colnames(S) <- rownames(S) <- graph::nodes(graph)
+
+ # Plot the correlation matrix of S
+ plotCorGraph(S)
+
+
+ S<-fitSgraph(graph = graph,S = S)
+ # Change the color range
+ plotCorGraph(S, colLim=c(-0.5,0.5))
+
+ # Visualize the adjacency matrix
+ plotCorGraph(S, type="cor", graph = graph)
+
+ # Show the partial correlation matrix
+ plotCorGraph(S, type="pcor", graph = graph)
+
+ # Plot the difference between two matrices
+ S2 <- S
+ # Change the element c~a
+ S2["a","c"] <- S2["c","a"]<- -0.1
+ plotCorGraph(S1=S, S2=S2)
+ plotCorGraph(S1=S, S2=S2, type="pcor")
+
+ S2<-fitSgraph(graph = graph,S = S2)
+ # Highlight the graphical structure
+ plotCorGraph(S1=S, S2=S2, type="pcor",graph = graph)
+ # Highlight the element c~a
+ plotCorGraph(S1=S, S2=S2, type="pcor",graph = graph,path = list(c("a","c")))
+
+ }
Loading required package: gRbase
Loading required package: graph
Loading required package: BiocGenerics
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
union, unique, unsplit, which.max, which.min
Attaching package: ‘graph’
The following objects are masked from ‘package:gRbase’:
addEdge, adj, connComp, edges, nodes, removeEdge, subGraph
Error: unable to find an inherited method for function ‘nodes’ for signature ‘object = "igraph"’
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 0.6
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘simPATHy.Rmd’ using rmarkdown
Quitting from lines 46-49 [unnamed-chunk-5] (simPATHy.Rmd)
Error: processing vignette 'simPATHy.Rmd' failed with diagnostics:
unable to find an inherited method for function 'nodes' for signature 'object = "igraph"'
--- failed re-building ‘simPATHy.Rmd’
SUMMARY: processing the following file failed:
‘simPATHy.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 0.6
Check: examples
Result: ERROR
Running examples in ‘simPATHy-Ex.R’ failed
The error most likely occurred in:
> ### Name: plotCorGraph
> ### Title: Plot correlation or partial correlation matrix
> ### Aliases: plotCorGraph
>
> ### ** Examples
>
> if( require(gRbase) & require(graph)){
+ graph <- gRbase::ug(~a:b, ~a:c, ~c:d, ~b:d, ~b:c)
+
+ S <- matrix(c(2, 0.8,0.5,-0.3,
+ 0.8,1.5,0.6,-0.7,
+ 0.5,0.6,1, 0.7,
+ -0.3,-0.7,0.7,3), ncol=4,nrow=4)
+ colnames(S) <- rownames(S) <- graph::nodes(graph)
+
+ # Plot the correlation matrix of S
+ plotCorGraph(S)
+
+
+ S<-fitSgraph(graph = graph,S = S)
+ # Change the color range
+ plotCorGraph(S, colLim=c(-0.5,0.5))
+
+ # Visualize the adjacency matrix
+ plotCorGraph(S, type="cor", graph = graph)
+
+ # Show the partial correlation matrix
+ plotCorGraph(S, type="pcor", graph = graph)
+
+ # Plot the difference between two matrices
+ S2 <- S
+ # Change the element c~a
+ S2["a","c"] <- S2["c","a"]<- -0.1
+ plotCorGraph(S1=S, S2=S2)
+ plotCorGraph(S1=S, S2=S2, type="pcor")
+
+ S2<-fitSgraph(graph = graph,S = S2)
+ # Highlight the graphical structure
+ plotCorGraph(S1=S, S2=S2, type="pcor",graph = graph)
+ # Highlight the element c~a
+ plotCorGraph(S1=S, S2=S2, type="pcor",graph = graph,path = list(c("a","c")))
+
+ }
Loading required package: gRbase
Loading required package: graph
Loading required package: BiocGenerics
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Attaching package: ‘graph’
The following objects are masked from ‘package:gRbase’:
addEdge, adj, connComp, edges, nodes, removeEdge, subGraph
Error: unable to find an inherited method for function ‘nodes’ for signature ‘object = "igraph"’
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-x86_64
Version: 0.6
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘simPATHy.Rmd’ using rmarkdown
Quitting from lines 46-49 [unnamed-chunk-5] (simPATHy.Rmd)
Error: processing vignette 'simPATHy.Rmd' failed with diagnostics:
unable to find an inherited method for function 'nodes' for signature 'object = "igraph"'
--- failed re-building ‘simPATHy.Rmd’
SUMMARY: processing the following file failed:
‘simPATHy.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64
Version: 0.6
Check: examples
Result: ERROR
Running examples in ‘simPATHy-Ex.R’ failed
The error most likely occurred in:
> ### Name: plotCorGraph
> ### Title: Plot correlation or partial correlation matrix
> ### Aliases: plotCorGraph
>
> ### ** Examples
>
> if( require(gRbase) & require(graph)){
+ graph <- gRbase::ug(~a:b, ~a:c, ~c:d, ~b:d, ~b:c)
+
+ S <- matrix(c(2, 0.8,0.5,-0.3,
+ 0.8,1.5,0.6,-0.7,
+ 0.5,0.6,1, 0.7,
+ -0.3,-0.7,0.7,3), ncol=4,nrow=4)
+ colnames(S) <- rownames(S) <- graph::nodes(graph)
+
+ # Plot the correlation matrix of S
+ plotCorGraph(S)
+
+
+ S<-fitSgraph(graph = graph,S = S)
+ # Change the color range
+ plotCorGraph(S, colLim=c(-0.5,0.5))
+
+ # Visualize the adjacency matrix
+ plotCorGraph(S, type="cor", graph = graph)
+
+ # Show the partial correlation matrix
+ plotCorGraph(S, type="pcor", graph = graph)
+
+ # Plot the difference between two matrices
+ S2 <- S
+ # Change the element c~a
+ S2["a","c"] <- S2["c","a"]<- -0.1
+ plotCorGraph(S1=S, S2=S2)
+ plotCorGraph(S1=S, S2=S2, type="pcor")
+
+ S2<-fitSgraph(graph = graph,S = S2)
+ # Highlight the graphical structure
+ plotCorGraph(S1=S, S2=S2, type="pcor",graph = graph)
+ # Highlight the element c~a
+ plotCorGraph(S1=S, S2=S2, type="pcor",graph = graph,path = list(c("a","c")))
+
+ }
Loading required package: gRbase
Loading required package: graph
Loading required package: BiocGenerics
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
union, unique, unsplit, which.max, which.min
Attaching package: ‘graph’
The following objects are masked from ‘package:gRbase’:
addEdge, adj, connComp, edges, nodes, removeEdge, subGraph
Error: unable to find an inherited method for function ‘nodes’ for signature ‘object = "igraph"’
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.6
Check: examples
Result: ERROR
Running examples in ‘simPATHy-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotCorGraph
> ### Title: Plot correlation or partial correlation matrix
> ### Aliases: plotCorGraph
>
> ### ** Examples
>
> if( require(gRbase) & require(graph)){
+ graph <- gRbase::ug(~a:b, ~a:c, ~c:d, ~b:d, ~b:c)
+
+ S <- matrix(c(2, 0.8,0.5,-0.3,
+ 0.8,1.5,0.6,-0.7,
+ 0.5,0.6,1, 0.7,
+ -0.3,-0.7,0.7,3), ncol=4,nrow=4)
+ colnames(S) <- rownames(S) <- graph::nodes(graph)
+
+ # Plot the correlation matrix of S
+ plotCorGraph(S)
+
+
+ S<-fitSgraph(graph = graph,S = S)
+ # Change the color range
+ plotCorGraph(S, colLim=c(-0.5,0.5))
+
+ # Visualize the adjacency matrix
+ plotCorGraph(S, type="cor", graph = graph)
+
+ # Show the partial correlation matrix
+ plotCorGraph(S, type="pcor", graph = graph)
+
+ # Plot the difference between two matrices
+ S2 <- S
+ # Change the element c~a
+ S2["a","c"] <- S2["c","a"]<- -0.1
+ plotCorGraph(S1=S, S2=S2)
+ plotCorGraph(S1=S, S2=S2, type="pcor")
+
+ S2<-fitSgraph(graph = graph,S = S2)
+ # Highlight the graphical structure
+ plotCorGraph(S1=S, S2=S2, type="pcor",graph = graph)
+ # Highlight the element c~a
+ plotCorGraph(S1=S, S2=S2, type="pcor",graph = graph,path = list(c("a","c")))
+
+ }
Loading required package: gRbase
Loading required package: graph
Loading required package: BiocGenerics
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Attaching package: ‘graph’
The following objects are masked from ‘package:gRbase’:
addEdge, adj, connComp, edges, nodes, removeEdge, subGraph
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function ‘nodes’ for signature ‘"igraph"’
Calls: <Anonymous> -> <Anonymous>
Execution halted
Flavors: r-patched-linux-x86_64, r-release-linux-x86_64
Version: 0.6
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘simPATHy.Rmd’ using rmarkdown
Quitting from lines 46-49 [unnamed-chunk-5] (simPATHy.Rmd)
Error: processing vignette 'simPATHy.Rmd' failed with diagnostics:
unable to find an inherited method for function 'nodes' for signature '"igraph"'
--- failed re-building ‘simPATHy.Rmd’
SUMMARY: processing the following file failed:
‘simPATHy.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-patched-linux-x86_64, r-release-linux-x86_64
Version: 0.6
Check: package dependencies
Result: NOTE
Packages suggested but not available for checking: 'clipper', 'topologyGSA'
Flavors: r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-arm64
Version: 0.6
Check: examples
Result: ERROR
Running examples in 'simPATHy-Ex.R' failed
The error most likely occurred in:
> ### Name: plotCorGraph
> ### Title: Plot correlation or partial correlation matrix
> ### Aliases: plotCorGraph
>
> ### ** Examples
>
> if( require(gRbase) & require(graph)){
+ graph <- gRbase::ug(~a:b, ~a:c, ~c:d, ~b:d, ~b:c)
+
+ S <- matrix(c(2, 0.8,0.5,-0.3,
+ 0.8,1.5,0.6,-0.7,
+ 0.5,0.6,1, 0.7,
+ -0.3,-0.7,0.7,3), ncol=4,nrow=4)
+ colnames(S) <- rownames(S) <- graph::nodes(graph)
+
+ # Plot the correlation matrix of S
+ plotCorGraph(S)
+
+
+ S<-fitSgraph(graph = graph,S = S)
+ # Change the color range
+ plotCorGraph(S, colLim=c(-0.5,0.5))
+
+ # Visualize the adjacency matrix
+ plotCorGraph(S, type="cor", graph = graph)
+
+ # Show the partial correlation matrix
+ plotCorGraph(S, type="pcor", graph = graph)
+
+ # Plot the difference between two matrices
+ S2 <- S
+ # Change the element c~a
+ S2["a","c"] <- S2["c","a"]<- -0.1
+ plotCorGraph(S1=S, S2=S2)
+ plotCorGraph(S1=S, S2=S2, type="pcor")
+
+ S2<-fitSgraph(graph = graph,S = S2)
+ # Highlight the graphical structure
+ plotCorGraph(S1=S, S2=S2, type="pcor",graph = graph)
+ # Highlight the element c~a
+ plotCorGraph(S1=S, S2=S2, type="pcor",graph = graph,path = list(c("a","c")))
+
+ }
Loading required package: gRbase
Loading required package: graph
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Attaching package: 'graph'
The following objects are masked from 'package:gRbase':
addEdge, adj, connComp, edges, nodes, removeEdge, subGraph
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'nodes' for signature '"igraph"'
Calls: <Anonymous> -> <Anonymous>
Execution halted
Flavors: r-release-windows-x86_64, r-oldrel-windows-x86_64
Version: 0.6
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building 'simPATHy.Rmd' using rmarkdown
Quitting from lines 46-49 [unnamed-chunk-5] (simPATHy.Rmd)
Error: processing vignette 'simPATHy.Rmd' failed with diagnostics:
unable to find an inherited method for function 'nodes' for signature '"igraph"'
--- failed re-building 'simPATHy.Rmd'
SUMMARY: processing the following file failed:
'simPATHy.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavors: r-release-windows-x86_64, r-oldrel-windows-x86_64
Version: 0.6
Check: package dependencies
Result: ERROR
Package required but not available: ‘qpgraph’
Packages suggested but not available for checking: 'clipper', 'topologyGSA'
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Flavor: r-oldrel-macos-x86_64