CRAN Package Check Results for Package simPATHy

Last updated on 2019-10-13 10:47:09 CEST.

Check Details

Version: 0.2
Check: dependencies in R code
Result: NOTE
    Missing or unexported objects:
     'gRbase::is.DG.graphNEL' 'gRbase::is.TUG.graphNEL'
     'gRbase::is.UG.graphNEL'
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-windows-ix86+x86_64

Version: 0.2
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
    Loading required package: parallel
    
    Attaching package: 'BiocGenerics'
    
    The following objects are masked from 'package:parallel':
    
     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
     clusterExport, clusterMap, parApply, parCapply, parLapply,
     parLapplyLB, parRapply, parSapply, parSapplyLB
    
    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, 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, which.max, which.min
    
    Error: 'is.DG.graphNEL' is not an exported object from 'namespace:gRbase'
    Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64

Version: 0.2
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building 'simPATHy.Rmd' using rmarkdown
    Quitting from lines 54-56 (simPATHy.Rmd)
    Error: processing vignette 'simPATHy.Rmd' failed with diagnostics:
    'is.DG.graphNEL' is not an exported object from 'namespace:gRbase'
    --- 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, r-patched-linux-x86_64, r-release-linux-x86_64

Version: 0.2
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
    Loading required package: parallel
    
    Attaching package: ‘BiocGenerics’
    
    The following objects are masked from ‘package:parallel’:
    
     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
     clusterExport, clusterMap, parApply, parCapply, parLapply,
     parLapplyLB, parRapply, parSapply, parSapplyLB
    
    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, 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, which.max, which.min
    
    Error: 'is.DG.graphNEL' is not an exported object from 'namespace:gRbase'
    Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-patched-solaris-x86, r-release-windows-ix86+x86_64

Version: 0.2
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building ‘simPATHy.Rmd’ using rmarkdown
    Quitting from lines 54-56 (simPATHy.Rmd)
    Error: processing vignette 'simPATHy.Rmd' failed with diagnostics:
    'is.DG.graphNEL' is not an exported object from 'namespace:gRbase'
    --- 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-ix86+x86_64, r-release-windows-ix86+x86_64

Version: 0.2
Check: installed package size
Result: NOTE
     installed size is 5.1Mb
     sub-directories of 1Mb or more:
     data 2.0Mb
     doc 2.7Mb
Flavor: r-patched-solaris-x86

Version: 0.2
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building ‘simPATHy.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    Quitting from lines 54-56 (simPATHy.Rmd)
    Error: processing vignette 'simPATHy.Rmd' failed with diagnostics:
    'is.DG.graphNEL' is not an exported object from 'namespace:gRbase'
    --- failed re-building ‘simPATHy.Rmd’
    
    SUMMARY: processing the following file failed:
     ‘simPATHy.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-patched-solaris-x86

Version: 0.2
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: ‘topologyGSA’
Flavor: r-release-osx-x86_64

Version: 0.2
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building ‘simPATHy.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    Quitting from lines 252-258 (simPATHy.Rmd)
    Error: processing vignette 'simPATHy.Rmd' failed with diagnostics:
    there is no package called 'topologyGSA'
    --- failed re-building ‘simPATHy.Rmd’
    
    SUMMARY: processing the following file failed:
     ‘simPATHy.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-release-osx-x86_64

Version: 0.2
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-osx-x86_64