CRAN Package Check Results for Package simPATHy

Last updated on 2017-09-26 01:47:52.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.2 1.30 38.31 39.61 OK
r-devel-linux-x86_64-debian-gcc 0.2 1.44 38.37 39.81 OK
r-devel-linux-x86_64-fedora-clang 0.2 78.00 OK
r-devel-linux-x86_64-fedora-gcc 0.2 77.22 OK
r-devel-windows-ix86+x86_64 0.2 4.00 70.00 74.00 OK
r-patched-linux-x86_64 0.2 1.18 29.59 30.78 ERROR
r-patched-solaris-x86 0.2 83.20 ERROR
r-release-linux-x86_64 0.2 1.17 39.32 40.49 OK
r-release-windows-ix86+x86_64 0.2 4.00 71.00 75.00 OK
r-release-osx-x86_64 0.2 ERROR
r-oldrel-windows-ix86+x86_64 0.2 4.00 71.00 75.00 OK
r-oldrel-osx-x86_64 0.2 OK

Check Details

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: simPATHy
    > ### Title: Simulate data from a graphical model
    > ### Aliases: simPATHy
    >
    > ### ** Examples
    >
    > if(require(gRbase) & require(graph)){
    +
    + ## Directed graph
    + ## sub-graph Acute Myel... Leukemia
    + graph<-gRbase::dag(~867:25+867:613+5295:867+5294:867+
    + + 207:5295+207:5294+4193:207+3551:207+
    + + 4792:3551+7157:4193+3265:6654+
    + + 3845:6654+6654:2885+2885:25+2885:613)
    + genes<-graph::nodes(graph)
    +
    + # covariance matrix of the reference condition
    + data<-t(chimera[genes,colnames(chimera)==1])
    + S<-cov(data)
    + S<-fitSgraph(graph,S)
    +
    + # select path to dysregulate
    + path<-list(c("613","867"),c("867","5295"),c("5295","207"),
    + c("207","4193"),c("4193","7157"))
    + ## ..or select the path in an interactive plot
    + # path<-getPathShiny(graph)
    +
    + # select parameters of the dysregulation
    + min<-c(2,8,2,0.1,0.5)
    + max<-c(2,10,2,4,0.5)
    + prob<-c(1,0,0,0.5,1)
    +
    + # activation, switch, switch, random, deactivation
    + dys<-cbind(min,max,prob)
    + rownames(dys)<-sapply(path,paste,collapse = "~")
    + dys
    +
    + set.seed(123)
    + # main function
    + Result<-simPATHy(graph,path,S,min,max,prob)
    + class(Result)
    + names(Result)
    +
    + # simulated data from two conditions
    + round(Result$dataset[c(1:3,501:503),1:5],3)
    +
    + # Summary
    + easyLookDys(Result)
    + # ..or interactive summary
    + # easyLookShiny(resObj=Result,graph=graph)
    +
    +
    + # Visualization
    + plotCorGraph(S1=Result$S1,S2 = Result$S2,graph = graph,path = path,colLim = c(-0.3,0.3))
    + plotGraphNELD3(S1=Result$S1,S2 = Result$S2,graph = graph,colLim = c(-0.3,0.3))
    + rm(list=ls())
    +
    +
    + ## Undirected graph
    + graph <- gRbase::ug(~a:b, ~a:c, ~c:d, ~b:d, ~b:c)
    + # when reference condition covariance matrix is not supplied simPATHy generate a random one
    + Result_ug<-simPATHy(graph)
    + easyLookDys(Result_ug)
    + plotGraphNELD3(S1=Result_ug$S1,S2 = Result_ug$S2,graph = graph,colLim = c(-0.5,0.5))
    +
    + }
    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, cbind, colMeans, colSums, colnames, do.call,
     duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
     lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
     pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
     setdiff, sort, table, tapply, union, unique, unsplit, which,
     which.max, which.min
    
    Error in dimnames(x) <- dn :
     length of 'dimnames' [1] not equal to array extent
    Calls: rownames<- -> rownames<-
    Execution halted
Flavor: r-patched-linux-x86_64

Version: 0.2
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    Quitting from lines 150-154 (simPATHy.Rmd)
    Error: processing vignette ‘simPATHy.Rmd’ failed with diagnostics:
    length of ‘dimnames’ [1] not equal to array extent
    Execution halted
Flavor: r-patched-linux-x86_64

Version: 0.2
Check: installed package size
Result: NOTE
     installed size is 5.0Mb
     sub-directories of 1Mb or more:
     data 2.0Mb
     doc 2.7Mb
Flavor: r-patched-solaris-x86

Version: 0.2
Check: examples
Result: ERROR
    Running examples in ‘simPATHy-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: simPATHy
    > ### Title: Simulate data from a graphical model
    > ### Aliases: simPATHy
    >
    > ### ** Examples
    >
    > if(require(gRbase) & require(graph)){
    +
    + ## Directed graph
    + ## sub-graph Acute Myel... Leukemia
    + graph<-gRbase::dag(~867:25+867:613+5295:867+5294:867+
    + + 207:5295+207:5294+4193:207+3551:207+
    + + 4792:3551+7157:4193+3265:6654+
    + + 3845:6654+6654:2885+2885:25+2885:613)
    + genes<-graph::nodes(graph)
    +
    + # covariance matrix of the reference condition
    + data<-t(chimera[genes,colnames(chimera)==1])
    + S<-cov(data)
    + S<-fitSgraph(graph,S)
    +
    + # select path to dysregulate
    + path<-list(c("613","867"),c("867","5295"),c("5295","207"),
    + c("207","4193"),c("4193","7157"))
    + ## ..or select the path in an interactive plot
    + # path<-getPathShiny(graph)
    +
    + # select parameters of the dysregulation
    + min<-c(2,8,2,0.1,0.5)
    + max<-c(2,10,2,4,0.5)
    + prob<-c(1,0,0,0.5,1)
    +
    + # activation, switch, switch, random, deactivation
    + dys<-cbind(min,max,prob)
    + rownames(dys)<-sapply(path,paste,collapse = "~")
    + dys
    +
    + set.seed(123)
    + # main function
    + Result<-simPATHy(graph,path,S,min,max,prob)
    + class(Result)
    + names(Result)
    +
    + # simulated data from two conditions
    + round(Result$dataset[c(1:3,501:503),1:5],3)
    +
    + # Summary
    + easyLookDys(Result)
    + # ..or interactive summary
    + # easyLookShiny(resObj=Result,graph=graph)
    +
    +
    + # Visualization
    + plotCorGraph(S1=Result$S1,S2 = Result$S2,graph = graph,path = path,colLim = c(-0.3,0.3))
    + plotGraphNELD3(S1=Result$S1,S2 = Result$S2,graph = graph,colLim = c(-0.3,0.3))
    + rm(list=ls())
    +
    +
    + ## Undirected graph
    + graph <- gRbase::ug(~a:b, ~a:c, ~c:d, ~b:d, ~b:c)
    + # when reference condition covariance matrix is not supplied simPATHy generate a random one
    + Result_ug<-simPATHy(graph)
    + easyLookDys(Result_ug)
    + plotGraphNELD3(S1=Result_ug$S1,S2 = Result_ug$S2,graph = graph,colLim = c(-0.5,0.5))
    +
    + }
    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, cbind, colMeans, colSums, colnames, do.call,
     duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
     lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
     pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
     setdiff, sort, table, tapply, union, unique, unsplit, which,
     which.max, which.min
    
    Error in dimnames(x) <- dn :
     length of 'dimnames' [1] not equal to array extent
    Calls: rownames<- -> rownames<-
    Execution halted
Flavor: r-patched-solaris-x86

Version: 0.2
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    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 150-154 (simPATHy.Rmd)
    Error: processing vignette 'simPATHy.Rmd' failed with diagnostics:
    length of 'dimnames' [1] not equal to array extent
    Execution halted
Flavor: r-patched-solaris-x86

Version: 0.2
Check: package dependencies
Result: ERROR
    Packages required but not available: ‘gRbase’ ‘graph’ ‘qpgraph’
    
    Packages suggested but not available for checking: ‘clipper’ ‘topologyGSA’
    
    See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
    manual.
Flavor: r-release-osx-x86_64