CRAN Package Check Results for Package CePa

Last updated on 2014-10-02 01:48:12.

Check Details

Version: 0.5
Check: dependencies in R code
Result: NOTE
    Packages in Depends field not imported from:
     ‘igraph’ ‘snow’
     These packages need to be imported from (in the NAMESPACE file)
     for when this namespace is loaded but not attached.
    See the information on DESCRIPTION files in the chapter ‘Creating R
    packages’ of the ‘Writing R Extensions’ manual.
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-osx-x86_64-clang, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-ix86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 0.5
Check: R code for possible problems
Result: NOTE
    centrality: no visible global function definition for ‘vcount’
    centrality: no visible global function definition for ‘degree’
    centrality: no visible global function definition for ‘betweenness’
    cepa.all.parallel.by.snow: no visible global function definition for
     ‘makeCluster’
    cepa.all.parallel.by.snow: no visible global function definition for
     ‘clusterCall’
    cepa.all.parallel.by.snow: no visible global function definition for
     ‘clusterApply’
    cepa.all.parallel.by.snow: no visible global function definition for
     ‘stopCluster’
    generate.pathway: no visible global function definition for
     ‘graph.edgelist’
    pathway.nodes: no visible global function definition for ‘vcount’
    pathway.nodes: no visible global function definition for
     ‘get.vertex.attribute’
    plot.igraph2: no visible binding for global variable ‘layout.random’
    plot.igraph2: no visible global function definition for ‘V’
    plot.igraph2: no visible global function definition for ‘E’
    plot.igraph2: no visible global function definition for ‘get.edgelist’
    plot.igraph2: no visible global function definition for ‘ecount’
    plotGraph: no visible global function definition for ‘V’
    plotGraph: no visible global function definition for ‘V<-’
    plotGraph: no visible global function definition for ‘E’
    plotGraph: no visible global function definition for ‘E<-’
    plotGraph : layout.method: no visible global function definition for
     ‘layout.reingold.tilford’
    radiality: no visible global function definition for ‘shortest.paths’
    radiality: no visible global function definition for ‘vcount’
    radiality: no visible global function definition for ‘diameter’
    reach: no visible global function definition for ‘E’
    reach: no visible global function definition for ‘shortest.paths’
    report: no visible global function definition for ‘write.graph’
    spread: no visible global function definition for ‘E’
    spread: no visible global function definition for ‘shortest.paths’
    
    Found the following calls to attach():
    File ‘CePa/R/report.R’:
     attach(replacement, warn.conflicts = FALSE)
    See section ‘Good practice’ in ‘?attach’.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Version: 0.5
Check: Rd line widths
Result: NOTE
    Rd file 'cepa.Rd':
     \usage lines wider than 90 characters:
     cepa(dif = NULL, bk = NULL, mat = NULL, label = NULL, pc, pathway = NULL, id = NULL, cen = "equal.weight",
     cen.name = if(is.function(cen)) deparse(substitute(cen)) else if(mode(cen) == "name") deparse(cen) else cen,
    
    Rd file 'cepa.all.Rd':
     \examples lines wider than 100 characters:
     label = read.cls("http://mcube.nju.edu.cn/jwang/lab/soft/cepa/P53.cls", treatment="MUT", control="WT")
    
    Rd file 'cepa.all.parallel.Rd':
     \usage lines wider than 90 characters:
     cepa.all.parallel(dif = NULL, bk = NULL, mat = NULL, label = NULL, pc, cen = default.centralities,
     \examples lines wider than 100 characters:
     label = read.cls("http://mcube.nju.edu.cn/jwang/lab/soft/cepa/P53.cls", treatment="MUT", control="WT")
    
    Rd file 'cepa.ora.Rd':
     \usage lines wider than 90 characters:
     cen.name = if(is.function(cen)) deparse(substitute(cen)) else if(mode(cen) == "name") deparse(cen) else cen,
    
    Rd file 'cepa.univariate.Rd':
     \usage lines wider than 90 characters:
     cen.name = if(is.function(cen)) deparse(substitute(cen)) else if(mode(cen) == "name") deparse(cen) else cen,
    
    Rd file 'cepa.univariate.all.Rd':
     \examples lines wider than 100 characters:
     label = read.cls("http://mcube.nju.edu.cn/jwang/lab/soft/cepa/P53.cls", treatment="MUT", control="WT")
    
    Rd file 'plotGraph.Rd':
     \usage lines wider than 90 characters:
     graph.node.max.size = 20, graph.node.min.size = 3, graph.layout.method = NULL, ...)
    
    Rd file 'read.cls.Rd':
     \examples lines wider than 100 characters:
     label = read.cls("http://mcube.nju.edu.cn/jwang/lab/soft/cepa/P53.cls", treatment="MUT", control="WT")
    
    Rd file 'report.Rd':
     \usage lines wider than 90 characters:
     template.file = paste(system.file(package = "CePa"), "/extdata/cepa.template", sep=""),
    
    These lines will be truncated in the PDF manual.
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-patched-linux-x86_64, r-release-linux-x86_64

Version: 0.5
Check: R code for possible problems
Result: NOTE
    centrality: no visible global function definition for ‘vcount’
    centrality: no visible global function definition for ‘degree’
    centrality: no visible global function definition for ‘betweenness’
    cepa.all.parallel.by.snow: no visible global function definition for
     ‘makeCluster’
    cepa.all.parallel.by.snow: no visible global function definition for
     ‘clusterCall’
    cepa.all.parallel.by.snow: no visible global function definition for
     ‘clusterApply’
    cepa.all.parallel.by.snow: no visible global function definition for
     ‘stopCluster’
    generate.pathway: no visible global function definition for
     ‘graph.edgelist’
    pathway.nodes: no visible global function definition for ‘vcount’
    pathway.nodes: no visible global function definition for
     ‘get.vertex.attribute’
    plot.igraph2: no visible binding for global variable ‘layout.random’
    plot.igraph2: no visible global function definition for ‘V’
    plot.igraph2: no visible global function definition for ‘E’
    plot.igraph2: no visible global function definition for ‘get.edgelist’
    plot.igraph2: no visible global function definition for ‘ecount’
    plotGraph: no visible global function definition for ‘V’
    plotGraph: no visible global function definition for ‘V<-’
    plotGraph: no visible global function definition for ‘E’
    plotGraph: no visible global function definition for ‘E<-’
    plotGraph : layout.method: no visible global function definition for
     ‘layout.reingold.tilford’
    radiality: no visible global function definition for ‘shortest.paths’
    radiality: no visible global function definition for ‘vcount’
    radiality: no visible global function definition for ‘diameter’
    reach: no visible global function definition for ‘E’
    reach: no visible global function definition for ‘shortest.paths’
    report: no visible global function definition for ‘write.graph’
    spread: no visible global function definition for ‘E’
    spread: no visible global function definition for ‘shortest.paths’
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang, r-devel-windows-ix86+x86_64

Version: 0.5
Check: R code for possible problems
Result: NOTE
    Found the following calls to attach():
    File ‘CePa/R/report.R’:
     attach(replacement, warn.conflicts = FALSE)
    See section ‘Good practice’ in ‘?attach’.
Flavors: r-patched-linux-x86_64, r-release-linux-x86_64