CRAN Package Check Results for Package CePa

Last updated on 2015-08-31 04:48:36.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.5 1.22 25.67 26.88 NOTE
r-devel-linux-x86_64-debian-gcc 0.5 1.22 25.48 26.70 NOTE
r-devel-linux-x86_64-fedora-clang 0.5 54.41 NOTE
r-devel-linux-x86_64-fedora-gcc 0.5 52.01 NOTE
r-devel-osx-x86_64-clang 0.5 51.37 NOTE
r-devel-windows-ix86+x86_64 0.5 9.00 51.00 60.00 NOTE
r-patched-linux-x86_64 0.5 1.22 26.54 27.75 NOTE
r-patched-solaris-sparc 0.5 334.20 NOTE
r-patched-solaris-x86 0.5 77.40 NOTE
r-release-linux-x86_64 0.5 1.42 26.93 28.36 NOTE
r-release-osx-x86_64-mavericks 0.5 NOTE
r-release-windows-ix86+x86_64 0.5 7.00 72.00 79.00 NOTE
r-oldrel-windows-ix86+x86_64 0.5 9.00 57.00 66.00 NOTE

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.
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-x86_64, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 0.5
Check: S3 generic/method consistency
Result: NOTE
    Found the following apparent S3 methods exported but not registered:
     plot.cepa plot.cepa.all plot.pathway.catalogue print.cepa
     print.cepa.all print.pathway.catalogue
    See section ‘Registering S3 methods’ in 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-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, 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: no visible global function definition for ‘read.table’
    cepa.all: no visible global function definition for ‘read.table’
    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’
    cepa.ora: no visible global function definition for ‘read.table’
    cepa.ora: no visible global function definition for ‘quantile’
    cepa.ora: no visible global function definition for ‘rbinom’
    cepa.ora.all: no visible global function definition for ‘read.table’
    cepa.univariate: no visible global function definition for ‘prcomp’
    cepa.univariate: no visible global function definition for ‘predict’
    cepa.univariate: no visible global function definition for ‘quantile’
    cepa.univariate.all: no visible global function definition for ‘prcomp’
    cepa.univariate.all: no visible global function definition for
     ‘predict’
    generate.pathway: no visible global function definition for
     ‘graph.edgelist’
    get_color: no visible global function definition for ‘col2rgb’
    get_color: no visible global function definition for ‘rgb’
    jitt: no visible global function definition for ‘runif’
    nodeLevelFun.tvalue: no visible global function definition for ‘var’
    p.heatmap: no visible binding for global variable ‘p.adjust’
    p.heatmap: no visible global function definition for ‘plot’
    p.heatmap: no visible global function definition for ‘text’
    p.heatmap: no visible global function definition for ‘layout’
    p.heatmap: no visible global function definition for ‘lcm’
    p.heatmap: no visible global function definition for ‘par’
    p.heatmap: no visible global function definition for ‘rect’
    p.table: no visible binding for global variable ‘p.adjust’
    pathway.nodes: no visible global function definition for ‘vcount’
    pathway.nodes: no visible global function definition for
     ‘get.vertex.attribute’
    pathwayLevelFun.median: no visible global function definition for
     ‘median’
    pathwayLevelFun.rank: no visible global function definition for
     ‘wilcox.test’
    plot.cepa.all: no visible global function definition for ‘plot’
    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 ‘plot’
    plot.igraph2: no visible global function definition for ‘box’
    plot.igraph2: no visible global function definition for ‘points’
    plot.igraph2: no visible global function definition for ‘text’
    plot.igraph2: no visible global function definition for ‘get.edgelist’
    plot.igraph2: no visible global function definition for ‘par’
    plot.igraph2: no visible global function definition for ‘segments’
    plot.igraph2: no visible global function definition for ‘ecount’
    plot.igraph2: no visible global function definition for ‘polygon’
    plot.pathway.catalogue: no visible global function definition for ‘par’
    plot.pathway.catalogue: no visible global function definition for
     ‘plot’
    plot.pathway.catalogue: no visible global function definition for
     ‘abline’
    plotGraph: no visible global function definition for ‘plot’
    plotGraph: no visible global function definition for ‘text’
    plotGraph: no visible global function definition for ‘par’
    plotGraph: no visible global function definition for ‘rgb’
    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’
    plotGraph: no visible global function definition for ‘legend’
    plotGraph: no visible global function definition for ‘rect’
    plotGraph: no visible global function definition for ‘title’
    plotNull: no visible global function definition for ‘plot’
    plotNull: no visible global function definition for ‘text’
    plotNull: no visible global function definition for ‘par’
    plotNull: no visible global function definition for ‘rgb’
    plotNull: no visible global function definition for ‘matplot’
    plotNull: no visible global function definition for ‘points’
    plotNull: no visible global function definition for ‘legend’
    plotNull: no visible global function definition for ‘abline’
    plotNull: no visible global function definition for ‘hist’
    plotNull: no visible global function definition for ‘box’
    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’
    read.gct: no visible global function definition for ‘read.table’
    report: no visible global function definition for ‘png’
    report: no visible global function definition for ‘plot’
    report: no visible global function definition for ‘dev.off’
    report: no visible binding for global variable ‘p.adjust’
    report: no visible global function definition for ‘write.graph’
    report: no visible global function definition for ‘write.table’
    spread: no visible global function definition for ‘E’
    spread: no visible global function definition for ‘shortest.paths’
    table.content: no visible binding for global variable ‘p.adjust’
    Undefined global functions or variables:
     E E<- V V<- abline betweenness box clusterApply clusterCall col2rgb
     degree dev.off diameter ecount get.edgelist get.vertex.attribute
     graph.edgelist hist layout layout.random layout.reingold.tilford lcm
     legend makeCluster matplot median p.adjust par plot png points
     polygon prcomp predict quantile rbinom read.table rect rgb runif
     segments shortest.paths stopCluster text title var vcount wilcox.test
     write.graph write.table
    Consider adding
     importFrom("grDevices", "col2rgb", "dev.off", "png", "rgb")
     importFrom("graphics", "abline", "box", "hist", "layout", "lcm",
     "legend", "matplot", "par", "plot", "points", "polygon",
     "rect", "segments", "text", "title")
     importFrom("stats", "median", "p.adjust", "prcomp", "predict",
     "quantile", "rbinom", "runif", "var", "wilcox.test")
     importFrom("utils", "read.table", "write.table")
    to your NAMESPACE.
    
    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: no visible global function definition for ‘read.table’
    cepa.all: no visible global function definition for ‘read.table’
    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’
    cepa.ora: no visible global function definition for ‘read.table’
    cepa.ora: no visible global function definition for ‘quantile’
    cepa.ora: no visible global function definition for ‘rbinom’
    cepa.ora.all: no visible global function definition for ‘read.table’
    cepa.univariate: no visible global function definition for ‘prcomp’
    cepa.univariate: no visible global function definition for ‘predict’
    cepa.univariate: no visible global function definition for ‘quantile’
    cepa.univariate.all: no visible global function definition for ‘prcomp’
    cepa.univariate.all: no visible global function definition for
     ‘predict’
    generate.pathway: no visible global function definition for
     ‘graph.edgelist’
    get_color: no visible global function definition for ‘col2rgb’
    get_color: no visible global function definition for ‘rgb’
    jitt: no visible global function definition for ‘runif’
    nodeLevelFun.tvalue: no visible global function definition for ‘var’
    p.heatmap: no visible binding for global variable ‘p.adjust’
    p.heatmap: no visible global function definition for ‘plot’
    p.heatmap: no visible global function definition for ‘text’
    p.heatmap: no visible global function definition for ‘layout’
    p.heatmap: no visible global function definition for ‘lcm’
    p.heatmap: no visible global function definition for ‘par’
    p.heatmap: no visible global function definition for ‘rect’
    p.table: no visible binding for global variable ‘p.adjust’
    pathway.nodes: no visible global function definition for ‘vcount’
    pathway.nodes: no visible global function definition for
     ‘get.vertex.attribute’
    pathwayLevelFun.median: no visible global function definition for
     ‘median’
    pathwayLevelFun.rank: no visible global function definition for
     ‘wilcox.test’
    plot.cepa.all: no visible global function definition for ‘plot’
    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 ‘plot’
    plot.igraph2: no visible global function definition for ‘box’
    plot.igraph2: no visible global function definition for ‘points’
    plot.igraph2: no visible global function definition for ‘text’
    plot.igraph2: no visible global function definition for ‘get.edgelist’
    plot.igraph2: no visible global function definition for ‘par’
    plot.igraph2: no visible global function definition for ‘segments’
    plot.igraph2: no visible global function definition for ‘ecount’
    plot.igraph2: no visible global function definition for ‘polygon’
    plot.pathway.catalogue: no visible global function definition for ‘par’
    plot.pathway.catalogue: no visible global function definition for
     ‘plot’
    plot.pathway.catalogue: no visible global function definition for
     ‘abline’
    plotGraph: no visible global function definition for ‘plot’
    plotGraph: no visible global function definition for ‘text’
    plotGraph: no visible global function definition for ‘par’
    plotGraph: no visible global function definition for ‘rgb’
    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’
    plotGraph: no visible global function definition for ‘legend’
    plotGraph: no visible global function definition for ‘rect’
    plotGraph: no visible global function definition for ‘title’
    plotNull: no visible global function definition for ‘plot’
    plotNull: no visible global function definition for ‘text’
    plotNull: no visible global function definition for ‘par’
    plotNull: no visible global function definition for ‘rgb’
    plotNull: no visible global function definition for ‘matplot’
    plotNull: no visible global function definition for ‘points’
    plotNull: no visible global function definition for ‘legend’
    plotNull: no visible global function definition for ‘abline’
    plotNull: no visible global function definition for ‘hist’
    plotNull: no visible global function definition for ‘box’
    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’
    read.gct: no visible global function definition for ‘read.table’
    report: no visible global function definition for ‘png’
    report: no visible global function definition for ‘plot’
    report: no visible global function definition for ‘dev.off’
    report: no visible binding for global variable ‘p.adjust’
    report: no visible global function definition for ‘write.graph’
    report: no visible global function definition for ‘write.table’
    spread: no visible global function definition for ‘E’
    spread: no visible global function definition for ‘shortest.paths’
    table.content: no visible binding for global variable ‘p.adjust’
    Undefined global functions or variables:
     E E<- V V<- abline betweenness box clusterApply clusterCall col2rgb
     degree dev.off diameter ecount get.edgelist get.vertex.attribute
     graph.edgelist hist layout layout.random layout.reingold.tilford lcm
     legend makeCluster matplot median p.adjust par plot png points
     polygon prcomp predict quantile rbinom read.table rect rgb runif
     segments shortest.paths stopCluster text title var vcount wilcox.test
     write.graph write.table
    Consider adding
     importFrom("grDevices", "col2rgb", "dev.off", "png", "rgb")
     importFrom("graphics", "abline", "box", "hist", "layout", "lcm",
     "legend", "matplot", "par", "plot", "points", "polygon",
     "rect", "segments", "text", "title")
     importFrom("stats", "median", "p.adjust", "prcomp", "predict",
     "quantile", "rbinom", "runif", "var", "wilcox.test")
     importFrom("utils", "read.table", "write.table")
    to your NAMESPACE.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-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’
    Undefined global functions or variables:
     E E<- V V<- betweenness clusterApply clusterCall degree diameter
     ecount get.edgelist get.vertex.attribute graph.edgelist layout.random
     layout.reingold.tilford makeCluster shortest.paths stopCluster vcount
     write.graph
Flavor: r-devel-osx-x86_64-clang

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-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-patched-solaris-sparc, r-patched-solaris-x86, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64