CRAN Package Check Results for Package sparcl

Last updated on 2015-07-07 23:48:06.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.0.3 0.83 17.11 17.94 NOTE
r-devel-linux-x86_64-debian-gcc 1.0.3 0.80 16.01 16.81 NOTE
r-devel-linux-x86_64-fedora-clang 1.0.3 31.76 NOTE
r-devel-linux-x86_64-fedora-gcc 1.0.3 29.85 NOTE
r-devel-osx-x86_64-clang 1.0.3 27.40 NOTE
r-devel-windows-ix86+x86_64 1.0.3 6.00 40.00 46.00 NOTE
r-patched-linux-x86_64 1.0.3 2.90 16.84 19.74 NOTE
r-patched-solaris-sparc 1.0.3 236.30 NOTE
r-patched-solaris-x86 1.0.3 50.90 NOTE
r-release-linux-x86_64 1.0.3 0.86 16.48 17.34 NOTE
r-release-osx-x86_64-mavericks 1.0.3 OK
r-release-windows-ix86+x86_64 1.0.3 7.00 39.00 46.00 OK
r-oldrel-windows-ix86+x86_64 1.0.3 7.00 40.00 47.00 OK

Check Details

Version: 1.0.3
Check: S3 generic/method consistency
Result: NOTE
    Found the following apparent S3 methods exported but not registered:
     plot.HierarchicalSparseCluster plot.HierarchicalSparseCluster.permute
     plot.KMeansSparseCluster plot.KMeansSparseCluster.permute
     print.HierarchicalSparseCluster
     print.HierarchicalSparseCluster.permute print.KMeansSparseCluster
     print.KMeansSparseCluster.permute
    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: 1.0.3
Check: R code for possible problems
Result: NOTE
    ColorDendrogram: no visible global function definition for ‘plot’
    ColorDendrogram: no visible global function definition for ‘segments’
    GetUW: no visible global function definition for ‘rnorm’
    GetUW: no visible global function definition for ‘as.dist’
    HierarchicalSparseCluster: no visible binding for global variable ‘sd’
    HierarchicalSparseCluster: no visible global function definition for
     ‘hclust’
    HierarchicalSparseCluster: no visible global function definition for
     ‘as.dist’
    HierarchicalSparseCluster: no visible global function definition for
     ‘cor’
    HierarchicalSparseCluster.permute: no visible binding for global
     variable ‘sd’
    HierarchicalSparseCluster.wrapper: no visible binding for global
     variable ‘var’
    HierarchicalSparseCluster.wrapper: no visible global function
     definition for ‘write.table’
    KMeansSparseCluster: no visible global function definition for ‘kmeans’
    KMeansSparseCluster: no visible global function definition for ‘rnorm’
    KMeansSparseCluster.permute: no visible binding for global variable
     ‘sd’
    UpdateCs: no visible global function definition for ‘kmeans’
    UpdateCs: no visible global function definition for ‘dist’
    output.cluster.files.fun: no visible global function definition for
     ‘write.table’
    output.matrix: no visible global function definition for ‘write.table’
    plot.HierarchicalSparseCluster: no visible global function definition
     for ‘par’
    plot.HierarchicalSparseCluster: no visible global function definition
     for ‘plot’
    plot.HierarchicalSparseCluster.permute: no visible global function
     definition for ‘plot’
    plot.HierarchicalSparseCluster.permute: no visible global function
     definition for ‘lines’
    plot.KMeansSparseCluster: no visible global function definition for
     ‘par’
    plot.KMeansSparseCluster: no visible global function definition for
     ‘plot’
    plot.KMeansSparseCluster.permute: no visible global function definition
     for ‘plot’
    plot.KMeansSparseCluster.permute: no visible global function definition
     for ‘lines’
    read.gct: no visible global function definition for ‘read.table’
    Undefined global functions or variables:
     as.dist cor dist hclust kmeans lines par plot read.table rnorm sd
     segments var write.table
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

Version: 1.0.3
Check: Rd line widths
Result: NOTE
    Rd file 'ColorDendrogram.Rd':
     \usage lines wider than 90 characters:
     ColorDendrogram(hc, y, main = "", branchlength = 0.7, labels = NULL, xlab = NULL, sub = NULL, ylab = "", cex.main = NULL)
    
    Rd file 'HierarchicalSparseCluster.Rd':
     \usage lines wider than 90 characters:
     HierarchicalSparseCluster(x=NULL, dists=NULL,method=c("average","complete", "single","centroid"),
     wbound=NULL,niter=15,dissimilarity=c("squared.distance","absolute.value"), uorth=NULL,silent=FALSE,
     \examples lines wider than 100 characters:
     # faster than sparsehc <- HierarchicalSparseCluster(x=x,wbound=perm.out$bestw, method="complete")
     sparsehc <- HierarchicalSparseCluster(dists=perm.out$dists, wbound=perm.out$bestw, method="complete", dissimilarity="absolute.value")
    
    Rd file 'HierarchicalSparseCluster.permute.Rd':
     \examples lines wider than 100 characters:
     sparsehc <- HierarchicalSparseCluster(dists=perm.out$dists, wbound=perm.out$bestw, method="complete")
    
    Rd file 'HierarchicalSparseCluster.wrapper.Rd':
     \usage lines wider than 90 characters:
     HierarchicalSparseCluster.wrapper(file, method=c("average", "complete", "single", "centroid"),
     "single","centroid"),output.cluster.files=TRUE,outputfile.prefix=NULL,maxnumgenes=5000,standardize.arrays=TRUE)
    
    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