CRAN Package Check Results for Package sparcl

Last updated on 2016-12-28 23:47:37.

Flavor	Version	T_install	T_check	T_total	Status	Flags
r-devel-linux-x86_64-debian-clang	1.0.3	0.99	20.41	21.40	NOTE
r-devel-linux-x86_64-debian-gcc	1.0.3	0.94	20.59	21.52	NOTE
r-devel-linux-x86_64-fedora-clang	1.0.3			37.80	NOTE	--no-stop-on-test-error
r-devel-linux-x86_64-fedora-gcc	1.0.3			32.50	NOTE	--no-stop-on-test-error
r-devel-macos-x86_64-clang	1.0.3			27.64	NOTE	--no-stop-on-test-error
r-devel-windows-ix86+x86_64	1.0.3	6.00	48.00	54.00	NOTE
r-patched-linux-x86_64	1.0.3	0.91	18.85	19.76	NOTE
r-patched-solaris-sparc	1.0.3			223.30	NOTE
r-patched-solaris-x86	1.0.3			48.30	NOTE
r-release-linux-x86_64	1.0.3	0.86	18.81	19.67	NOTE
r-release-osx-x86_64-mavericks	1.0.3				NOTE
r-release-windows-ix86+x86_64	1.0.3	5.00	49.00	54.00	NOTE
r-oldrel-windows-ix86+x86_64	1.0.3	6.00	49.00	55.00	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-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
    Consider adding
     importFrom("graphics", "lines", "par", "plot", "segments")
     importFrom("stats", "as.dist", "cor", "dist", "hclust", "kmeans",
     "rnorm", "sd", "var")
     importFrom("utils", "read.table", "write.table")
    to your NAMESPACE file.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, 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

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-patched-linux-x86_64, r-release-linux-x86_64

Version: 1.0.3
Flags: --no-stop-on-test-error
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-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-macos-x86_64-clang

Version: 1.0.3
Flags: --no-stop-on-test-error
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
    Consider adding
     importFrom("graphics", "lines", "par", "plot", "segments")
     importFrom("stats", "as.dist", "cor", "dist", "hclust", "kmeans",
     "rnorm", "sd", "var")
     importFrom("utils", "read.table", "write.table")
    to your NAMESPACE file.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-macos-x86_64-clang

Version: 1.0.3
Flags: --no-stop-on-test-error
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-fedora-clang, r-devel-linux-x86_64-fedora-gcc