Last updated on 2016-12-28 23:47:37.
Flavor | Version | Tinstall | Tcheck | Ttotal | 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 |
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