R Development Page

provenance log file (check_x86_64_windows)

* using log directory 'R:/run/building/build_2015-04-14-23-04/RF_PKG_CHECK/PKGS/provenance.Rcheck'
* using R version 3.1.3 Patched (2015-03-16 r68170)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--as-cran'
* checking for file 'provenance/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'provenance' version '0.1-3'
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Martin Rittner '
New submission
* checking package namespace information ... OK
* checking package dependencies ... NOTE
  No repository set, so cyclic dependency check skipped
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'provenance' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
Non-standard file/directory found at top level:
  'noninst'
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls to packages already attached by Depends:
  'MASS' 'ggplot2' 'scales'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'CDFt' 'MASS' 'ggplot2' 'reshape2' 'scales'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
clustree: no visible binding for global variable 'y'
clustree: no visible binding for global variable 'yend'
clustree: no visible binding for global variable 'x'
clustree: no visible binding for global variable 'xend'
dissimilarity: no visible global function definition for
  'KolmogorovSmirnov'
dissimilarity: no visible global function definition for
  'CramerVonMisesTwoSamples'
plotKDE: no visible global function definition for 'trans_breaks'
plotKDE: no visible global function definition for 'pretty_breaks'
plotKDE: no visible global function definition for 'melt'
plotKDE: no visible global function definition for 'rel'
plotKDE: no visible global function definition for 'ggplot'
plotKDE: no visible global function definition for 'geom_density'
plotKDE: no visible global function definition for 'aes'
plotKDE: no visible binding for global variable 'x'
plotKDE: no visible binding for global variable 'd'
plotKDE: no visible binding for global variable 'type'
plotKDE: no visible global function definition for 'stat_bin'
plotKDE: no visible binding for global variable 'age'
plotKDE: no visible binding for global variable '..ncount..'
plotKDE: no visible binding for global variable 'bw'
plotKDE: no visible global function definition for 'geom_segment'
plotKDE: no visible global function definition for 'geom_point'
plotKDE: no visible global function definition for 'geom_text'
plotKDE: no visible binding for global variable 'y'
plotKDE: no visible global function definition for 'scale_x_continuous'
plotKDE: no visible global function definition for 'scale_fill_manual'
plotKDE: no visible global function definition for 'guides'
plotKDE: no visible global function definition for 'guide_legend'
plotKDE: no visible global function definition for 'facet_grid'
plotKDE: no visible global function definition for 'theme'
plotKDE: no visible global function definition for 'element_blank'
plotKDE: no visible global function definition for 'element_rect'
plotMDS: no visible global function definition for 'ggplot'
plotMDS: no visible global function definition for 'geom_segment'
plotMDS: no visible global function definition for 'geom_point'
plotMDS: no visible global function definition for 'aes_string'
plotMDS: no visible global function definition for 'aes'
plotMDS: no visible binding for global variable 'x'
plotMDS: no visible binding for global variable 'y'
plotMDS: no visible global function definition for 'geom_text'
plotMDS: no visible global function definition for 'brewer_pal'
plotMDS: no visible global function definition for 'scale_fill_manual'
plotMDS: no visible global function definition for 'scale_shape_manual'
plotMDS: no visible global function definition for 'theme'
plotMDS: no visible global function definition for 'element_blank'
plotMDS: no visible global function definition for 'element_rect'
plotMDS: no visible global function definition for 'coord_equal'
plotMDS: no visible global function definition for 'xlim'
plotMDS: no visible global function definition for 'ylim'
plotMDS: no visible global function definition for 'guides'
plotMDS: no visible global function definition for 'guide_legend'
plotShepard: no visible global function definition for 'Shepard'
plotShepard: no visible global function definition for 'ggplot'
plotShepard: no visible global function definition for 'geom_point'
plotShepard: no visible global function definition for 'aes'
plotShepard: no visible binding for global variable 'x'
plotShepard: no visible binding for global variable 'y'
plotShepard: no visible global function definition for 'geom_step'
plotShepard: no visible binding for global variable 'yf'
plotShepard: no visible global function definition for 'geom_text'
* checking Rd files ... NOTE
prepare_Rd: clustree.Rd:28-30: Dropping empty section \details
prepare_Rd: clustree.Rd:31-37: Dropping empty section \value
prepare_Rd: clustree.Rd:44-46: Dropping empty section \note
prepare_Rd: clustree.Rd:38-40: Dropping empty section \references
prepare_Rd: clustree.Rd:53-54: Dropping empty section \examples
prepare_Rd: dissimilarity.Rd:19-21: Dropping empty section \details
prepare_Rd: dissimilarity.Rd:22-28: Dropping empty section \value
prepare_Rd: dissimilarity.Rd:46-48: Dropping empty section \examples
prepare_Rd: kde.Rd:33-35: Dropping empty section \details
prepare_Rd: kdeGUI.Rd:19-21: Dropping empty section \details
prepare_Rd: kdeGUI.Rd:22-28: Dropping empty section \value
prepare_Rd: kdeGUI.Rd:29-30: Dropping empty section \references
prepare_Rd: kdeGUI.Rd:44-46: Dropping empty section \seealso
prepare_Rd: kdeGUI.Rd:47-48: Dropping empty section \examples
prepare_Rd: kdemds-package.Rd:27-29: Dropping empty section \references
prepare_Rd: kdemds-package.Rd:32-35: Dropping empty section \seealso
prepare_Rd: kdemds-package.Rd:36-38: Dropping empty section \examples
prepare_Rd: plotKDE.Rd:61-63: Dropping empty section \details
prepare_Rd: plotKDE.Rd:64-70: Dropping empty section \value
prepare_Rd: plotKDE.Rd:85-87: Dropping empty section \seealso
prepare_Rd: plotKDE.Rd:88-89: Dropping empty section \examples
prepare_Rd: plotMDS.Rd:44-45: Dropping empty section \details
prepare_Rd: plotMDS.Rd:46-52: Dropping empty section \value
prepare_Rd: plotMDS.Rd:66-68: Dropping empty section \seealso
prepare_Rd: plotMDS.Rd:69-71: Dropping empty section \examples
prepare_Rd: plotShepard.Rd:31-33: Dropping empty section \details
prepare_Rd: plotShepard.Rd:34-40: Dropping empty section \value
prepare_Rd: plotShepard.Rd:47-49: Dropping empty section \note
prepare_Rd: plotShepard.Rd:41-43: Dropping empty section \references
prepare_Rd: plotShepard.Rd:56-57: Dropping empty section \examples
prepare_Rd: provenance-package.Rd:27-29: Dropping empty section \references
prepare_Rd: provenance-package.Rd:32-35: Dropping empty section \seealso
prepare_Rd: provenance-package.Rd:36-38: Dropping empty section \examples
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'plotKDE.Rd':
  \usage lines wider than 90 characters:
     plotKDE(data, title, limits = c(0, 3000), breaks = NA, bandwidth = NULL, fcolour = NA, splitat = NA, plotonly = names(data), periods =  ... [TRUNCATED]

These lines will be truncated in the PDF manual.
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'Kfun' 'Perm.Test' 'Rf' 'adapt.f' 'akde' 'dXY' 'fak' 'fk' 'jkde'
  'lambda' 'pkde' 'sig2.con' 'skde'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... WARNING
Functions or methods with usage in documentation object 'kde' but not in code:
  kde

Functions or methods with usage in documentation object 'kdeGUI' but not in code:
  kdeGUI

Codoc mismatches from documentation object 'dissimilarity':
dissimilarity
  Code: function(data, metric = "K-S")
  Docs: function(data)
  Argument names in code not in docs:
    metric

Codoc mismatches from documentation object 'plotKDE':
plotKDE
  Code: function(data, title, limits = c(0, 3000), breaks = NA_real_,
                 bandwidth = NA, fcolour = NA, splitat = NA, plotonly =
                 names(data), classes = NA, periods = FALSE, hist =
                 FALSE, markers = "none", order = TRUE, logx = FALSE,
                 method = "botev", ...)
  Docs: function(data, title, limits = c(0, 3000), breaks = NA,
                 bandwidth = NULL, fcolour = NA, splitat = NA, plotonly
                 = names(data), periods = FALSE, classes = NA, hist =
                 FALSE, markers = "none", order = TRUE, logx = FALSE,
                 method = "botev", ...)
  Mismatches in argument names:
    Position: 9 Code: classes Docs: periods
    Position: 10 Code: periods Docs: classes
  Mismatches in argument default values:
    Name: 'bandwidth' Code: NA Docs: NULL

Codoc mismatches from documentation object 'plotMDS':
plotMDS
  Code: function(mds, diss, col = "", sym = "", nearest = TRUE, labels
                 = TRUE, symbols = TRUE, fcolour = NA, stretch = FALSE,
                 axes = FALSE, expand = FALSE)
  Docs: function(mds, diss, col = "area", sym = "", nearest = TRUE,
                 labels = TRUE, symbols = TRUE)
  Argument names in code not in docs:
    fcolour stretch axes expand
  Mismatches in argument default values:
    Name: 'col' Code: "" Docs: "area"

* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'plotKDE'
  '...'

Documented arguments not in \usage in documentation object 'plotMDS':
  'stretch'

Bad \usage lines found in documentation object 'clustree':
  clustree<-function(atree,orientation=c(1:4),type=c(1,2),positions=NULL)

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking examples ... ERROR
Running examples in 'provenance-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: kde
> ### Title: Gaussian kernel density estimator
> ### Aliases: kde optimal_bw
> ### Keywords: ~kwd1 ~kwd2
> 
> ### ** Examples
> 
> data=c(rnorm(10^3),rnorm(10^3)*2+30)
> d=kde(data)
Error: could not find function "kde"
Execution halted
Run time: 40.54 seconds.