R Development Page

luck log file (check_x86_64_linux)

Thu Aug 18 14:52:25 2016: Checking package luck (SVN revision 6) ...
* using log directory ‘/mnt/building/build_2016-08-18-12-24/RF_PKG_CHECK/PKGS/luck.Rcheck’
* using R version 3.3.1 Patched (2016-08-17 r71112)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--as-cran’
* checking for file ‘luck/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘luck’ version ‘0.9’
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Gero Walter ’

New submission

The Title field should be in title case, current version then in title case:
‘Generalized iLUCK models’
‘Generalized iLUCK Models’

The Date field is over a month old.
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘luck’ can be installed ... [1s/1s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* 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 ... NOTE
Warning: no function found corresponding to methods exports from ‘luck’ for: ‘show’

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘TeachingDemos’ ‘methods’
  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 ... WARNING
  ‘data<-’ ‘n0<-’ ‘n<-’ ‘rawData<-’ ‘tau<-’ ‘tauN<-’ ‘y0<-’
  ‘\S4method{data<-}{LuckModel}’ ‘\S4method{n0<-}{LuckModel}’
  ‘\S4method{n<-}{LuckModelData}’
  ‘\S4method{rawData<-}{ExponentialData}’
  ‘\S4method{rawData<-}{ScaledNormalData}’
  ‘\S4method{tau<-}{LuckModelData}’ ‘\S4method{tauN<-}{LuckModelData}’
  ‘\S4method{y0<-}{LuckModel}’
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.ExponentialDataMeanN: no visible global function definition for ‘new’
.ExponentialDataSimulate: no visible global function definition for
  ‘rexp’
.ExponentialDataVector: no visible global function definition for ‘new’
.LuckModelDataMatrix: no visible global function definition for ‘new’
.LuckModelDataVectors: no visible global function definition for ‘new’
.ScaledNormalDataMeanN: no visible global function definition for ‘new’
.ScaledNormalDataSimulate: no visible global function definition for
  ‘rnorm’
.ScaledNormalDataVector: no visible global function definition for
  ‘new’
.plotLuck: no visible global function definition for ‘polygon’
.plotLuckAugAnno: no visible global function definition for ‘mtext’
.plotLuckAugAnno: no visible global function definition for ‘title’
.plotLuckAugNum: no visible global function definition for ‘text’
.plotLuckAugRect: no visible global function definition for ‘lines’
.showLuckModels : .oneNoneY: no visible global function definition for
  ‘show’
.showLuckModels : .oneNtwoY: no visible global function definition for
  ‘show’
.showLuckModels : .twoNoneY: no visible global function definition for
  ‘show’
.showLuckModels : .twoNtwoY: no visible global function definition for
  ‘show’
ExponentialData: no visible global function definition for ‘is’
ExponentialData: no visible global function definition for ‘new’
ExponentialLuckModel: no visible global function definition for ‘new’
ExponentialLuckModel: no visible global function definition for ‘is’
LuckModel: no visible global function definition for ‘new’
LuckModel: no visible global function definition for ‘is’
ScaledNormalData: no visible global function definition for ‘is’
ScaledNormalData: no visible global function definition for ‘new’
ScaledNormalLuckModel: no visible global function definition for ‘new’
ScaledNormalLuckModel: no visible global function definition for ‘is’
wrapOptim: no visible global function definition for ‘optim’
wrapOptim: no visible global function definition for ‘optimize’
wrapOptim: multiple local function definitions for ‘fn1’ with different
  formal arguments
cdfplot,LuckModel: no visible global function definition for ‘polygon’
cdfplot,LuckModel: no visible global function definition for ‘lines’
show,ExponentialData: no visible global function definition for ‘var’
show,ScaledNormalData: no visible global function definition for ‘var’
singleCdf,ExponentialLuckModel: no visible global function definition
  for ‘pgamma’
singleCdf,ScaledNormalLuckModel: no visible global function definition
  for ‘pnorm’
singleHdi,ExponentialLuckModel : qga: no visible global function
  definition for ‘qgamma’
singleHdi,ExponentialLuckModel: no visible global function definition
  for ‘hpd’
singleHdi,ScaledNormalLuckModel: no visible global function definition
  for ‘qnorm’
Undefined global functions or variables:
  hpd is lines mtext new optim optimize pgamma pnorm polygon qgamma
  qnorm rexp rnorm show text title var
Consider adding
  importFrom("graphics", "lines", "mtext", "polygon", "text", "title")
  importFrom("methods", "is", "new", "show")
  importFrom("stats", "optim", "optimize", "pgamma", "pnorm", "qgamma",
             "qnorm", "rexp", "rnorm", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').

Found the following calls to data() loading into the global environment:
File ‘luck/R/00-02_LuckModel.r’:
  data(object)
  data(object)
  data(object)
  data(object)
  data(object)
  data(object)
  data(object)
File ‘luck/R/00-04_unionHdiLuckModel.r’:
  data(object)
  data(object)
File ‘luck/R/00-05_plotLuckModel.r’:
  data(.object)
  data(.object)
File ‘luck/R/00-06_cdfplotLuckModel.r’:
  data(object)
  data(object)
File ‘luck/R/01-02_ScaledNormal.r’:
  data(arg1)
  data(arg1)
File ‘luck/R/02-02_Exponential.r’:
  data(arg1)
  data(arg1)
See section ‘Good practice’ in ‘?data’.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'cdfplot-methods.Rd':
  \examples lines wider than 100 characters:
     scn1 <- ScaledNormalLuckModel(n0=c(2,10), y0=c(3, 4), data=ScaledNormalData(mean=mean(rnorm(5)), n=5))

These lines will be truncated in the PDF manual.
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'cdfplot-methods':
cdfplot
  Code: function(object, ...)
  Docs: function(object, xvec = 100, epsilon = 1e-05, control =
                 controlList(), ylim = c(0, 1), vertdist = TRUE, ...)
  Argument names in docs not in code:
    xvec epsilon control ylim vertdist
  Mismatches in argument names:
    Position: 2 Code: ... Docs: xvec

Codoc mismatches from documentation object 'plot-methods':
plot
  Code: function(x, y, ...)
  Docs: function(x, y, control = controlList(), add = FALSE, ...)
  Argument names in docs not in code:
    control add
  Mismatches in argument names:
    Position: 3 Code: ... Docs: control

Codoc mismatches from documentation object 'singleCdf-methods':
singleCdf
  Code: function(object, ...)
  Docs: function(object, n, y, x)
  Argument names in code not in docs:
    ...
  Argument names in docs not in code:
    n y x
  Mismatches in argument names:
    Position: 2 Code: ... Docs: n

Codoc mismatches from documentation object 'singleHdi-methods':
singleHdi
  Code: function(object, ...)
  Docs: function(object, n, y, gamma)
  Argument names in code not in docs:
    ...
  Argument names in docs not in code:
    n y gamma
  Mismatches in argument names:
    Position: 2 Code: ... Docs: n

Codoc mismatches from documentation object 'unionHdi-methods':
unionHdi
  Code: function(object, ...)
  Docs: function(object, gamma = 0.95, posterior = FALSE)
  Argument names in code not in docs:
    ...
  Argument names in docs not in code:
    gamma posterior
  Mismatches in argument names:
    Position: 2 Code: ... Docs: gamma

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking examples ... [4s/4s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘00-01_LuckModelData_Tests.R’
  Running ‘00-02_LuckModel_Tests.R’
  Running ‘00-03_utilLuckModel_Tests.R’
  Running ‘00-05_plotLuckModel_Tests.R’
  Running ‘01-01_ScaledNormalData_Tests.R’
  Running ‘01-02_ScaledNormal_Tests.R’
  Running ‘02-01_ExponentialData_Tests.R’
  Running ‘02-02_Exponential_Tests.R’
 [5s/6s] OK
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 5 NOTEs
See
  ‘/mnt/building/build_2016-08-18-12-24/RF_PKG_CHECK/PKGS/luck.Rcheck/00check.log’
for details.


Run time: 41.84 seconds.