R Development Page

gdistanalyst log file (check_x86_64_linux)

Fri Feb 15 12:36:38 2013: Checking package gdistanalyst (SVN revision 216) ...
* using log directory ‘/mnt/building/build_2013-02-15-08-50/RF_PKG_CHECK/PKGS/gdistanalyst.Rcheck’
* using R version 2.15.2 Patched (2013-02-13 r61942)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘gdistanalyst/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gdistanalyst’ version ‘1.0’
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Jacob van Etten ’
New submission
* 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 whether package ‘gdistanalyst’ can be installed ... [13s/40s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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 ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.rbga.bin: warning in sample(c(rep(0, zeroToOneRatio), 1), vars, rep =
  TRUE): partial argument match of 'rep' to 'replace'
RobustRegDist: warning in .rbga.bin2(forml, formterms, dat, p = p, iter
  = iter, maxNoImprove = maxNoImprove, mutationNo = mutationNo, popSize
  = popSize, evalFunc = .evalFunc, verbose = verbose, n = n): partial
  argument match of 'iter' to 'iters'
gbm.step.dist: warning in assign("x.data", x.data, env = globalenv()):
  partial argument match of 'env' to 'envir'
gbm.step.dist: warning in assign("y.data", y.data, env = globalenv()):
  partial argument match of 'env' to 'envir'
.PredToExpDist: no visible global function definition for ‘E’
.SFToDD: no visible global function definition for ‘lengths’
.SFToDD: possible error in DiscreteDistribution(supp = supp, probs =
  probs): unused argument(s) (probs = probs)
.reconstructOrder: no visible global function definition for
  ‘.matrIndex’
* checking Rd files ... NOTE
prepare_Rd: PSA.Rd:38: Dropping empty section \keyword
prepare_Rd: PSA.Rd:33: Dropping empty section \seealso
prepare_Rd: PSA.Rd:34-36: Dropping empty section \examples
prepare_Rd: WeitzmanCalc.Rd:30-31: Dropping empty section \note
prepare_Rd: WeitzmanCalc.Rd:32: Dropping empty section \seealso
prepare_Rd: WeitzmanUtility.Rd:28-29: Dropping empty section \note
prepare_Rd: WeitzmanUtility.Rd:30: Dropping empty section \seealso
prepare_Rd: permRegDist.Rd:36: Dropping empty section \keyword
prepare_Rd: permRegDist.Rd:28-30: Dropping empty section \note
prepare_Rd: permRegDist.Rd:31: Dropping empty section \seealso
prepare_Rd: permRegDist.Rd:32-34: Dropping empty section \examples
prepare_Rd: robustReg.Rd:43: Dropping empty section \keyword
prepare_Rd: robustReg.Rd:27-29: Dropping empty section \value
prepare_Rd: robustReg.Rd:35-37: Dropping empty section \note
prepare_Rd: robustReg.Rd:38: Dropping empty section \seealso
prepare_Rd: robustReg.Rd:39-41: Dropping empty section \examples
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘ASD’ ‘MRD’ ‘NNSA’ ‘RobustRegDist’ ‘WeitzmanPredict’ ‘distIndex’
  ‘dmSq’ ‘exclOutl’ ‘gbm.step.dist’ ‘matrIndex’ ‘writeArlequin’
  ‘writeNexus’
All user-level objects in a package should have documentation entries.
See the chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'distanceFromLevel':
distanceFromLevel
  Code: function(level, fun, diag = FALSE)
  Docs: function(levels, fun, diag = FALSE)
  Argument names in code not in docs:
    level
  Argument names in docs not in code:
    levels
  Mismatches in argument names:
    Position: 1 Code: level Docs: levels

Codoc mismatches from documentation object 'permReg':
permReg
  Code: function(forml, perms = 99, method = "residual", data = NULL)
  Docs: function(forml, perm, method, data)
  Argument names in code not in docs:
    perms
  Argument names in docs not in code:
    perm
  Mismatches in argument names:
    Position: 2 Code: perms Docs: perm
  Mismatches in argument default values:
    Name: 'method' Code: "residual" Docs: 
    Name: 'data' Code: NULL Docs: 

* checking Rd \usage sections ... WARNING
Bad \usage lines found in documentation object 'robustRegDist':
  robustReg(forml, dat, p, iter, popSize, maxNoImprove mutationNo, verbose)

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 the 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 ‘gdistanalyst-Ex.R’ failed
The error most likely occurred in:

> ### Name: WeitzmanCalc
> ### Title: Auxiliary function to calculate Weitzman's Utility Index
> ### Aliases: WeitzmanCalc
> ### Keywords: spatial
> 
> ### ** Examples
> 
> #Example from Thaon d'Arnoldi (1998), data originally presented in Weitzman (1992)
> 
> distObj <- dist(matrix(nrow=4,ncol=4))
> distObj[] <- c(357,532,498,477,488,126)
> 
> WeitzmanCalc(c(1,0,1), distObj)
[1] 981
> WeitzmanCalc2(c(4,2,3,1), distObj)
Error: could not find function "WeitzmanCalc2"
Execution halted
Run time: 432.56 seconds.