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pknng log file (check_x86_64_linux)

Thu Jul 31 18:15:48 2014: Checking package pknng (SVN revision 49) ...
* using log directory ‘/mnt/building/build_2014-07-31-18-04/RF_PKG_CHECK/PKGS/pknng.Rcheck’
* using R version 3.1.1 Patched (2014-07-30 r66281)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘pknng/DESCRIPTION’ ... OK
* this is package ‘pknng’ version ‘0.1-1’
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Ariel E. Baya ’
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 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 ‘pknng’ can be installed ... [4s/8s] 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 ... 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
Package in Depends field not imported from: ‘cluster’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'pknng.alledges.Rd':
  \examples lines wider than 100 characters:
     ## Calculates knn-graph (k=3) using euclidean metric, penalization and nearest point for groups union

Rd file 'pknng.allsubgraphs.Rd':
  \examples lines wider than 100 characters:
     ## Calculates knn-graph (k=3) using euclidean metric, penalization and nearest point for groups union

Rd file 'pknng.apcluster.Rd':
  \examples lines wider than 100 characters:
     ## Calculates knn-graph (k=3) using euclidean metric, penalization and nearest point for groups union

Rd file 'pknng.getmink.Rd':
  \examples lines wider than 100 characters:
     ## Calculates knn-graph using euclidean metric, penalization and return a sparse matrix (does not use Floyd)
     ## Calculates knn-graph using euclidean metric, penalization and return a matrix with distance to all pairs of points (uses Floyd)
     ## Calculates knn-graph using mutual information, penalization and return a sparse matrix (does not use Floyd)

Rd file 'pknng.minspan.Rd':
  \examples lines wider than 100 characters:
     ## Calculates knn-graph (k=3) using euclidean metric, penalization and nearest point for groups union

These lines will be truncated in the PDF manual.
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘NVI.list’ ‘cormetric’ ‘eucmetric’ ‘histfun’ ‘mi_estimator’
  ‘mi_metric’ ‘multiscale.rbf’ ‘mutualInf’ ‘pknng.insider’
  ‘rbf.dot.multiscale’
Undocumented data sets:
  ‘data’
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
Functions or methods with usage in documentation object 'pknng.alledges' but not in code:
  pknng.alledges

Functions or methods with usage in documentation object 'pknng.allsubgraphs' but not in code:
  pknng.allsubgraphs

Functions or methods with usage in documentation object 'pknng.apcluster' but not in code:
  pknng.apclustert

Functions or methods with usage in documentation object 'pknng.kconnect' but not in code:
  pknng.kconnect

Functions or methods with usage in documentation object 'pknng.minspan' but not in code:
  pknng.minspan

Functions or methods with usage in documentation object 'pknng.report' but not in code:
  pknng.report

Codoc mismatches from documentation object 'pknng':
pknng
  Code: function(X, k, fixed.k = 0, diss = F, cte = 3, mu = "mean",
                 method = "euclidean", conn = "one", penalize = 1, path
                 = "dijkstra", MinGroup = 0, silent = T, SMP = T)
  Docs: function(X, k, diss = T, cte = 3, mu = "mean", method =
                 "euclidean", conn = "one", penalize = 1)
  Argument names in code not in docs:
    fixed.k path MinGroup silent SMP
  Mismatches in argument names (first 3):
    Position: 3 Code: fixed.k Docs: diss
    Position: 4 Code: diss Docs: cte
    Position: 5 Code: cte Docs: mu
  Mismatches in argument default values:
    Name: 'diss' Code: F Docs: T

* checking Rd \usage sections ... WARNING
Objects in \usage without \alias in documentation object 'pknng.apcluster':
  ‘pknng.apclustert’

Bad \usage lines found in documentation object 'pknng.cormetric':
  pknng.cormetric (data))
Bad \usage lines found in documentation object 'pknng.eucmetric':
  pknng.eucmetric (data))
Bad \usage lines found in documentation object 'pknng.getmink':
  pknng.getmink (X,method="euclidean",return.matrix=FALSE,penalize=1))
Bad \usage lines found in documentation object 'pknng.mutualmetric':
  pknng.mutualmetric (data,bins=0))

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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... WARNING
Non-portable flags in variable 'PKG_CFLAGS':
  -fopenmp -std=gnu99 -fgnu89-inline
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... WARNING
File ‘/mnt/building/build_2014-07-31-18-04/RF_PKG_CHECK/PKGS/pknng.Rcheck/pknng/libs/pknng.so’:
  Found ‘abort’, possibly from ‘abort’ (C)
    Object: ‘fib.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking examples ... ERROR
Running examples in ‘pknng-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pknng.alledges
> ### Title: Connects a set of point using the minimum number of edges
> ### Aliases: pknng.alledges
> ### Keywords: graphs
> 
> ### ** Examples
> 
> ## Calculates knn-graph (k=3) using euclidean metric, penalization and nearest point for groups union
> 
> library(pknng)
> library(cluster)
> rm(list=ls())
> 
> data(croissants,package="pknng")
Warning in data(croissants, package = "pknng") :
  data set ‘croissants’ not found
> 
> # number of clusters
> centers<- length(unique(croissants2d[,3]))
Error in unique(croissants2d[, 3]) : object 'croissants2d' not found
Execution halted
Run time: 53.74 seconds.