R Development Page

RMacoqui log file (check_x86_64_windows)

* using log directory 'R:/run/building/build_2018-10-05-14-08/RF_PKG_CHECK/PKGS/RMacoqui.Rcheck'
* using R version 3.5.1 Patched (2018-09-27 r75383)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--as-cran'
* checking for file 'RMacoqui/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RMacoqui' version '1.0'
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Ramon Hidalgo '

New submission

The Title field should be in title case, current version then in title case:
'Identifying and describing chorotypes based on similarity between species distributions'
'Identifying and Describing Chorotypes Based on Similarity Between Species Distributions'

The Description field should not start with the package name,
  'This package' or similar.

The Date field is over a month old.
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... NOTE
Found the following apparent object files/libraries:
  libs/i386/RMacoqui.dll libs/x64/RMacoqui.dll
Object files/libraries should not be included in a source package.
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking serialization versions ... OK
* checking whether package 'RMacoqui' 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:
  'libs'
* 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
* loading checks for arch 'i386'
** 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 use of S3 registration ... OK
* loading checks for arch 'x64'
** 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 use of S3 registration ... OK
* checking dependencies in R code ... WARNING
'library' or 'require' calls not declared from:
  'tcltk' 'tcltk2'
'library' or 'require' calls in package code:
  'tcltk' 'tcltk2'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in 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
File 'RMacoqui/R/zzz.R':
  .onLoad calls:
    cat("Package RMACOQUI load \n (last revision July-2015)\n\n")
    cat("RMacoqui develops a probability procedure for the identification of chorotypes,  \n")
    cat("i.e. distribution patterns shared by a group of species, which can be operatively   \n")
    cat("identified within an area (Baroni-Urbani et al., 1978).  \n")
    cat("This method was first published by Marquez et al. (1997),  \n")
    cat("based on  a prior proposal for detecting biogeographic boundaries (Real et al., 1992),  \n")
    cat("and with a mathematic rationale derived from McCoy et al. (1986).  \n")
    cat("The method for chorotype identification was later enhanced by Munoz et al. (2003)  \n")
    cat("and Real et al. (2008), and was updated and contextualized under a fuzzy logic framework  \n")
    cat("by Olivero et al. (2011).  \n")
    cat("RMacoqui outputs  are also useful as the basis for delimiting biogeographic regions  \n")
    cat("and transition zones with the support of the fuzzy logic (Olivero et al. 2013).  \n")
    cat("\n\n")

Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in '?.onAttach'.

Package RMACOQUI load 
 (last revision July-2015)

RMacoqui develops a probability procedure for the identification of chorotypes,  
i.e. distribution patterns shared by a group of species, which can be operatively   
identified within an area (Baroni-Urbani et al., 1978).  
This method was first published by Marquez et al. (1997),  
based on  a prior proposal for detecting biogeographic boundaries (Real et al., 1992),  
and with a mathematic rationale derived from McCoy et al. (1986).  
The method for chorotype identification was later enhanced by Munoz et al. (2003)  
and Real et al. (2008), and was updated and contextualized under a fuzzy logic framework  
by Olivero et al. (2011).  
RMacoqui outputs  are also useful as the basis for delimiting biogeographic regions  
and transition zones with the support of the fuzzy logic (Olivero et al. 2013).  


cLogicaDifusa: no visible binding for global variable 'lang'
centropia: no visible binding for global variable 'lang'
cmDCor: no visible binding for global variable 'lang'
cmProx: no visible global function definition for 'cor'
cmatrizsignoscor: no visible global function definition for 'cor.test'
cmsignos: no visible global function definition for 'cor.test'
cvaloresmac: no visible global function definition for 'pchisq'
fuzzy.Clusters: no visible binding for global variable 'lang'
maccluster: no visible global function definition for 'plot'
maccluster: no visible global function definition for 'text'
print.tclArrayVar : toExcel: no visible global function definition for
  'write.xls'
print.tclArrayVar : toTxt: no visible global function definition for
  'write.csv'
print.tclArrayVar: no visible binding for global variable 'etbt2Excel'
print.tclArrayVar: no visible binding for global variable 'etbt2Txt'
print.tclArrayVar: no visible binding for global variable
  'etbtOrdenClus'
print.tclArrayVar: no visible binding for global variable 'OrdClus'
print.tclArrayVar: no visible binding for global variable
  'etbtOrdenIni'
print.tclArrayVar: no visible binding for global variable 'OrdIni'
ver.matRmacoqui: no visible global function definition for 'is'
ver.matRmacoqui: no visible binding for global variable 'lang'
verMatriz: no visible binding for global variable 'lang'
verMatriz : salvarTxt: no visible binding for global variable 'lang'
verMatriz : salvarTxt: no visible binding for global variable 'then'
verMatriz : salvarTxt: no visible global function definition for
  'write.csv'
Undefined global functions or variables:
  OrdClus OrdIni cor cor.test etbt2Excel etbt2Txt etbtOrdenClus
  etbtOrdenIni is lang pchisq plot text then write.csv write.xls
Consider adding
  importFrom("graphics", "plot", "text")
  importFrom("methods", "is")
  importFrom("stats", "cor", "cor.test", "pchisq")
  importFrom("utils", "write.csv")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').

Found the following assignments to the global environment:
File 'RMacoqui/R/macoqui.R':
  assign("lang", lang, .GlobalEnv)
* checking Rd files ... WARNING
RMacoqui-package.Rd: non-ASCII input and no declared encoding
prepare_Rd: amphib.Rd:7-8: Dropping empty section \description
prepare_Rd: amphib.Rd:13-14: Dropping empty section \details
prepare_Rd: amphib.Rd:15-16: Dropping empty section \source
prepare_Rd: amphib.Rd:17-18: Dropping empty section \references
checkRd: (5) amphib.Rd:0-24: Must have a \description
prepare_Rd: fuzzy.Clusters.Rd:55: Dropping empty section \keyword
prepare_Rd: fuzzy.Clusters.Rd:56: Dropping empty section \keyword
prepare_Rd: fuzzy.Clusters.Rd:44-45: Dropping empty section \note
prepare_Rd: fuzzy.Clusters.Rd:39-40: Dropping empty section \references
prepare_Rd: locCorot.Rd:40: Dropping empty section \keyword
prepare_Rd: locCorot.Rd:41: Dropping empty section \keyword
prepare_Rd: locCorot.Rd:24-25: Dropping empty section \references
prepare_Rd: locCorotGrupos.Rd:43: Dropping empty section \keyword
prepare_Rd: locCorotGrupos.Rd:44: Dropping empty section \keyword
prepare_Rd: locCorotGrupos.Rd:25-26: Dropping empty section \references
prepare_Rd: macoqui.Rd:65-66: Dropping empty section \note
prepare_Rd: simil.Rd:7-8: Dropping empty section \description
prepare_Rd: simil.Rd:13-14: Dropping empty section \details
prepare_Rd: simil.Rd:15-16: Dropping empty section \source
prepare_Rd: simil.Rd:17-18: Dropping empty section \references
checkRd: (5) simil.Rd:0-23: Must have a \description
prepare_Rd: ver.matRmacoqui.Rd:90: Dropping empty section \keyword
prepare_Rd: ver.matRmacoqui.Rd:91: Dropping empty section \keyword
prepare_Rd: ver.matRmacoqui.Rd:17-18: Dropping empty section \details
prepare_Rd: ver.matRmacoqui.Rd:46-47: Dropping empty section \references
problem found in 'RMacoqui-package.Rd'
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* 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 pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... NOTE
File 'RMacoqui/libs/i386/RMacoqui.dll':
  Found no calls to: 'R_registerRoutines', 'R_useDynamicSymbols'
File 'RMacoqui/libs/x64/RMacoqui.dll':
  Found no calls to: 'R_registerRoutines', 'R_useDynamicSymbols'

It is good practice to register native routines and to disable symbol
search.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking examples ...
** running examples for arch 'i386' ... NOTE
Examples with CPU or elapsed time > 5s
                  user system elapsed
RMacoqui-package 49.37   0.54   49.95
ver.matRmacoqui  49.16   0.41   49.60
locCorotGrupos   26.39   0.14   26.54
locCorot         23.15   0.09   23.24
** running examples for arch 'x64' ... NOTE
Examples with CPU or elapsed time > 5s
                  user system elapsed
RMacoqui-package 60.17   0.23   60.44
ver.matRmacoqui  59.66   0.31   59.97
locCorotGrupos   31.96   0.18   32.15
locCorot         27.91   0.13   28.03
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 7 NOTEs
See
  'R:/run/building/build_2018-10-05-14-08/RF_PKG_CHECK/PKGS/RMacoqui.Rcheck/00check.log'
for details.


Run time: 377.51 seconds.