v0.2.1: First CRAN available version

See also on CRAN: https://cran.r-project.org/web/packages/gmum.r/

.Rbuildignore

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+^.*\.Rproj$
+^\.Rproj\.user$
+^\.travis\.yml$

.gitignore

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+# Compiled Object files
+*.slo
+*.lo
+*.o
+*.obj
+*.gch
+
+# Compiled Dynamic libraries
+*.so
+*.dylib
+*.dll
+
+# Co
+
+# Compiled Static libraries
+*.lai
+*.la
+*.a
+*.lib
+
+# Executables
+*.exe
+*.out
+*.app
+
+obj/*
+
+## Core latex/pdflatex auxiliary files:
+*.aux
+*.lof
+*.log
+*.lot
+*.fls
+*.out
+*.toc
+
+## Intermediate documents:
+*.dvi
+# these rules might exclude image files for figures etc.
+# *.ps
+# *.eps
+# *.pdf
+
+## Bibliography auxiliary files (bibtex/biblatex/biber):
+*.bbl
+*.bcf
+*.blg
+*-blx.aux
+*-blx.bib
+*.run.xml
+
+## Build tool auxiliary files:
+*.fdb_latexmk
+*.synctex.gz
+*.synctex.gz(busy)
+*.pdfsync
+
+## Auxiliary and intermediate files from other packages:
+
+# algorithms
+*.alg
+*.loa
+
+# amsthm
+*.thm
+
+# beamer
+*.nav
+*.snm
+*.vrb
+
+# glossaries
+*.acn
+*.acr
+*.glg
+*.glo
+*.gls
+
+# hyperref
+*.brf
+
+# listings
+*.lol
+
+# makeidx
+*.idx
+*.ilg
+*.ind
+*.ist
+
+# minitoc
+*.maf
+*.mtc
+*.mtc0
+
+# minted
+*.pyg
+
+# nomencl
+*.nlo
+
+# sagetex
+*.sagetex.sage
+*.sagetex.py
+*.sagetex.scmd
+
+# sympy
+*.sout
+*.sympy
+sympy-plots-for-*.tex/
+
+# todonotes
+*.tdo
+
+# xindy
+*.xdy
+
+*.so
+*.o
+*.a
+
+# R history files etc.
+.Rbuildignore
+.Rhistory
+.Rproj.user
+.RData
+..Rcheck
+*.Rproj
+
+# Vim files
+*~
+*.swp
+
+#
+Debug
+.cproject
+.project
+.settings
+..Rcheck/
+
+# file with main for tests
+src/main.cpp
+test/cpp/svm/svm_test_model.txt
+test/cpp/svm/libsvm_test
+
+# log file
+tests/cpp/cec/extra/valgrind/*.txt
+
+# Autogenerated by testthat
+tests/testthat/Rplots.pdf
+
+# Test outputs
+tests/testthat/trans_predictions
+trans_predictions
+
+# svm big data
+inst/data_sets/svm/colon-cancer
+inst/data_sets/svm
+
+.depend/
+build/
 *.so
 *.o
+*.d
+*.bin
+*~
+data/
+/TestParts/
+/TestIntegrationFix/
+
+.idea/
+
+# compiled samples
+demo/samples/*.html
+
+# misc
+*.log

.travis.yml

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+# Sample .travis.yml for R projects.
+#
+# see the wiki:
+#   https://github.com/craigcitro/r-travis/wiki
+
+language: c
+
+sudo: required
+
+before_install:
+  - curl -OL http://raw.github.com/craigcitro/r-travis/master/scripts/travis-tool.sh
+  - chmod 755 ./travis-tool.sh
+  - ./travis-tool.sh bootstrap
+  # Test datasets
+  - cd inst/dev/datasets/svm/ && ./download_large.sh && cd ../../../..
+  - cd inst/dev/datasets/svm/ && ./download_transduction.sh && cd ../../../..
+
+install:
+  - ./travis-tool.sh install_deps
+  # Install dependencies of R tests
+  - Rscript -e 'library("devtools"); library("methods"); options(repos=c(CRAN="http://cran.rstudio.com")); install_deps(dependencies = "Suggests")'
+
+script: ./travis-tool.sh run_tests
+
+after_failure:
+  - ./travis-tool.sh dump_logs
+
+notifications:
+  email:
+    on_success: change
+    on_failure: change

CMakeLists.txt

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+cmake_minimum_required(VERSION 3.0)
+project(gmumr_project)
+
+list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_LIST_DIR}/cmake")
+find_package(R)
+
+set(INCLUDE_DIR ${PROJECT_SOURCE_DIR}/inst/include CACHE PATH "Path to include directory")
+set(SRC_DIR ${PROJECT_SOURCE_DIR}/src CACHE PATH "Path to gmum.r library source files")
+set(TESTS_DIR ${PROJECT_SOURCE_DIR}/tests/cpp CACHE PATH "Path to C++ tests directory")
+set(TEST_DATA_PATH ${PROJECT_SOURCE_DIR}/inst/dev/datasets CACHE PATH "Path to test input data directory")
+set(GMUM_INCLUDE ${INCLUDE_DIR} ${INCLUDE_DIR}/cec ${INCLUDE_DIR}/gng ${INCLUDE_DIR}/svm ${INCLUDE_DIR}/svmlight ${INCLUDE_DIR}/utils CACHE TYPE LIST)
+
+set(CMAKE_SKIP_BUILD_RPATH  FALSE)
+set(CMAKE_BUILD_WITH_INSTALL_RPATH FALSE) 
+set(CMAKE_INSTALL_RPATH "${SRC_DIR}")
+set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
+
+add_definitions(-DNDEBUG -DNDEBUG_GMUM -DNDEBUG_GMUM_2 -DRCPP_INTERFACE -DARMA_64BIT_WORD)
+include_directories(${GMUM_INCLUDE} ${R_INCLUDE_DIR})
+link_directories(${R_LIB_DIRS})
+
+add_subdirectory(${SRC_DIR})
+add_subdirectory(${TESTS_DIR})

DESCRIPTION

@@ -1,13 +1,32 @@
 Package: gmum.r
+Version: 0.2.1
+Date: 2015-09-25
+Title: GMUM Machine Learning Group Package
 Type: Package
-Title: Package with models proposed by GMUM group at Jagiellonian University
-Version: 1.0
-Date: 2014-02-25
-Author: Stanislaw Jastrzebski
-Maintainer: Stanislaw Jastrzebski <[email protected]>
-Description: More about what it does (maybe more than one line)
-License: MIT
-Depends:
-    Rcpp (>= 0.10.4)
-LinkingTo: Rcpp
+Author: Wojciech Czarnecki, Stanislaw Jastrzebski, Marcin Data, Igor Sieradzki, Mateusz Bruno-Kaminski, Karol Jurek, Piotr Kowenzowski, Michal Pletty, Konrad Talik, Maciej Zgliczynski
+Maintainer: Stanislaw Jastrzebski <[email protected]>
+Description: Direct R interface to Support Vector Machine libraries ('LIBSVM' and 'SVMLight') and efficient C++ implementations of Growing Neural Gas and models developed by 'GMUM' group (Cross Entropy Clustering and 2eSVM).
+License: MIT + file LICENSE
+Repository: CRAN
+Imports:
+    ggplot2 (>= 1.0.0),
+    stats, 
+    igraph,
+    SparseM,
+    Matrix,
+    httr,
+    Rcpp (>= 0.11.6),
+    methods,
+    grid
+LinkingTo: Rcpp, RcppArmadillo, BH
 NeedsCompilation: yes
+LazyData: yes
+Suggests:
+    car,
+    caret,
+    e1071,
+    klaR,
+    testthat,
+    mlbench
+URL: https://github.com/gmum/gmum.r
+BugReports: https://github.com/gmum/gmum.r/issues

LICENSE

@@ -1,20 +1,2 @@
-The MIT License (MIT)
-
-Copyright (c) 2013 GyMnasiUM
-
-Permission is hereby granted, free of charge, to any person obtaining a copy of
-this software and associated documentation files (the "Software"), to deal in
-the Software without restriction, including without limitation the rights to
-use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
-the Software, and to permit persons to whom the Software is furnished to do so,
-subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
-FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
-COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
-IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
-CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+YEAR: 2015
+COPYRIGHT HOLDER: GMUM <[email protected]>