rbbt-util 5.14.29 → 5.14.30

checksums.yaml

@@ -1,7 +1,7 @@
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-  metadata.gz: 1ed65d89a02680821214ab3141ef167565045291
-  data.tar.gz: 95402199abefb0228dc7788731a1c2b0487c9bf6
+  metadata.gz: 961b2aefbda7865869a3c58926e8b14ecde80ecb
+  data.tar.gz: def79057ef14b73031ec710b40b420f4e5356350
 SHA512:
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-  data.tar.gz: 25b4bf073c68ee563eb17d77b00af6a38f9d25d10520f834167bb94e6b8daea866c048264f97a9b6afc2917d7d32b16c4b41a52aa123176541b3e84f8bd83b3b
+  metadata.gz: 691ab8d3aec9159ba632b5124a2f00dbadd8bb661e20d9e2c3999d54df939bec38042acdfbcde49474ce476056ca2c458c4019287ad9a4e014e5ee5a814d7732
+  data.tar.gz: 3813a6152181ca3e3d59248adc13e28189d9dac7ed8efaa5df1c30c3e41df4d79091692ce415c9529c24fc94a723e9558821a681d08585d596810c510eb86cb2

data/lib/rbbt/annotations.rb

@@ -128,6 +128,8 @@ module Annotated
       @shared_annotations = true
     end
 
+    object.extend AnnotatedArray if AnnotatedArray === self and Array === object
+
     object
   end
 

data/lib/rbbt/association/item.rb

@@ -84,6 +84,7 @@ module AssociationItem
 
     value = self.value
     value.collect{|v|
+      raise "No info for pair; not registered in index" if v.nil?
       Hash[*fields.zip(v).flatten]
     }
   end
@@ -103,6 +104,12 @@ module AssociationItem
     tsv
   end
 
+  property :filter => :array do |*args,&block|
+    keys = tsv.select(*args,&block).keys
+    keys = self.annotate Annotated.purge(keys)
+    keys
+  end
+
   def self.incidence(pairs, key_field = nil, &block)
     matrix = {}
     targets = []

data/lib/rbbt/knowledge_base.rb

@@ -15,7 +15,6 @@ class KnowledgeBase
     end
   end
 
-
   def setup(name, matches, reverse = false)
     AssociationItem.setup matches, self, name, reverse
   end
@@ -64,7 +63,12 @@ class KnowledgeBase
       db_name = [database, name] * "@"
       file, kb_options = kb.registry[database]
       options = {}
+      options[:entity_options] = kb_options[:entity_options]
       options[:undirected] = true if kb_options and kb_options[:undirected]
+      if kb.entity_options
+        options[:entity_options] = kb.entity_options.merge(options[:entity_options] || {})
+      end
+
       register(db_name, nil, options) do
         kb.get_database(database)
       end
@@ -158,9 +162,9 @@ class KnowledgeBase
     key = name.to_s + "_" + Misc.digest(Misc.fingerprint([name,options,format,namespace]))
     @databases[key] ||= 
       begin 
-        Persist.memory("Database:" << [key, dir] * "@") do
+        file, registered_options = registry[name]
+        database = Persist.memory("Database:" << [key, dir] * "@") do
           persist_file = dir.databases[key]
-          file, registered_options = registry[name]
 
           options = Misc.add_defaults options, :persist_file => persist_file, :namespace => namespace, :format => format
           options = Misc.add_defaults options, registered_options if registered_options
@@ -180,6 +184,10 @@ class KnowledgeBase
 
           database
         end
+
+        database.entity_options ||= {}
+        database.entity_options.merge! registered_options[:entity_options] if registered_options.include? :entity_options
+        database
       end
   end
 
@@ -247,8 +255,10 @@ class KnowledgeBase
     options = entity_options[Entity.formats[type]] || {}
     options[:format] = @format[type] if @format.include? :type
     options = {:organism => namespace}.merge(options)
-    if database_name and (database = get_database(database_name)).entity_options
-      options = options.merge database.entity_options
+    if database_name and 
+      (database = get_database(database_name)).entity_options and
+      (database = get_database(database_name)).entity_options[type]
+      options = options.merge database.entity_options[type] 
     end
     options
   end
@@ -299,7 +309,7 @@ class KnowledgeBase
 
   def identify_target(name, entity)
     database = get_database(name, :persist => true)
-    return entity if Symbol === entity or (String === entity and database.values.collect{|v| v.first}.compact.flatten.include?(entity))
+    return entity if Symbol === entity #or (String === entity) # and database.values.collect{|v| v.first}.compact.flatten.include?(entity))
     target = target(name)
 
     @identifiers[name] ||= {}
@@ -347,7 +357,7 @@ class KnowledgeBase
 
   def parents(name, entity)
     repo = get_index name
-    setup(name, repo.reverse.match(entity))
+    setup(name, repo.reverse.match(entity), true)
   end
 
   def neighbours(name, entity)

data/lib/rbbt/tsv/accessor.rb

@@ -39,8 +39,11 @@ module TSV
     return entity unless defined? Entity
     entity = entity if options.delete :dup_array
     if (template = entity_templates[field]) and template.respond_to?(:annotate)
-      entity = template.annotate(entity.frozen? ? entity.dup : entity)
-      entity.extend AnnotatedArray if Array === entity
+      if String === entity or Array === entity
+        entity = entity.dup if entity.frozen? 
+        template.annotate entity
+        entity.extend AnnotatedArray if Array === entity
+      end
       entity
     else
       if entity_templates.include? field
@@ -49,8 +52,11 @@ module TSV
         template = Misc.prepare_entity("TEMPLATE", field, options)
         if template.respond_to?(:annotate)
           entity_templates[field] = template
-          entity = template.annotate(entity.frozen? ? entity.dup : entity)
-          entity.extend AnnotatedArray if Array === entity
+          if String === entity or Array === entity
+            entity = entity.dup if entity.frozen? 
+            template.annotate entity
+            entity.extend AnnotatedArray if Array === entity
+          end
           entity
         else
           entity_templates[field] = nil

data/lib/rbbt/tsv/manipulate.rb

@@ -558,7 +558,6 @@ module TSV
     field_pos = identify_field field
 
     through do |key, values|
-      next if values.nil?
 
       case
       when type == :single
@@ -566,7 +565,7 @@ module TSV
       when type == :flat
         field_values = values
       else
-        next if values[field_pos].nil? 
+        next if values.nil?
         field_values = values[field_pos]
       end
 

data/lib/rbbt/tsv/util.rb

@@ -177,6 +177,11 @@ module TSV
     TSV.identify_field(key_field, fields, field)
   end
 
+  def rename_field(field, new)
+    self.fields = self.fields.collect{|f| f == field ? new : f }
+    self
+  end
+
   def to_list
     new = {}
     case type
@@ -220,8 +225,14 @@ module TSV
         new[k] = [[v]]
       end
     when :list
-      through do |k,v|
-        new[k] = v.collect{|e| [e]}
+      if block_given?
+        through do |k,v|
+          new[k] = v.collect{|e| yield e}
+        end
+      else
+        through do |k,v|
+          new[k] = v.collect{|e| [e]}
+        end
       end
     end
     self.annotate(new)

data/lib/rbbt/util/R/eval.rb

@@ -1,17 +1,69 @@
+require 'rbbt/util/R'
+require 'rserve'
+
+# Hack to make it work with local sockets
+module Rserve
+  module TCPSocket 
+    def self.new(hostname, port_number)
+      raise "Socket at #{hostname} not found" unless File.exists? hostname
+      @s = Socket.unix hostname
+    end
+  end
+end
+
 module R
+  PID = Process.pid
   def self.instance
     @@instance ||= begin
-                     require 'rserve'
-                     @@server_process = CMD.cmd('R CMD Rserve --vanilla', :pipe => true)
-                     Rserve::Connection.new
+                     @@socket_file = Rbbt.tmp.R_sockets[R::PID].find
+
+                     FileUtils.mkdir_p File.dirname(@@socket_file) unless File.directory?(File.dirname(@@socket_file))
+
+                     begin
+
+                       if not File.exists? @@socket_file
+
+                         @@instance_process = Process.fork do
+                           args = %w(CMD Rserve --vanilla --quiet --RS-socket)
+                           args << "'#{@@socket_file}'"
+
+                           bin_path = "R"
+                           cmd = bin_path + " " + args*" "
+                           exec(ENV, cmd)
+                         end
+                         sleep 1
+                       end
+
+                       begin
+                        i = Rserve::Connection.new :hostname => @@socket_file
+                        i.eval "source('#{UTIL}');" 
+                        i
+                       rescue Exception
+                         raise TryAgain
+                       end
+                     rescue Exception
+                       Process.kill :INT, @@instance_process if defined? @@instance_process and @@instance_process
+                       FileUtils.rm @@socket_file if File.exists? @@socket_file
+                       retry if TryAgain === $!
+                       raise $!
+                     end
                    end
   end
 
-  def self.eval(cmd)
-    instance.eval(cmd).payload.first
+  def self._eval(cmd)
+    instance.eval(cmd)
   end
 
   def self.eval_a(cmd)
-    instance.eval(cmd).payload
+    _eval(cmd).payload
+  end
+
+  def self.eval(cmd)
+    eval_a(cmd).first
+  end
+
+  def self.eval_run(cmd)
+    _eval(cmd)
   end
+
 end

data/lib/rbbt/util/R/model.rb

@@ -0,0 +1,76 @@
+require 'rbbt/util/R'
+
+module R
+
+  class << self
+    attr_accessor :model_dir
+
+    def self.model_dir=(model_dir)
+      @model_dir = Path === model_dir ? model_dir : Path.setup(model_dir)
+    end
+    def self.model_dir
+      @model_dir ||= Rbbt.var.R.models
+    end
+  end
+
+
+  self.model_dir = Rbbt.var.R.models
+  class Model
+
+    attr_accessor :name, :formula
+    def initialize(name, formula)
+      @name = name
+      @formula = formula
+    end
+
+    def model_file
+      @model_file ||= R.model_dir[Misc.name2basename([name, Misc.name2basename(formula)] * ": ")].find
+    end
+
+    def update(tsv, field = "Prediction")
+      tsv.R <<-EOF, :R_method => :eval
+model = rbbt.model.load('#{model_file}');
+model = update(model, data);
+save(model, file='#{model_file}');
+      EOF
+    end
+
+    def self.groom(tsv, formula)
+      tsv = tsv.to_list if tsv.type == :single
+
+      if formula.include? tsv.key_field and not tsv.fields.include? tsv.key_field
+        tsv = tsv.add_field tsv.key_field do |k,v|
+          k
+        end
+      end
+
+      tsv
+    end
+
+    def predict(tsv, field = "Prediction")
+      tsv = Model.groom tsv, formula 
+      tsv.R <<-EOF, :R_method => :eval, :key => tsv.key_field
+model = rbbt.model.load('#{model_file}');
+data$#{field} = predict(model, data);
+      EOF
+    end
+
+    def exists?
+      File.exists? model_file
+    end
+
+    def fit(tsv, method='lm', args = {})
+      args_str = ""
+      args_str = args.collect{|name,value| [name,R.ruby2R(value)] * "=" } * ", "
+      args_str = ", " << args_str unless args_str.empty?
+
+      tsv = Model.groom(tsv, formula)
+
+      FileUtils.mkdir_p File.dirname(model_file) unless File.exists?(File.dirname(model_file))
+      tsv.R <<-EOF, :R_method => :shell
+model = rbbt.model.fit(data, #{formula}, method=#{method}#{args_str})
+save(model, file='#{model_file}')
+      EOF
+    end
+  end
+end

data/lib/rbbt/util/R.rb

@@ -26,7 +26,7 @@ source('#{UTIL}');
     Log.debug{"R Script:\n#{ cmd }"}
 
     if options.delete :monitor
-      io = CMD.cmd('R --vanilla', options.merge(:in => cmd, :pipe => true, :log => true))
+      io = CMD.cmd('R --vanilla --quiet', options.merge(:in => cmd, :pipe => true, :log => true))
       while line = io.gets
         puts line
       end
@@ -40,7 +40,7 @@ source('#{UTIL}');
     TmpFile.with_file do |init_file|
        Open.write(init_file) do |f|
           f.puts "# Loading basic rbbt environment"
-          f.puts "library(utils);\n"
+          f.puts "library(utils, quietly=TRUE);\n"
           f.puts "source('#{R::UTIL}');\n"
           f.puts 
           f.puts script
@@ -117,13 +117,37 @@ end
 
 module TSV
 
-  def R(script, open_options = {})
-    TmpFile.with_file do |f|
+  def R(script, source = nil, open_options = {})
+    open_options, source = source, nil if Hash === source
+
+    source = [source] if String === source
+
+    require_sources  = source.collect{|source|
+      "source('#{source}');"
+    } * ";\n" if Array === source and source.any?
+
+    script = require_sources + "\n\n" + script if require_sources
+
+    r_options = Misc.pull_keys open_options, :R
+    r_options[:debug] = true if r_options[:method] == :debug
+    if r_options.delete :debug
+      r_options[:monitor] = true
+      r_options[:method] = :shell
+      erase = false
+    else
+      erase = true
+    end
+
+    tsv_R_option_str = r_options.delete :open
+    tsv_R_option_str = ", "  + tsv_R_option_str if String === tsv_R_option_str and not tsv_R_option_str.empty?
+
+    raw = open_options.delete :raw
+    TmpFile.with_file nil, erase do |f|
       Open.write(f, self.to_s)
 
       script = <<-EOF
 ## Loading tsv into data
-data = rbbt.tsv('#{f}');
+data = rbbt.tsv('#{f}'#{tsv_R_option_str});
 
 #{script.strip}
 
@@ -131,12 +155,16 @@ data = rbbt.tsv('#{f}');
 if (! is.null(data)){ rbbt.tsv.write('#{f}', data); }
       EOF
 
-      r_options = Misc.pull_keys open_options, :R
-      io = R.run script, r_options
 
+      case r_options.delete :method
+      when :eval
+        R.eval_run script
+      else 
+        R.run script, r_options
+      end
 
       open_options = Misc.add_defaults open_options, :type => :list
-      if open_options[:raw]
+      if raw
         Open.read(f)
       else
         tsv = TSV.open(f, open_options) unless open_options[:ignore_output]

data/lib/rbbt/util/log.rb

@@ -269,7 +269,7 @@ def ppp(message)
   stack = caller
   puts "#{Log.color :cyan, "PRINT:"} " << stack.first
   puts ""
-  puts Log.color(:cyan, "=> ") << message
+  puts Log.color(:cyan, "=> ") << message.to_s
   puts ""
 end
 

data/lib/rbbt/util/misc/inspect.rb

@@ -2,6 +2,10 @@ module Misc
   ARRAY_MAX_LENGTH = 1000
   STRING_MAX_LENGTH = ARRAY_MAX_LENGTH * 10
 
+  def self.name2basename(file)
+    sanitize_filename(file.gsub("/",'>').gsub("~", '-'))
+  end
+
   def self.sanitize_filename(filename, length = 254)
     if filename.length > length
       if filename =~ /(\..{2,9})$/
@@ -157,7 +161,7 @@ module Misc
 
       end
 
-      str << "_" << hash2md5(v.info) if defined? Annotated and Annotated === v
+      str << "_" << hash2md5(v.info) if defined? Annotated and Annotated === v and not AssociationItem === v
     end
     hash.unnamed = unnamed if hash.respond_to? :unnamed
 

data/lib/rbbt/workflow/definition.rb

@@ -97,13 +97,19 @@ module Workflow
   
   def export_exec(*names)
     exec_exports.concat names
+    exec_exports.uniq!
+    exec_exports
   end
 
   def export_asynchronous(*names)
     asynchronous_exports.concat names
+    asynchronous_exports.uniq!
+    asynchronous_exports
   end
 
   def export_synchronous(*names)
     synchronous_exports.concat names
+    synchronous_exports.uniq!
+    synchronous_exports
   end
 end

data/share/Rlib/util.R

@@ -207,9 +207,12 @@ rbbt.init <- function(data, new){
     }
 }
 
-rbbt.this.script = system("rbbt_Rutil.rb", intern =T)
+rbbt.this.script = NULL;
 
 rbbt.reload <- function (){
+    if (is.null(rbbt.this.script)){
+        rbbt.this.script = system("rbbt_Rutil.rb", intern =T)
+    }
     source(rbbt.this.script)
 }
 
@@ -302,7 +305,8 @@ rbbt.plot.matrix <- function(x, ...){
 }
 
 rbbt.log <- function(m){
-    cat(paste(m,"\n"), file = stderr())
+    head = "R-Rbbt"
+    cat(paste(head, "> ", m,"\n",sep=""), file = stderr())
 }
 
 rbbt.ddd <- function(o){
@@ -310,3 +314,128 @@ rbbt.ddd <- function(o){
     cat("\n", file = stderr())
 }
 
+
+
+# {{{ MODELS
+
+
+rbbt.model.fit <- function(data, formula, method=lm, ...){
+    method(formula, data = data, ...);
+}
+
+rbbt.model.groom <- function(data, variables = NULL, classes = NULL, formula = NULL){
+    names = names(data)
+    if (is.null(variables)){
+        if (is.null(formula)){
+            variables = names
+        }
+        variables = names[names %in% all.vars(formula)]
+    }
+
+    data.groomed = data[,variables]
+
+    if (! is.null(classes)){
+        if (is.character(classes)){ classes = rep(classes,dim(data.groomed)[2]) }
+        i = 1
+        for (class in classes){
+            v = data.groomed[, i]
+            v = switch(class, numeric =as.numeric(v), character = as.character(v), factor = as.factor(v), boolean = as.logical(v), logical = as.logical(v))
+            data.groomed[,i] = v
+            i = i+1
+        }
+    }
+
+    data.groomed
+}
+
+rbbt.model.predict <- function(model, data, ...){
+    predictions = predict(model, newdata = data, ...);
+    predictions
+}
+
+rbbt.loaded.models = list();
+rbbt.model.load <- function(file, force = F){
+    if (is.null(rbbt.loaded.models[[file]])){
+        load(file)
+        rbbt.loaded.models[[file]] = model
+    }
+    rbbt.loaded.models[[file]]
+}
+
+rbbt.pull.keys <- function(items, key){
+    pulled = list()
+    rest = list()
+
+    names = names(items)
+
+    prefix = paste("^",key,'.',sep='')
+    matches = grep(prefix, names)
+
+    for (i in seq(1,length(names))){
+        if (i %in% matches){
+            name = names[i]
+            name = sub(prefix, "", name)
+            pulled[[name]] = items[[i]]
+        }else{
+            name = names[i]
+            rest[[name]] = items[[i]]
+        }
+    }
+    
+    list(pulled=pulled, rest=rest)
+}
+
+rbbt.model.add_fit <- function(data, formula, method, classes=NULL, ...){
+    data.groomed = rbbt.model.groom(data, formula=formula, classes = classes);
+
+    args = list(...)
+    args.pull = rbbt.pull.keys(args, 'predict')
+    predict.args = args.pull$pulled
+
+    args.pull = rbbt.pull.keys(args.pull$rest, 'fit')
+
+    fit.args = args.pull$pulled
+    args.rest = args.pull$rest
+
+    fit.args =c(fit.args, args.rest)
+    predict.args =c(predict.args, args.rest)
+
+    fit.args[["data"]] = data.groomed
+    fit.args[["formula"]] = formula
+    fit.args[["method"]] = method
+
+    model = do.call(rbbt.model.fit, fit.args);
+
+    response = rbbt.model.formula.reponse(formula)
+    data.groomed[[response]] = NULL
+
+    predict.args[["model"]] = model
+    predict.args[["data"]] = data.groomed
+
+    predictions = do.call(rbbt.model.predict,predict.args)
+
+    data$Prediction = predictions;
+    data
+}
+
+rbbt.model.formula.reponse <- function(formula){
+    tt <- terms(formula)
+    vars <- as.character(attr(tt, "variables"))[-1] ## [1] is the list call
+    response.index <- attr(tt, "response") # index of response var
+    as.character(vars[response.index])
+}
+
+rbbt.model.inpute <- function(data, formula, ...){
+    data = rbbt.model.add_fit(data, formula=formula, ...)
+
+    response = rbbt.model.formula.reponse(formula)
+
+    rows = rownames(data)
+    missing = rows[is.na(data[,c(response)])]
+
+    predictions = data[missing, "Prediction"]
+
+    data[missing,c(response)] = predictions
+#    data$Prediction = NULL
+    data
+}

data/test/rbbt/test_resource.rb

@@ -30,7 +30,6 @@ class TestTSV < Test::Unit::TestCase
       tsv = {"a" => 1, "b" => 2}
       TSV.setup(tsv, :key_field => "Letter", :fields => ["Value"], :type => :single)
     end
-    iii TestResource.tmp.test.test_tsv.produce
     Log.tsv TestResource.tmp.test.test_tsv.tsv
   end
 

data/test/rbbt/util/R/test_eval.rb

@@ -3,7 +3,7 @@ require 'rbbt/util/R/eval'
 
 class TestREval < Test::Unit::TestCase
   def test_get
-    Misc.benchmark(100) do
+    Misc.benchmark(1000) do
       a = R.eval <<-EOF
     p = 12
     a = p * 2
@@ -12,5 +12,32 @@ class TestREval < Test::Unit::TestCase
       assert_equal 12 * 2, a
     end
   end
+
+  def test_TSV_fork
+    tsv = TSV.setup({"1" => "1"},:type => :single)
+      a = tsv.R <<-EOF, :R_method => :eval
+    p = 12
+    a = p * 2
+    c(a)
+      EOF
+
+      pid = Process.fork do
+        a = tsv.R <<-EOF, :R_method => :eval
+    p = 12
+    a = p * 2
+    c(a)
+        EOF
+      end
+      s = Process.waitpid2 pid
+  end
+
+  def test_TSV
+    tsv = TSV.setup({"1" => "1"},:type => :single)
+      a = tsv.R <<-EOF, :R_method => :eval
+    p = 12
+    a = p * 2
+    c(a)
+      EOF
+  end
 end
 

data/test/rbbt/util/R/test_model.rb

@@ -0,0 +1,52 @@
+require File.join(File.expand_path(File.dirname(__FILE__)), '../../..', 'test_helper.rb')
+require 'rbbt/util/R/model'
+
+class TestRModel < Test::Unit::TestCase
+  def model
+  end
+
+  def _test_fit
+    data = TSV.setup({}, :key_field => "Dose", :fields => ["Response"], :type => :single)
+    10.times do 
+      x = rand(10)
+      y = 10 + 3 * x + rand * 4
+      data[x] = y
+    end
+
+    model = R::Model.new "Test fit 2", "Response ~ Dose"
+
+    model.fit(data, method='drm', :fct => "LL.3()") unless model.exists?
+
+    x = 5
+    y = 10 + 3 * x 
+    input = TSV.setup({"new 1" => [x]}, :key_field => "Code", :fields => ["Dose"], :type => :single)
+    puts model.predict(input).to_s
+    pred = model.predict(input)["new 1"]["Prediction"].to_f
+    assert pred > y and pred < y + 4
+  end
+
+  def test_add_fit
+    tsv = TSV.open datafile_test('dose_response'), :type => :list
+    tsv = tsv.slice(["Dose", "Response"])
+
+    result = tsv.R <<-EOF, :R_debug => true
+library(drc, quietly=T)
+library(txtplot)
+data = rbbt.model.add_fit(data, Response ~ Dose, method=drm, classes='numeric', fct=LL.4(),na.action=na.omit)
+txtplot(data$Dose, data$Response)
+txtplot(data$Dose, data$Prediction)
+    EOF
+    ppp result
+  end
+
+  def _test_add_inpute
+    tsv = TSV.open datafile_test('dose_response'), :type => :list
+
+    result = tsv.R <<-EOF, :R_debug => true
+library(drc, quietly=T)
+data = rbbt.model.inpute(data, CI ~ Dose, method=drm, classes='numeric', fct=LL.4(), na.action=na.exclude)
+    EOF
+
+    assert_equal result.size, result.column("CI").values.flatten.reject{|p| p.nil? or p.empty? or p == "NA"}.length
+  end
+end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.14.29
+  version: 5.14.30
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-09-19 00:00:00.000000000 Z
+date: 2014-09-29 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -187,6 +187,7 @@ files:
 - lib/rbbt/tsv/util.rb
 - lib/rbbt/util/R.rb
 - lib/rbbt/util/R/eval.rb
+- lib/rbbt/util/R/model.rb
 - lib/rbbt/util/chain_methods.rb
 - lib/rbbt/util/cmd.rb
 - lib/rbbt/util/color.rb
@@ -340,6 +341,7 @@ files:
 - test/rbbt/tsv/test_stream.rb
 - test/rbbt/tsv/test_util.rb
 - test/rbbt/util/R/test_eval.rb
+- test/rbbt/util/R/test_model.rb
 - test/rbbt/util/concurrency/processes/test_socket.rb
 - test/rbbt/util/concurrency/test_processes.rb
 - test/rbbt/util/concurrency/test_threads.rb
@@ -419,6 +421,7 @@ test_files:
 - test/rbbt/util/test_semaphore.rb
 - test/rbbt/util/test_misc.rb
 - test/rbbt/util/test_tmpfile.rb
+- test/rbbt/util/R/test_model.rb
 - test/rbbt/util/R/test_eval.rb
 - test/rbbt/test_packed_index.rb
 - test/rbbt/test_association.rb