diff --git a/lib/jekyll/commands/new.rb b/lib/jekyll/commands/new.rb
index d348315a..ca5ed164 100644
--- a/lib/jekyll/commands/new.rb
+++ b/lib/jekyll/commands/new.rb
@@ -36,7 +36,7 @@ module Jekyll
           end
         end
 
-        puts "New jekyll site installed in #{new_blog_path}."
+        Jekyll.logger.info "New jekyll site installed in #{new_blog_path}."
       end
 
       def self.create_blank_site(path)
diff --git a/lib/jekyll/convertible.rb b/lib/jekyll/convertible.rb
index cce7460b..9d00d703 100644
--- a/lib/jekyll/convertible.rb
+++ b/lib/jekyll/convertible.rb
@@ -50,9 +50,9 @@ module Jekyll
           self.data = SafeYAML.load($1)
         end
       rescue SyntaxError => e
-        puts "YAML Exception reading #{File.join(base, name)}: #{e.message}"
+        Jekyll.logger.warn "YAML Exception reading #{File.join(base, name)}: #{e.message}"
       rescue Exception => e
-        puts "Error reading file #{File.join(base, name)}: #{e.message}"
+        Jekyll.logger.warn "Error reading file #{File.join(base, name)}: #{e.message}"
       end
 
       self.data ||= {}
diff --git a/lib/jekyll/site.rb b/lib/jekyll/site.rb
index 5ebf3c20..a86ca5e2 100644
--- a/lib/jekyll/site.rb
+++ b/lib/jekyll/site.rb
@@ -396,13 +396,11 @@ module Jekyll
 
     def relative_permalinks_deprecation_method
       if config['relative_permalinks'] && has_relative_page?
-        $stderr.puts # Places newline after "Generating..."
         Jekyll.logger.warn "Deprecation:", "Starting in 2.0, permalinks for pages" +
                                             " in subfolders must be relative to the" +
                                             " site source directory, not the parent" +
                                             " directory. Check http://jekyllrb.com/docs/upgrading/"+
                                             " for more info."
-        $stderr.print Jekyll.logger.formatted_topic("") + "..." # for "done."
       end
     end