rbbt-util 5.21.72 → 5.21.73

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: e69da003714cab274f0880e0d64e401e32a7e8eb
+  metadata.gz: 67fc2edc5af1bf247a71c9e19a7cef289741cfd6
+  data.tar.gz: 1c23e84e67396dec836260de5c6f07f0709bffe8
 SHA512:
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+  data.tar.gz: 3444eee6813fdff76b847fadb93e230d721afbe90a61edf1aed27e91c6a4e97bf57c9a1fb75749c211a1159ccfa88114df64d1603b57fe0e9b18a84089a02c02

data/lib/rbbt/util/R.rb

@@ -40,7 +40,7 @@ source('#{UTIL}');
     Log.debug{"R Script:\n#{ cmd }"}
 
     if monitor
-      io = CMD.cmd('R --vanilla --quiet', options.merge(:in => cmd, :pipe => true, :log => true))
+      io = CMD.cmd('R --quiet', options.merge(:in => cmd, :pipe => true, :log => true))
       while line = io.gets
         puts line
       end

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

@@ -74,7 +74,7 @@ module R
 
                          sh_pid = Process.fork do
                            #args = %w(CMD Rserve --vanilla --quiet --RS-socket)
-                           args = %w(--vanilla --quiet --RS-socket)
+                           args = %w(--quiet --RS-socket)
                            args << "'#{socket_file}'"
                            args << "--RS-workdir"
                            args << "'#{workdir}'"

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.21.72
+  version: 5.21.73
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2017-02-15 00:00:00.000000000 Z
+date: 2017-02-17 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -506,83 +506,83 @@ signing_key:
 specification_version: 4
 summary: Utilities for the Ruby Bioinformatics Toolkit (rbbt)
 test_files:
-- test/test_helper.rb
+- test/rbbt/test_workflow.rb
 - test/rbbt/resource/test_path.rb
-- test/rbbt/association/test_item.rb
-- test/rbbt/association/test_database.rb
-- test/rbbt/association/test_open.rb
-- test/rbbt/association/test_index.rb
-- test/rbbt/association/test_util.rb
-- test/rbbt/util/test_concurrency.rb
-- test/rbbt/util/test_log.rb
-- test/rbbt/util/test_chain_methods.rb
-- test/rbbt/util/test_simpleopt.rb
-- test/rbbt/util/simpleopt/test_parse.rb
-- test/rbbt/util/simpleopt/test_get.rb
-- test/rbbt/util/simpleopt/test_setup.rb
 - test/rbbt/util/test_cmd.rb
-- test/rbbt/util/test_semaphore.rb
-- test/rbbt/util/concurrency/test_threads.rb
-- test/rbbt/util/concurrency/processes/test_socket.rb
-- test/rbbt/util/concurrency/test_processes.rb
-- test/rbbt/util/test_tmpfile.rb
-- test/rbbt/util/test_open.rb
-- test/rbbt/util/test_filecache.rb
-- test/rbbt/util/R/test_eval.rb
-- test/rbbt/util/R/test_model.rb
+- test/rbbt/util/simpleopt/test_setup.rb
+- test/rbbt/util/simpleopt/test_get.rb
+- test/rbbt/util/simpleopt/test_parse.rb
+- test/rbbt/util/test_chain_methods.rb
 - test/rbbt/util/test_simpleDSL.rb
-- test/rbbt/util/log/test_progress.rb
-- test/rbbt/util/test_colorize.rb
-- test/rbbt/util/test_R.rb
+- test/rbbt/util/test_log.rb
+- test/rbbt/util/test_open.rb
 - test/rbbt/util/misc/test_lock.rb
-- test/rbbt/util/misc/test_pipes.rb
+- test/rbbt/util/misc/test_multipart_payload.rb
 - test/rbbt/util/misc/test_bgzf.rb
+- test/rbbt/util/misc/test_pipes.rb
 - test/rbbt/util/misc/test_omics.rb
-- test/rbbt/util/misc/test_multipart_payload.rb
+- test/rbbt/util/test_concurrency.rb
+- test/rbbt/util/test_R.rb
+- test/rbbt/util/log/test_progress.rb
+- test/rbbt/util/test_colorize.rb
+- test/rbbt/util/test_simpleopt.rb
 - test/rbbt/util/test_excel2tsv.rb
+- test/rbbt/util/test_filecache.rb
+- test/rbbt/util/concurrency/test_processes.rb
+- test/rbbt/util/concurrency/test_threads.rb
+- test/rbbt/util/concurrency/processes/test_socket.rb
+- 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/entity/test_identifiers.rb
+- test/rbbt/test_association.rb
+- test/rbbt/knowledge_base/test_traverse.rb
+- test/rbbt/knowledge_base/test_registry.rb
+- test/rbbt/knowledge_base/test_entity.rb
+- test/rbbt/knowledge_base/test_enrichment.rb
+- test/rbbt/knowledge_base/test_syndicate.rb
+- test/rbbt/knowledge_base/test_query.rb
+- test/rbbt/test_resource.rb
 - test/rbbt/test_entity.rb
+- test/rbbt/test_knowledge_base.rb
+- test/rbbt/annotations/test_util.rb
+- test/rbbt/association/test_index.rb
+- test/rbbt/association/test_item.rb
+- test/rbbt/association/test_open.rb
+- test/rbbt/association/test_util.rb
+- test/rbbt/association/test_database.rb
+- test/rbbt/test_tsv.rb
 - test/rbbt/workflow/step/test_dependencies.rb
-- test/rbbt/workflow/test_doc.rb
-- test/rbbt/workflow/test_step.rb
 - test/rbbt/workflow/test_task.rb
-- test/rbbt/test_association.rb
-- test/rbbt/test_knowledge_base.rb
-- test/rbbt/tsv/parallel/test_traverse.rb
-- test/rbbt/tsv/parallel/test_through.rb
+- test/rbbt/workflow/test_step.rb
+- test/rbbt/workflow/test_doc.rb
+- test/rbbt/test_monitor.rb
+- test/rbbt/test_persist.rb
+- test/rbbt/test_annotations.rb
+- test/rbbt/persist/test_tsv.rb
+- test/rbbt/persist/tsv/test_lmdb.rb
+- test/rbbt/persist/tsv/test_kyotocabinet.rb
+- test/rbbt/persist/tsv/test_sharder.rb
+- test/rbbt/persist/tsv/test_cdb.rb
+- test/rbbt/persist/tsv/test_tokyocabinet.rb
+- test/rbbt/persist/tsv/test_leveldb.rb
+- test/rbbt/tsv/test_field_index.rb
 - test/rbbt/tsv/test_parallel.rb
-- test/rbbt/tsv/test_excel.rb
-- test/rbbt/tsv/test_accessor.rb
+- test/rbbt/tsv/test_index.rb
+- test/rbbt/tsv/test_matrix.rb
 - test/rbbt/tsv/test_change_id.rb
+- test/rbbt/tsv/test_parser.rb
 - test/rbbt/tsv/test_stream.rb
+- test/rbbt/tsv/test_util.rb
+- test/rbbt/tsv/test_excel.rb
+- test/rbbt/tsv/test_accessor.rb
 - test/rbbt/tsv/test_filter.rb
-- test/rbbt/tsv/test_matrix.rb
 - test/rbbt/tsv/test_attach.rb
 - test/rbbt/tsv/test_manipulate.rb
-- test/rbbt/tsv/test_field_index.rb
-- test/rbbt/tsv/test_index.rb
-- test/rbbt/tsv/test_util.rb
-- test/rbbt/tsv/test_parser.rb
-- test/rbbt/test_packed_index.rb
-- test/rbbt/test_persist.rb
+- test/rbbt/tsv/parallel/test_through.rb
+- test/rbbt/tsv/parallel/test_traverse.rb
 - test/rbbt/test_fix_width_table.rb
-- test/rbbt/knowledge_base/test_traverse.rb
-- test/rbbt/knowledge_base/test_entity.rb
-- test/rbbt/knowledge_base/test_query.rb
-- test/rbbt/knowledge_base/test_enrichment.rb
-- test/rbbt/knowledge_base/test_syndicate.rb
-- test/rbbt/knowledge_base/test_registry.rb
-- test/rbbt/entity/test_identifiers.rb
-- test/rbbt/test_monitor.rb
-- test/rbbt/test_workflow.rb
-- test/rbbt/test_annotations.rb
-- test/rbbt/annotations/test_util.rb
-- test/rbbt/test_resource.rb
-- test/rbbt/persist/tsv/test_tokyocabinet.rb
-- test/rbbt/persist/tsv/test_kyotocabinet.rb
-- test/rbbt/persist/tsv/test_lmdb.rb
-- test/rbbt/persist/tsv/test_leveldb.rb
-- test/rbbt/persist/tsv/test_cdb.rb
-- test/rbbt/persist/tsv/test_sharder.rb
-- test/rbbt/persist/test_tsv.rb
-- test/rbbt/test_tsv.rb
+- test/test_helper.rb