BioC experimental data: CHECK report for OnassisJavaLibs on malbec1

Package: OnassisJavaLibs

Version: 0.99.8

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings OnassisJavaLibs_0.99.8.tar.gz

StartedAt: 2017-08-15 10:58:32 -0400 (Tue, 15 Aug 2017)

EndedAt: 2017-08-15 10:58:49 -0400 (Tue, 15 Aug 2017)

EllapsedTime: 17.0 seconds

RetCode: 0

Status:  OK

CheckDir: OnassisJavaLibs.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings OnassisJavaLibs_0.99.8.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.6-data-experiment/meat/OnassisJavaLibs.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OnassisJavaLibs/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OnassisJavaLibs’ version ‘0.99.8’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... NOTE
Found the following non-portable file paths:
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-algo/src/main/java/slib/graph/algo/accessor/GraphAccessor.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-algo/src/main/java/slib/graph/algo/extraction/metric/DepthAnalyserAG.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-algo/src/main/java/slib/graph/algo/extraction/package-info.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-algo/src/main/java/slib/graph/algo/extraction/reduction/dag/GraphReduction_DAG_Ranwez_2011.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-algo/src/main/java/slib/graph/algo/extraction/reduction/dag/GraphReduction_Transitive.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-algo/src/main/java/slib/graph/algo/extraction/rvf/AncestorEngine.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-algo/src/main/java/slib/graph/algo/extraction/rvf/DescendantEngine.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-algo/src/main/java/slib/graph/algo/extraction/rvf/RVF.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-algo/src/main/java/slib/graph/algo/extraction/rvf/RVF_DAG.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-algo/src/main/java/slib/graph/algo/extraction/rvf/RVF_TAX.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-algo/src/main/java/slib/graph/algo/extraction/rvf/instances/InstancesAccessor.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-algo/src/main/java/slib/graph/algo/extraction/rvf/instances/impl/InstanceAccessor_RDF_TYPE.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-algo/src/main/java/slib/graph/algo/extraction/shortest_path/Dijkstra.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-algo/src/main/java/slib/graph/algo/extraction/traversal/GraphTraversal.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-algo/src/main/java/slib/graph/algo/extraction/traversal/classical/BFS.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-algo/src/main/java/slib/graph/algo/extraction/traversal/classical/DFS.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-algo/src/main/java/slib/graph/algo/extraction/utils/Color.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-algo/src/main/java/slib/graph/algo/extraction/utils/GAction.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-algo/src/main/java/slib/graph/algo/extraction/utils/GActionType.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-algo/src/main/java/slib/graph/algo/extraction/utils/GActionValidator.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-algo/src/main/java/slib/graph/algo/extraction/utils/GraphActionExecutor.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-algo/src/main/java/slib/graph/algo/extraction/utils/RooterDAG.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-algo/src/main/java/slib/graph/algo/extraction/validator/dag/Path.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-algo/src/main/java/slib/graph/algo/extraction/validator/dag/ValidatorDAG.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-algo/src/main/java/slib/graph/algo/metric/DepthAnalyserAG.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-algo/src/main/java/slib/graph/algo/reduction/dag/GraphReduction_DAG_Ranwez_2011.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-algo/src/main/java/slib/graph/algo/reduction/dag/GraphReduction_Transitive.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-algo/src/main/java/slib/graph/algo/shortest_path/Dijkstra.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-algo/src/main/java/slib/graph/algo/traversal/GraphTraversal.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-algo/src/main/java/slib/graph/algo/traversal/classical/BFS.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-algo/src/main/java/slib/graph/algo/traversal/classical/DFS.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-algo/src/main/java/slib/graph/algo/utils/GAction.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-algo/src/main/java/slib/graph/algo/utils/GActionType.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-algo/src/main/java/slib/graph/algo/utils/GActionValidator.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-algo/src/main/java/slib/graph/algo/utils/GraphActionExecutor.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-algo/src/main/java/slib/graph/algo/utils/RooterDAG.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-algo/src/main/java/slib/graph/algo/validator/dag/Path.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-algo/src/main/java/slib/graph/algo/validator/dag/ValidatorDAG.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-io/src/main/java/slib/graph/io/loader/GraphLoader.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-io/src/main/java/slib/graph/io/loader/GraphLoaderGeneric.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-io/src/main/java/slib/graph/io/loader/annot/GraphLoader_TSVannot.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-io/src/main/java/slib/graph/io/loader/bio/gaf2/EvidenceCodeRules.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-io/src/main/java/slib/graph/io/loader/bio/gaf2/GraphLoader_GAF_2.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-io/src/main/java/slib/graph/io/loader/bio/mesh/GraphLoader_MESH_XML.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-io/src/main/java/slib/graph/io/loader/bio/mesh/MeshConcept.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-io/src/main/java/slib/graph/io/loader/bio/mesh/MeshXMLHandler.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-io/src/main/java/slib/graph/io/loader/bio/obo/GraphLoader_OBO_1_2.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-io/src/main/java/slib/graph/io/loader/bio/obo/utils/OboRelationship.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-io/src/main/java/slib/graph/io/loader/bio/obo/utils/OboTerm.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-io/src/main/java/slib/graph/io/loader/bio/obo/utils/OboType.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-io/src/main/java/slib/graph/io/loader/bio/snomedct/GraphLoaderSnomedCT_RF2.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-io/src/main/java/slib/graph/io/loader/csv/CSV_Mapping.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-io/src/main/java/slib/graph/io/loader/csv/CSV_StatementTemplate.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-io/src/main/java/slib/graph/io/loader/csv/CSV_StatementTemplate_Constraint.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-io/src/main/java/slib/graph/io/loader/csv/GraphLoader_CSV.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-io/src/main/java/slib/graph/io/loader/csv/StatementTemplateElement.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-io/src/main/java/slib/graph/io/loader/csv/StatementTemplate_Constraint_Type.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-io/src/main/java/slib/graph/io/loader/rdf/RDFLoader.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-io/src/main/java/slib/graph/io/loader/rdf/SlibRdfHandler.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-io/src/main/java/slib/graph/io/loader/slibformat/GraphLoader_SLIB.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-io/src/main/java/slib/graph/io/loader/utils/filter/graph/Filter.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-io/src/main/java/slib/graph/io/loader/utils/filter/graph/FilterCst.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-io/src/main/java/slib/graph/io/loader/utils/filter/graph/FilterGraph.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-io/src/main/java/slib/graph/io/loader/utils/filter/graph/gaf2/FilterGraph_GAF2.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-io/src/main/java/slib/graph/io/loader/utils/filter/graph/gaf2/FilterGraph_GAF2_cst.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-io/src/main/java/slib/graph/io/loader/utils/filter/graph/metrics/FilterGraph_Metrics.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-io/src/main/java/slib/graph/io/loader/utils/filter/graph/metrics/FilterGraph_Metrics_cst.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-io/src/main/java/slib/graph/io/loader/utils/filter/graph/repo/FilterRepository.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-io/src/main/java/slib/graph/io/loader/wordnet/GraphLoader_Wordnet.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-io/src/main/java/slib/graph/io/plotter/GraphPlotter_Graphviz.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-io/src/main/java/slib/graph/io/util/GActionValidator.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-io/src/main/java/slib/graph/io/util/GDataValidator.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-model-impl/src/main/java/slib/graph/model/impl/graph/elements/Edge.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-model-impl/src/main/java/slib/graph/model/impl/graph/memory/GraphMemory.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-model-impl/src/main/java/slib/graph/model/impl/graph/weight/GWS_impl.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-model-impl/src/main/java/slib/graph/model/impl/repo/GraphRepositoryMemory.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-model-impl/src/main/java/slib/graph/model/impl/repo/URIFactoryMemory.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-model-impl/src/main/java/slib/graph/model/impl/utils/GraphUtils.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-model/src/main/java/slib/graph/model/graph/elements/E.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-model/src/main/java/slib/graph/model/graph/utils/Direction.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-model/src/main/java/slib/graph/model/graph/utils/WalkConstraint.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-model/src/main/java/slib/graph/model/graph/weight/GWS.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-model/src/main/java/slib/graph/model/repo/GraphRepository.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-model/src/main/java/slib/graph/model/repo/URIFactory.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-utils/src/main/java/slib/graph/utils/WalkConstraintGeneric.java
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-utils/src/main/java/slib/graph/utils/WalkConstraintUtils.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/Sim_Groupwise_Indirect.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/corpus/VocContextMatrixBuilder.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/graph/framework/dag/Sim_Framework_DAG_Set_Bader_2003.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/graph/framework/dag/Sim_Framework_DAG_Set_Batet_2010.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/graph/framework/dag/Sim_Framework_DAG_Set_Braun_Blanquet_1932.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/graph/framework/dag/Sim_Framework_DAG_Set_Dice_1945.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/graph/framework/dag/Sim_Framework_DAG_Set_Jaccard_1901.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/graph/framework/dag/Sim_Framework_DAG_Set_Knappe_2004.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/graph/framework/dag/Sim_Framework_DAG_Set_Korbel_2002.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/graph/framework/dag/Sim_Framework_DAG_Set_Maryland_Bridge_2003.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/graph/framework/dag/Sim_Framework_DAG_Set_Ochiai_1957.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/graph/framework/dag/Sim_Framework_DAG_Set_Simpson_1960.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/graph/framework/dag/Sim_Framework_DAG_Set_Sokal_Sneath_1963.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/graph/framework/dag/Sim_Framework_DAG_Set_Tversky_1977.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/graph/framework/dag/Sim_Framework_DAG_Set_abstract.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/graph/groupwise/dag/Sim_groupwise_DAG_Ali_Deane.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/graph/groupwise/dag/Sim_groupwise_DAG_GIC.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/graph/groupwise/dag/Sim_groupwise_DAG_LP.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/graph/groupwise/dag/Sim_groupwise_DAG_Lee_2004.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/graph/groupwise/dag/Sim_groupwise_DAG_NTO.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/graph/groupwise/dag/Sim_groupwise_DAG_NTO_MAX.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/graph/groupwise/dag/Sim_groupwise_DAG_TO.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/graph/groupwise/dag/Sim_groupwise_DAG_UI.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/graph/groupwise/dag/Sim_groupwise_DAG_abstract.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/graph/pairwise/dag/Dist_Pairwise_DAG.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/graph/pairwise/dag/IDist_Pairwise_DAG.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/graph/pairwise/dag/ISim_Pairwise_DAG.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/graph/pairwise/dag/Sim_Pairwise_DAG.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/graph/pairwise/dag/edge_based/Dist_DAG_edge_abstract.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/graph/pairwise/dag/edge_based/Dist_pairwise_DAG_edge_Rada_1989.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/graph/pairwise/dag/edge_based/Dist_pairwise_DAG_edge_Rada_LCA_1989.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/graph/pairwise/dag/edge_based/Sim_DAG_edge_abstract.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/graph/pairwise/dag/edge_based/Sim_pairwise_DAG_edge_Kyogoku_basic_2011.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/graph/pairwise/dag/edge_based/Sim_pairwise_DAG_edge_Leacock_Chodorow_1998.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/graph/pairwise/dag/edge_based/Sim_pairwise_DAG_edge_Pekar_Staab_2002.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/graph/pairwise/dag/edge_based/Sim_pairwise_DAG_edge_Rada_1989.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/graph/pairwise/dag/edge_based/Sim_pairwise_DAG_edge_Rada_LCA_1989.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/graph/pairwise/dag/edge_based/Sim_pairwise_DAG_edge_Stojanovic_2001.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/graph/pairwise/dag/edge_based/Sim_pairwise_DAG_edge_Wu_Palmer_1994.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/graph/pairwise/dag/edge_based/experimental/Sim_pairwise_DAG_edge_Al_Mubaid_2006.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/graph/pairwise/dag/edge_based/experimental/Sim_pairwise_DAG_edge_G_SESAME_2007.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/graph/pairwise/dag/edge_based/experimental/Sim_pairwise_DAG_edge_Resnik_1995.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/graph/pairwise/dag/edge_based/experimental/Sim_pairwise_DAG_edge_Slimani_2006.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/graph/pairwise/dag/edge_based/utils/SimDagEdgeUtils.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/graph/pairwise/dag/hybrid/Sim_DAG_hybrid_abstract.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/graph/pairwise/dag/hybrid/experimental/Sim_pairwise_DAG_edge_Li_2003.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/graph/pairwise/dag/hybrid/experimental/Sim_pairwise_DAG_hybrid_Ranwez_2006.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/graph/pairwise/dag/hybrid/experimental/Sim_pairwise_DAG_hybrid_Wang_2007.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/graph/pairwise/dag/hybrid/utils/SimDagHybridUtils.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/graph/pairwise/dag/node_based/Sim_DAG_node_abstract.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/graph/pairwise/dag/node_based/Sim_pairwise_DAG_node_Constants.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/graph/pairwise/dag/node_based/Sim_pairwise_DAG_node_Feature_Tversky_Contrast_Model.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/graph/pairwise/dag/node_based/Sim_pairwise_DAG_node_Feature_Tversky_Ratio_Model.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/graph/pairwise/dag/node_based/Sim_pairwise_DAG_node_GL.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/graph/pairwise/dag/node_based/Sim_pairwise_DAG_node_IC_Prop_Tversky_Contrast_Model.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/graph/pairwise/dag/node_based/Sim_pairwise_DAG_node_IC_Prop_Tversky_Ratio_Model.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/graph/pairwise/dag/node_based/Sim_pairwise_DAG_node_IC_Tversky_Contrast_Model.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/graph/pairwise/dag/node_based/Sim_pairwise_DAG_node_IC_Tversky_Ratio_Model.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/graph/pairwise/dag/node_based/Sim_pairwise_DAG_node_Jaccard_3W_IC.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/graph/pairwise/dag/node_based/Sim_pairwise_DAG_node_Jaccard_IC.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/graph/pairwise/dag/node_based/Sim_pairwise_DAG_node_Jiang_Conrath_1997.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/graph/pairwise/dag/node_based/Sim_pairwise_DAG_node_Jiang_Conrath_1997_Norm.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/graph/pairwise/dag/node_based/Sim_pairwise_DAG_node_Lin_1998.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/graph/pairwise/dag/node_based/Sim_pairwise_DAG_node_Resnik_1995.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/graph/pairwise/dag/node_based/Sim_pairwise_DAG_node_Schlicker_2006_SimRel.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/graph/pairwise/dag/node_based/Sim_pairwise_DAG_node_Sim_IC_2010.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/graph/pairwise/dag/node_based/experimental/Sim_pairwise_DAG_node_GL_GraSM.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/graph/pairwise/dag/node_based/experimental/Sim_pairwise_DAG_node_Harispe_2013.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/graph/pairwise/dag/node_based/experimental/Sim_pairwise_DAG_node_Lin_1998_GraSM.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/graph/pairwise/dag/node_based/experimental/Sim_pairwise_DAG_node_Mazandu_2012.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/graph/pairwise/dag/node_based/experimental/Sim_pairwise_DAG_node_Resnik_1995_Ancestors.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/graph/pairwise/dag/node_based/experimental/Sim_pairwise_DAG_node_Resnik_1995_Descendants.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/graph/pairwise/dag/node_based/experimental/Sim_pairwise_DAG_node_Resnik_1995_GraSM.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/graph/pairwise/dag/node_based/experimental/Sim_pairwise_DAG_node_Schlicker_3WJaccard_SimRel.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/graph/pairwise/dag/node_based/experimental/Sim_pairwise_DAG_node_Schlicker_GL_SimRel.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/graph/pairwise/dag/node_based/experimental/Sim_pairwise_DAG_node_Schlicker_Jaccard_SimRel.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/graph/pairwise/dag/node_based/experimental/Sim_pairwise_DAG_node_Schlicker_Tversky_SimRel.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/others/groupwise/direct/Sim_groupwise_Random.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/others/groupwise/direct/vector/VectorSpaceModel.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/others/groupwise/indirect/Sim_groupwise_Average.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/others/groupwise/indirect/Sim_groupwise_BestMatchAverage.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/others/groupwise/indirect/Sim_groupwise_BestMatchMax.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/others/groupwise/indirect/Sim_groupwise_Lord_2003.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/others/groupwise/indirect/Sim_groupwise_Max.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/others/groupwise/indirect/Sim_groupwise_Min.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/others/groupwise/indirect/experimental/Sim_groupwise_AVERAGE_NORMALIZED_GOSIM.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/others/groupwise/indirect/experimental/Sim_groupwise_MAX_NORMALIZED_GOSIM.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/others/pairwise/Sim_pairwise_Random.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/string/LevenshteinDistance.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/string/LevenshteinSimilarity.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/vector/CosineSimilarity.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/metrics/ic/annot/IC_annot_resnik_1995.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/metrics/ic/annot/IC_annot_resnik_1995_Normalized.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/metrics/ic/annot/IC_probOccurence_propagatted.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/metrics/ic/topo/ICi_ancestors_norm.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/metrics/ic/topo/ICi_depth_max_linear.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/metrics/ic/topo/ICi_depth_max_nonlinear.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/metrics/ic/topo/ICi_depth_min_nonlinear.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/metrics/ic/topo/ICi_harispe_2012.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/metrics/ic/topo/ICi_probOccurence.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/metrics/ic/topo/ICi_probOccurence_propagatted.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/metrics/ic/topo/ICi_resnik_1995.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/metrics/ic/topo/ICi_resnik_unpropagatted_1995.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/metrics/ic/topo/ICi_sanchez_2011.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/metrics/ic/topo/ICi_sanchez_2011_b_adapted.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/metrics/ic/utils/IC_Conf_Corpus.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/metrics/ic/utils/ProbOccurence.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/metrics/utils/LogBasedMetricInterface.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/metrics/vector/VectorWeight_Chabalier_2007.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/metrics/vector/VectorWeight_Chabalier_Propaggated.java
  OnassisJavaLibs/java/slib/slib-sml/src/main/resources/scripts/R/discriminative_power/plotDiscriminativePower.R
  OnassisJavaLibs/java/slib/slib-sml/src/main/resources/scripts/python/kegg_trembl_mapping/human_pathways_prots_kegg_mapping
  OnassisJavaLibs/java/slib/slib-sml/src/main/resources/scripts/python/kegg_trembl_mapping/keggToUniprot.py
  OnassisJavaLibs/java/slib/slib-sml/src/main/resources/scripts/python/kegg_trembl_mapping/pathways_prots
  OnassisJavaLibs/java/slib/slib-sml/src/main/resources/scripts/python/kegg_trembl_mapping/yeast_pathways_prots
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-algo/src/main/java/slib/graph/algo/extraction/reduction/dag
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-algo/src/main/java/slib/graph/algo/extraction/rvf/instances
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-algo/src/main/java/slib/graph/algo/extraction/rvf/instances/impl
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-algo/src/main/java/slib/graph/algo/extraction/shortest_path
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-algo/src/main/java/slib/graph/algo/extraction/traversal
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-algo/src/main/java/slib/graph/algo/extraction/traversal/classical
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-algo/src/main/java/slib/graph/algo/extraction/validator/dag
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-algo/src/main/java/slib/graph/algo/traversal/classical
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-io/src/main/java/slib/graph/io/loader/utils/filter/graph
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-io/src/main/java/slib/graph/io/loader/utils/filter/graph/gaf2
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-io/src/main/java/slib/graph/io/loader/utils/filter/graph/metrics
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-io/src/main/java/slib/graph/io/loader/utils/filter/graph/repo
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-model-impl/src/main/java/slib/graph/model/impl/graph/elements
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-model-impl/src/main/java/slib/graph/model/impl/graph/memory
  OnassisJavaLibs/java/slib/slib-graph/slib-graph-model-impl/src/main/java/slib/graph/model/impl/graph/weight
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/graph/pairwise/dag/edge_based
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/graph/pairwise/dag/edge_based/experimental
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/graph/pairwise/dag/edge_based/utils
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/graph/pairwise/dag/hybrid/experimental
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/graph/pairwise/dag/hybrid/utils
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/graph/pairwise/dag/node_based
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/graph/pairwise/dag/node_based/experimental
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/others/groupwise/direct/vector
  OnassisJavaLibs/java/slib/slib-sml/src/main/java/slib/sml/sm/core/measures/others/groupwise/indirect/experimental

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* checking for sufficient/correct file permissions ... OK
* checking whether package ‘OnassisJavaLibs’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 89.2Mb
  sub-directories of 1Mb or more:
    extdata  89.0Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
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File
  LICENSE
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* 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
* 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
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* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘rJava’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... NONE
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 5 NOTEs
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  ‘/home/biocbuild/bbs-3.6-data-experiment/meat/OnassisJavaLibs.Rcheck/00check.log’
for details.

* installing *source* package ‘OnassisJavaLibs’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (OnassisJavaLibs)