This page was generated on 2023年04月11日 14:50:27 -0400 (2023年4月11日).
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:OnassisJavaLibs.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings OnassisJavaLibs_1.20.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.16-data-experiment/meat/OnassisJavaLibs.Rcheck’ * using R version 4.2.3 (2023年03月15日) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * checking for file ‘OnassisJavaLibs/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘OnassisJavaLibs’ version ‘1.20.0’ * 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-sml/src/main/resources/scripts/python/pfam_uniprot_kb/buildUniprotKB_pfam_Mapping.py 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 Tarballs are only required to store paths of up to 100 bytes and cannot store those of more than 256 bytes, with restrictions including to 100 bytes for the final component. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * 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 89.1Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences. * checking top-level files ... NOTE File LICENSE is not mentioned in the DESCRIPTION file. * 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 * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * 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 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 ... ‘OnassisJavaLibs.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 5 NOTEs See ‘/home/biocbuild/bbs-3.16-data-experiment/meat/OnassisJavaLibs.Rcheck/00check.log’ for details.
OnassisJavaLibs.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL OnassisJavaLibs ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’ * installing *source* package ‘OnassisJavaLibs’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (OnassisJavaLibs)