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CHECK report for OnassisJavaLibs on malbec2

This page was generated on 2021-01-14 15:59:04 -0500 (Thu, 14 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE OnassisJavaLibs PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 253/385HostnameOS / ArchINSTALLBUILDCHECK
OnassisJavaLibs 1.13.0
Eugenia Galeota
Snapshot Date: 2021-01-14 09:00:13 -0500 (Thu, 14 Jan 2021)
URL: https://git.bioconductor.org/packages/OnassisJavaLibs
Branch: master
Last Commit: a612d9f
Last Changed Date: 2020-10-27 10:23:07 -0500 (Tue, 27 Oct 2020)
malbec2 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK  WARNINGS 

Summary

Package: OnassisJavaLibs
Version: 1.13.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:OnassisJavaLibs.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings OnassisJavaLibs_1.13.0.tar.gz
StartedAt: 2021-01-14 12:32:39 -0500 (Thu, 14 Jan 2021)
EndedAt: 2021-01-14 12:32:58 -0500 (Thu, 14 Jan 2021)
EllapsedTime: 18.9 seconds
RetCode: 0
Status:  OK 
CheckDir: OnassisJavaLibs.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:OnassisJavaLibs.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings OnassisJavaLibs_1.13.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-data-experiment/meat/OnassisJavaLibs.Rcheck’
* using R Under development (unstable) (2021-01-05 r79797)
* 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 ‘1.13.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 6 NOTEs
See
  ‘/home/biocbuild/bbs-3.13-data-experiment/meat/OnassisJavaLibs.Rcheck/00check.log’
for details.



Installation output

OnassisJavaLibs.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL OnassisJavaLibs
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/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)

Tests output


Example timings