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This page was generated on 2024-10-17 14:51 -0400 (Thu, 17 Oct 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4763
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 279/430HostnameOS / ArchINSTALLBUILDCHECK
OnassisJavaLibs 1.26.0  (landing page)
Eugenia Galeota
Snapshot Date: 2024-10-17 07:30 -0400 (Thu, 17 Oct 2024)
git_url: https://git.bioconductor.org/packages/OnassisJavaLibs
git_branch: RELEASE_3_19
git_last_commit: cd4b250
git_last_commit_date: 2024-04-30 10:48:41 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published

CHECK results for OnassisJavaLibs on nebbiolo1

To the developers/maintainers of the OnassisJavaLibs package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: OnassisJavaLibs
Version: 1.26.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:OnassisJavaLibs.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings OnassisJavaLibs_1.26.0.tar.gz
StartedAt: 2024-10-17 11:51:44 -0400 (Thu, 17 Oct 2024)
EndedAt: 2024-10-17 11:52:04 -0400 (Thu, 17 Oct 2024)
EllapsedTime: 20.0 seconds
RetCode: 0
Status:   OK  
CheckDir: OnassisJavaLibs.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:OnassisJavaLibs.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings OnassisJavaLibs_1.26.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-data-experiment/meat/OnassisJavaLibs.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.5 LTS
* using session charset: UTF-8
* checking for file ‘OnassisJavaLibs/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OnassisJavaLibs’ version ‘1.26.0’
* 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 87.1Mb
  sub-directories of 1Mb or more:
    extdata  87.0Mb
* 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 code 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 ... NOTE
checkRd: (-1) OnassisJavaLibs.Rd:18: Lost braces
    18 | /code{ mvn clean compile assembly:single  -Dlog4j.configuration=log4j2.properties}
       |      ^
checkRd: (-1) OnassisJavaLibs.Rd:27: Lost braces
    27 | /code{ mvn clean install }
       |      ^
checkRd: (-1) OnassisJavaLibs.Rd:32: Lost braces
    32 | /code{mvn clean install  assembly:single}
       |      ^
* 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 ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 6 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-data-experiment/meat/OnassisJavaLibs.Rcheck/00check.log’
for details.

Installation output

OnassisJavaLibs.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL OnassisJavaLibs
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-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)

Tests output


Example timings