############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf PDATK.buildbin-libdir && mkdir PDATK.buildbin-libdir && D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL --build --library=PDATK.buildbin-libdir PDATK_1.3.1.tar.gz ### ############################################################################## ############################################################################## * installing *source* package 'PDATK' ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'PDATK' finding HTML links ... done CSPC_MAE html ClinicalModel-class html ClinicalModel html CohortList-class html CohortList html ConsensusMetaclusteringModel-class html ConsensusMetaclusteringModel html CoxModel-class html CoxModel html GeneFuModel-class html GeneFuModel html ModelComparison-class html ModelComparison html NCSModel-class html NetworkCommunitySearchModel html PCOSP-class html PCOSP html PCOSP_or_ClinicalModel-class html PCOSP_or_RLS_or_RGA-class html RGAModel-class html RLSModel-class html RandomGeneAssignmentModel html RandomLabelShufflingModel html S4Model-class html SurvivalExperiment-class html SurvivalExperiment html SurvivalModel-class html SurvivalModel html assignColDataColumn html assignSubtypes-CohortList-list-method html assignSubtypes-SurvivalExperiment-data.frame-method html assignSubtypes html barPlotModelComparison-ClinicalModel-PCOSP_or_RLS_or_RGA-method html barPlotModelComparison html birnbaum html chen html cohortSubtypeDFs html compareModels-ModelComparison-SurvivalModel-method html compareModels-SurvivalModel-SurvivalModel-method html compareModels html densityPlotModelComparison-PCOSP_or_RLS_or_RGA-PCOSP_or_RLS_or_RGA-method html densityPlotModelComparison html dot-findAllCohortPairs html dot-randomSampleIndex html dropNotCensored-CohortList-method html dropNotCensored-SurvivalExperiment-method html dropNotCensored html existingClassifierData html findCommonGenes-CohortList-method html findCommonGenes-MultiAssayExperiment-method html findCommonGenes html findCommonSamples-CohortList-method html findCommonSamples html forestPlot-ModelComparison-method html forestPlot-PCOSP_or_ClinicalModel-method html forestPlot html getModelSeed-SurvivalModel-method html getModelSeed html getTopFeatures-MultiAssayExperiment-method html getTopFeatures-PCOSP-method html getTopFeatures-SummarizedExperiment-method html getTopFeatures html haiderSigScores html hasColDataColumns html merge-SurvivalExperiment-SurvivalExperiment-method html modelParams-S4Model-method html modelParams-set-S4Model-List_or_list_or_NULL-method html modelParams-set html modelParams html models-S4Model-method html models-SurvivalModel-method html models-set-S4Model-List_or_list_or_NULL-method html models-set-SurvivalModel-SimpleList-method html models-set html models html normalize-DFrame-method html normalize-MultiAssayExperiment-method html normalize-SummarizedExperiment-method html normalize-data.frame_or_matrix-method html normalsMAE html optimalKMinimizeAmbiguity html plotNetworkGraph-NCSModel-method html plotNetworkGraph html plotROC-PCOSP-method html plotROC html plotSurvivalCurves-CoxModel-method html plotSurvivalCurves html predictClasses-CohortList-ClinicalModel-method html predictClasses-CohortList-GeneFuModel-method html predictClasses-CohortList-PCOSP_or_RLS_or_RGA-method html predictClasses-ConsensusMetaclusteringModel-ANY-method html predictClasses-NCSModel-ANY-method html predictClasses-SurvivalExperiment-ClinicalModel-method html predictClasses-SurvivalExperiment-GeneFuModel-method html predictClasses-SurvivalExperiment-PCOSP_or_RLS_or_RGA-method html predictClasses html preprocessCaret html rankFeatures-MultiAssayExperiment-method html rankFeatures-SummarizedExperiment-method html rankFeatures html removeColDataFactorColumns html removeFactorColumns html renameColDataColumns html renameColumns html runGSEA-PCOSP-data.frame-method html runGSEA html sampleClinicalModel html sampleCohortList html sampleICGCmicro html samplePCOSPmodel html samplePCOSPpredList html samplePCSIsurvExp html sampleRGAmodel html sampleRLSmodel html sampleTrainedPCOSPmodel html sampleValPCOSPmodel html show-S4Model-method html subset-CohortList-method html trainData-S4Model-method html trainData-set-S4Model-method html trainData-set html trainData html trainModel-ClinicalModel-method html trainModel-ConsensusMetaclusteringModel-method html trainModel-CoxModel-method html trainModel-GeneFuModel-method html trainModel-NCSModel-method html trainModel-PCOSP-method html trainModel-RGAModel-method html trainModel-RLSModel-method html trainModel html validateModel-ClinicalModel-CohortList-method html validateModel-ClinicalModel-SurvivalExperiment-method html validateModel-ConsensusMetaclusteringModel-ConsensusMetaclusteringModel-method html validateModel-GeneFuModel-CohortList-method html validateModel-GeneFuModel-SurvivalExperiment-method html validateModel-PCOSP_or_RLS_or_RGA-CohortList-method html validateModel-PCOSP_or_RLS_or_RGA-SurvivalExperiment-method html validateModel html validationData-S4Model-method html validationData-SurvivalModel-method html validationData-set-S4Model-List_or_list_or_NULL-method html validationData-set-SurvivalModel-CohortList-method html validationData-set html validationData html validationStats-S4Model-method html validationStats-SurvivalModel-method html validationStats-set-S4Model-DFrame_or_data.frame_data.table_or_NULL-method html validationStats-set-SurvivalModel-data.frame-method html validationStats-set html validationStats html ** 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 * MD5 sums packaged installation of 'PDATK' as PDATK_1.3.1.zip * DONE (PDATK)