############################################################################## ############################################################################## ### ### Running command: ### ### /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD check --install=check:TCGAbiolinks.install-out.txt --library=/home/rapidbuild/bbs-3.21-bioc-rapid/R/site-library --timings TCGAbiolinks_2.35.3.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/TCGAbiolinks.Rcheck’ * using R Under development (unstable) (2025-01-20 r87609) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘TCGAbiolinks/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘TCGAbiolinks’ version ‘2.35.3’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 23 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * 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 ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘TCGAbiolinks’ can be installed ... OK * checking installed package size ... INFO installed size is 6.2Mb sub-directories of 1Mb or more: R 1.6Mb data 4.3Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * 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 whether startup messages can be suppressed ... OK * checking dependencies in R code ... WARNING '::' or ':::' import not declared from: ‘dnet’ * checking S3 generic/method consistency ... WARNING print: function(x, ...) print.header: function(text, type) See section ‘Generic functions and methods’ in the ‘Writing R Extensions’ manual. * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE GDCprepare_clinic: no visible binding for global variable ‘bcr_patient_barcode’ GDCprepare_clinic: no visible binding for global variable ‘days_to_last_followup’ GDCprepare_clinic: no visible binding for global variable ‘vital_status’ GDCquery : : no visible binding for global variable ‘submitter_id’ GDCquery : : no visible binding for global variable ‘is_ffpe’ GDCquery_clinic: no visible binding for global variable ‘submitter_id’ GDCquery_clinic: no visible global function definition for ‘across’ GDCquery_clinic: no visible global function definition for ‘everything’ GDCquery_clinic : : no visible binding for global variable ‘submitter_id’ GDCquery_clinic : : no visible global function definition for ‘across’ GDCquery_clinic : : no visible global function definition for ‘everything’ TCGAanalyze_DEA: no visible binding for global variable ‘barcode’ TCGAanalyze_DEA: no visible binding for global variable ‘clinical’ TCGAquery_recount2: no visible binding for global variable ‘rse_gene’ TCGAtumor_purity: no visible binding for global variable ‘Tumor.purity’ TCGAvisualize_oncoprint: no visible binding for global variable ‘value’ TCGAvisualize_starburst: no visible binding for global variable ‘gene_name’ TCGAvisualize_starburst: no visible binding for global variable ‘geFDR2’ TCGAvisualize_starburst: no visible binding for global variable ‘logFC’ TCGAvisualize_starburst: no visible binding for global variable ‘meFDR2’ TCGAvisualize_starburst: no visible binding for global variable ‘threshold.starburst’ TCGAvisualize_starburst: no visible binding for global variable ‘starburst.status’ colDataPrepare: no visible binding for global variable ‘sample_submitter_id’ colDataPrepare: no visible binding for global variable ‘submitter_id’ readExonQuantification: no visible binding for global variable ‘exon’ readExonQuantification: no visible binding for global variable ‘coordinates’ readSingleCellAnalysis : : no visible global function definition for ‘Read10X’ read_gene_expression_quantification : : no visible binding for '<<-' assignment to ‘assay.list’ read_gene_expression_quantification: no visible binding for global variable ‘assay.list’ Undefined global functions or variables: Read10X Tumor.purity across assay.list barcode bcr_patient_barcode clinical coordinates days_to_last_followup everything exon geFDR2 gene_name is_ffpe logFC meFDR2 rse_gene sample_submitter_id starburst.status submitter_id threshold.starburst value vital_status * checking Rd files ... WARNING DE_PCBC_stemSig.Rd: Sections \title, and \name must exist and be unique in Rd files EB_PCBC_stemSig.Rd: Sections \title, and \name must exist and be unique in Rd files ECTO_PCBC_stemSig.Rd: Sections \title, and \name must exist and be unique in Rd files GDCdownload.Rd: Sections \title, and \name must exist and be unique in Rd files GDCprepare.Rd: Sections \title, and \name must exist and be unique in Rd files GDCprepare_clinic.Rd: Sections \title, and \name must exist and be unique in Rd files Error writing to connection: No space left on device GDCquery_ATAC_seq.Rd: Sections \title, and \name must exist and be unique in Rd files GDCquery_clinic.Rd: Sections \title, and \name must exist and be unique in Rd files GeneSplitRegulon.Rd: Sections \title, and \name must exist and be unique in Rd files GenesCutID.Rd: Sections \title, and \name must exist and be unique in Rd files MESO_PCBC_stemSig.Rd: Sections \title, and \name must exist and be unique in Rd files PanCancerAtlas_subtypes.Rd: Sections \title, and \name must exist and be unique in Rd files SC_PCBC_stemSig.Rd: Sections \title, and \name must exist and be unique in Rd files TCGAVisualize_volcano.Rd: Sections \title, and \name must exist and be unique in Rd files TCGA_MolecularSubtype.Rd: Sections \title, and \name must exist and be unique in Rd files TCGAanalyze_Clustering.Rd: Sections \title, and \name must exist and be unique in Rd files Error writing to connection: No space left on device TCGAanalyze_DEA_Affy.Rd: Sections \title, and \name must exist and be unique in Rd files Error writing to connection: No space left on device TCGAanalyze_EA.Rd: Sections \title, and \name must exist and be unique in Rd files TCGAanalyze_EAcomplete.Rd: Sections \title, and \name must exist and be unique in Rd files TCGAanalyze_Filtering.Rd: Sections \title, and \name must exist and be unique in Rd files TCGAanalyze_LevelTab.Rd: Sections \title, and \name must exist and be unique in Rd files TCGAanalyze_Normalization.Rd: Sections \title, and \name must exist and be unique in Rd files TCGAanalyze_Pathview.Rd: Sections \title, and \name must exist and be unique in Rd files TCGAanalyze_Preprocessing.Rd: Sections \title, and \name must exist and be unique in Rd files TCGAanalyze_Stemness.Rd: Sections \title, and \name must exist and be unique in Rd files TCGAanalyze_SurvivalKM.Rd: Sections \title, and \name must exist and be unique in Rd files TCGAanalyze_analyseGRN.Rd: Sections \title, and \name must exist and be unique in Rd files TCGAanalyze_networkInference.Rd: Sections \title, and \name must exist and be unique in Rd files TCGAanalyze_survival.Rd: Sections \title, and \name must exist and be unique in Rd files TCGAbatch_Correction.Rd: Sections \title, and \name must exist and be unique in Rd files TCGAbiolinks-package.Rd: Sections \title, and \name must exist and be unique in Rd files Warning in for (i in seq_len(n)) { : closing unused connection 5 () Warning in for (i in seq_len(n)) { : closing unused connection 4 () Warning in for (i in seq_len(n)) { : closing unused connection 3 () TCGAprepare_Affy.Rd: Sections \title, and \name must exist and be unique in Rd files TCGAquery_MatchedCoupledSampleTypes.Rd: Sections \title, and \name must exist and be unique in Rd files TCGAquery_SampleTypes.Rd: Sections \title, and \name must exist and be unique in Rd files TCGAquery_recount2.Rd: Sections \title, and \name must exist and be unique in Rd files TCGAquery_subtype.Rd: Sections \title, and \name must exist and be unique in Rd files TCGAtumor_purity.Rd: Sections \title, and \name must exist and be unique in Rd files TCGAvisualize_BarPlot.Rd: Sections \title, and \name must exist and be unique in Rd files TCGAvisualize_EAbarplot.Rd: Sections \title, and \name must exist and be unique in Rd files Error writing to connection: No space left on device TCGAvisualize_PCA.Rd: Sections \title, and \name must exist and be unique in Rd files TCGAvisualize_SurvivalCoxNET.Rd: Sections \title, and \name must exist and be unique in Rd files Error writing to connection: No space left on device TCGAvisualize_oncoprint.Rd: Sections \title, and \name must exist and be unique in Rd files Error writing to connection: No space left on device TabSubtypesCol_merged.Rd: Sections \title, and \name must exist and be unique in Rd files Tumor.purity.Rd: Sections \title, and \name must exist and be unique in Rd files UseRaw_afterFilter.Rd: Sections \title, and \name must exist and be unique in Rd files batch.info.Rd: Sections \title, and \name must exist and be unique in Rd files bcgsc.ca_CHOL.IlluminaHiSeq_DNASeq.1.somatic.maf.Rd: Sections \title, and \name must exist and be unique in Rd files chol_maf.Rd: Sections \title, and \name must exist and be unique in Rd files classification.Rd: Sections \title, and \name must exist and be unique in Rd files clinBRCA.Rd: Sections \title, and \name must exist and be unique in Rd files clinical.biotab.Rd: Sections \title, and \name must exist and be unique in Rd files colDataPrepare.Rd: Sections \title, and \name must exist and be unique in Rd files dataBRCA.Rd: Sections \title, and \name must exist and be unique in Rd files dataDEGsFiltLevel.Rd: Sections \title, and \name must exist and be unique in Rd files dataREAD.Rd: Sections \title, and \name must exist and be unique in Rd files dataREAD_df.Rd: Sections \title, and \name must exist and be unique in Rd files dmc.non.parametric.Rd: Sections \title, and \name must exist and be unique in Rd files dmc.non.parametric.se.Rd: Sections \title, and \name must exist and be unique in Rd files gaiaCNVplot.Rd: Sections \title, and \name must exist and be unique in Rd files gbm.exp.harmonized.Rd: Sections \title, and \name must exist and be unique in Rd files gbm.exp.legacy.Rd: Sections \title, and \name must exist and be unique in Rd files geneInfo.Rd: Sections \title, and \name must exist and be unique in Rd files geneInfoHT.Rd: Sections \title, and \name must exist and be unique in Rd files get.GRCh.bioMart.Rd: Sections \title, and \name must exist and be unique in Rd files getAdjacencyBiogrid.Rd: Sections \title, and \name must exist and be unique in Rd files getDataCategorySummary.Rd: Sections \title, and \name must exist and be unique in Rd files getGDCInfo.Rd: Sections \title, and \name must exist and be unique in Rd files getGDCprojects.Rd: Sections \title, and \name must exist and be unique in Rd files getGistic.Rd: Sections \title, and \name must exist and be unique in Rd files getLinkedOmicsData.Rd: Sections \title, and \name must exist and be unique in Rd files getMC3MAF.Rd: Sections \title, and \name must exist and be unique in Rd files getManifest.Rd: Sections \title, and \name must exist and be unique in Rd files getNbCases.Rd: Sections \title, and \name must exist and be unique in Rd files getNbFiles.Rd: Sections \title, and \name must exist and be unique in Rd files getProjectSummary.Rd: Sections \title, and \name must exist and be unique in Rd files getResults.Rd: Sections \title, and \name must exist and be unique in Rd files getSampleFilesSummary.Rd: Sections \title, and \name must exist and be unique in Rd files getTSS.Rd: Sections \title, and \name must exist and be unique in Rd files get_IDs.Rd: Sections \title, and \name must exist and be unique in Rd files ggbiplot.Rd: Sections \title, and \name must exist and be unique in Rd files gliomaClassifier.Rd: Sections \title, and \name must exist and be unique in Rd files isServeOK.Rd: Sections \title, and \name must exist and be unique in Rd files matchedMetExp.Rd: Sections \title, and \name must exist and be unique in Rd files met.gbm.27k.Rd: Sections \title, and \name must exist and be unique in Rd files msi_results.Rd: Sections \title, and \name must exist and be unique in Rd files pancan2018.Rd: Sections \title, and \name must exist and be unique in Rd files splitAPICall.Rd: Sections \title, and \name must exist and be unique in Rd files tabSurvKMcompleteDEGs.Rd: Sections \title, and \name must exist and be unique in Rd files problems found in ‘DE_PCBC_stemSig.Rd’, ‘EB_PCBC_stemSig.Rd’, ‘ECTO_PCBC_stemSig.Rd’, ‘GDCdownload.Rd’, ‘GDCprepare.Rd’, ‘GDCprepare_clinic.Rd’, ‘GDCquery.Rd’, ‘GDCquery_ATAC_seq.Rd’, ‘GDCquery_clinic.Rd’, ‘GeneSplitRegulon.Rd’, ‘GenesCutID.Rd’, ‘MESO_PCBC_stemSig.Rd’, ‘PanCancerAtlas_subtypes.Rd’, ‘SC_PCBC_stemSig.Rd’, ‘TCGAVisualize_volcano.Rd’, ‘TCGA_MolecularSubtype.Rd’, ‘TCGAanalyze_Clustering.Rd’, ‘TCGAanalyze_DEA.Rd’, ‘TCGAanalyze_DEA_Affy.Rd’, ‘TCGAanalyze_DMC.Rd’, ‘TCGAanalyze_EA.Rd’, ‘TCGAanalyze_EAcomplete.Rd’, ‘TCGAanalyze_Filtering.Rd’, ‘TCGAanalyze_LevelTab.Rd’, ‘TCGAanalyze_Normalization.Rd’, ‘TCGAanalyze_Pathview.Rd’, ‘TCGAanalyze_Preprocessing.Rd’, ‘TCGAanalyze_Stemness.Rd’, ‘TCGAanalyze_SurvivalKM.Rd’, ‘TCGAanalyze_analyseGRN.Rd’, ‘TCGAanalyze_networkInference.Rd’, ‘TCGAanalyze_survival.Rd’, ‘TCGAbatch_Correction.Rd’, ‘TCGAbiolinks-package.Rd’, ‘TCGAprepare_Affy.Rd’, ‘TCGAquery_MatchedCoupledSampleTypes.Rd’, ‘TCGAquery_SampleTypes.Rd’, ‘TCGAquery_recount2.Rd’, ‘TCGAquery_subtype.Rd’, ‘TCGAtumor_purity.Rd’, ‘TCGAvisualize_BarPlot.Rd’, ‘TCGAvisualize_EAbarplot.Rd’, ‘TCGAvisualize_Heatmap.Rd’, ‘TCGAvisualize_PCA.Rd’, ‘TCGAvisualize_SurvivalCoxNET.Rd’, ‘TCGAvisualize_meanMethylation.Rd’, ‘TCGAvisualize_oncoprint.Rd’, ‘TCGAvisualize_starburst.Rd’, ‘TabSubtypesCol_merged.Rd’, ‘Tumor.purity.Rd’, ‘UseRaw_afterFilter.Rd’, ‘batch.info.Rd’, ‘bcgsc.ca_CHOL.IlluminaHiSeq_DNASeq.1.somatic.maf.Rd’, ‘chol_maf.Rd’, ‘classification.Rd’, ‘clinBRCA.Rd’, ‘clinical.biotab.Rd’, ‘colDataPrepare.Rd’, ‘dataBRCA.Rd’, ‘dataDEGsFiltLevel.Rd’, ‘dataREAD.Rd’, ‘dataREAD_df.Rd’, ‘dmc.non.parametric.Rd’, ‘dmc.non.parametric.se.Rd’, ‘gaiaCNVplot.Rd’, ‘gbm.exp.harmonized.Rd’, ‘gbm.exp.legacy.Rd’, ‘geneInfo.Rd’, ‘geneInfoHT.Rd’, ‘get.GRCh.bioMart.Rd’, ‘getAdjacencyBiogrid.Rd’, ‘getDataCategorySummary.Rd’, ‘getGDCInfo.Rd’, ‘getGDCprojects.Rd’, ‘getGistic.Rd’, ‘getLinkedOmicsData.Rd’, ‘getMC3MAF.Rd’, ‘getManifest.Rd’, ‘getNbCases.Rd’, ‘getNbFiles.Rd’, ‘getProjectSummary.Rd’, ‘getResults.Rd’, ‘getSampleFilesSummary.Rd’, ‘getTSS.Rd’, ‘get_IDs.Rd’, ‘ggbiplot.Rd’, ‘gliomaClassifier.Rd’, ‘isServeOK.Rd’, ‘matchedMetExp.Rd’, ‘met.gbm.27k.Rd’, ‘msi_results.Rd’, ‘pancan2018.Rd’, ‘splitAPICall.Rd’, ‘tabSurvKMcompleteDEGs.Rd’ * 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking R/sysdata.rda ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed TCGAanalyze_DEA 8.800 0.198 9.003 getManifest 6.833 0.070 133.279 GDCquery 1.623 0.027 15.849 GDCprepare_clinic 1.141 0.130 42.768 matchedMetExp 0.993 0.017 11.934 getResults 0.956 0.017 18.384 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... NOTE Package vignettes without corresponding tangle output: ‘analysis.Rmd’ ‘casestudy.Rmd’ ‘classifiers.Rmd’ ‘clinical.Rmd’ ‘download_prepare.Rmd’ ‘extension.Rmd’ ‘index.Rmd’ ‘mutation.Rmd’ ‘query.Rmd’ ‘stemness_score.Rmd’ ‘subtypes.Rmd’ * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 3 WARNINGs, 2 NOTEs See ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/TCGAbiolinks.Rcheck/00check.log’ for details.