############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TCGAbiolinks.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TCGAbiolinks_2.36.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/TCGAbiolinks.Rcheck’ * using R version 4.5.0 RC (2025-04-04 r88126) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘TCGAbiolinks/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘TCGAbiolinks’ version ‘2.36.0’ * 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 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 binding for global variable ‘days_to_follow_up’ GDCquery_clinic: no visible binding for global variable ‘disease_response’ 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’ getBarcodeInfo: no visible binding for global variable ‘days_to_follow_up’ getBarcodeInfo: no visible binding for global variable ‘disease_response’ 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_follow_up days_to_last_followup disease_response 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 ... 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 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 10.635 0.615 11.316 getManifest 8.235 0.167 158.038 TCGAanalyze_LevelTab 6.351 0.159 6.547 GDCquery 1.796 0.056 19.406 getDataCategorySummary 1.408 0.026 6.047 GDCprepare_clinic 1.285 0.123 52.445 getResults 1.226 0.043 20.276 matchedMetExp 0.957 0.037 22.538 GDCquery_ATAC_seq 0.327 0.032 7.522 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 WARNINGs, 1 NOTE See ‘/Users/biocbuild/bbs-3.21-bioc/meat/TCGAbiolinks.Rcheck/00check.log’ for details.