############################################################################## ############################################################################## ### ### 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_2.24.3.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/TCGAbiolinks.Rcheck’ * using R version 4.2.1 (2022-06-23) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘TCGAbiolinks/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘TCGAbiolinks’ version ‘2.24.3’ * 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 ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘TCGAbiolinks’ can be installed ... OK * checking installed package size ... NOTE installed size is 6.4Mb sub-directories of 1Mb or more: R 1.6Mb data 4.5Mb * 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 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 ... WARNING 'library' or 'require' call not declared from: ‘dplyr’ 'library' or 'require' calls in package code: ‘dplyr’ ‘maftools’ Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE GDCquery : : no visible binding for global variable ‘submitter_id’ GDCquery : : no visible binding for global variable ‘is_ffpe’ 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’ colDataPrepare: no visible binding for global variable ‘sample_type’ readExonQuantification: no visible binding for global variable ‘exon’ readExonQuantification: no visible binding for global variable ‘coordinates’ readGeneExpressionQuantification : : no visible binding for '<<-' assignment to ‘assay.list’ readGeneExpressionQuantification: no visible binding for global variable ‘assay.list’ readSingleCellAnalysis : : no visible global function definition for ‘Read10X’ Undefined global functions or variables: Read10X Tumor.purity assay.list barcode clinical coordinates exon geFDR2 gene_name is_ffpe logFC meFDR2 rse_gene sample_submitter_id sample_type starburst.status submitter_id threshold.starburst value * 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 GDCquery_clinic 26.420 0.421 43.368 getManifest 17.007 0.222 134.767 TCGAanalyze_DEA 15.335 0.313 15.675 TCGAanalyze_LevelTab 7.581 0.097 7.684 GDCquery_ATAC_seq 6.345 0.318 7.359 TCGAvisualize_meanMethylation 6.104 0.075 6.189 GDCdownload 5.566 0.208 53.977 TCGAanalyze_Filtering 5.527 0.057 5.589 GDCprepare_clinic 4.171 0.157 77.393 getDataCategorySummary 2.715 0.042 5.359 getResults 1.228 0.019 8.809 matchedMetExp 1.133 0.038 8.634 GDCquery 1.094 0.040 9.459 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * 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: 1 WARNING, 2 NOTEs See ‘/Users/biocbuild/bbs-3.15-bioc/meat/TCGAbiolinks.Rcheck/00check.log’ for details.