############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:TCGAbiolinks.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings TCGAbiolinks_2.27.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/TCGAbiolinks.Rcheck’ * using R version 4.3.0 alpha (2023-04-03 r84154) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.2 LTS * using session charset: UTF-8 * checking for file ‘TCGAbiolinks/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘TCGAbiolinks’ version ‘2.27.2’ * 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 ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘TCGAbiolinks’ can be installed ... OK * checking installed package size ... NOTE installed size is 6.5Mb 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 ... NOTE Problems with news in ‘NEWS’: Cannot process chunk/lines: Changing chunks.per.download to files.per.chunk * 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 loading without being on the library search path ... OK * checking startup messages can be suppressed ... 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 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’ 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 bcr_patient_barcode clinical coordinates days_to_last_followup exon geFDR2 gene_name is_ffpe logFC meFDR2 rse_gene sample_submitter_id sample_type 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 10.900 1.108 12.008 getManifest 7.792 0.130 77.032 TCGAanalyze_LevelTab 6.578 0.376 6.954 GDCdownload 2.969 0.296 35.804 GDCprepare_clinic 1.621 0.207 25.428 matchedMetExp 1.422 0.172 6.858 getDataCategorySummary 1.311 0.072 5.066 getResults 1.203 0.035 6.254 GDCquery 0.974 0.135 6.433 * 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 ... ‘analysis.Rmd’ using ‘UTF-8’... OK ‘casestudy.Rmd’ using ‘UTF-8’... OK ‘classifiers.Rmd’ using ‘UTF-8’... OK ‘clinical.Rmd’ using ‘UTF-8’... OK ‘download_prepare.Rmd’ using ‘UTF-8’... OK ‘extension.Rmd’ using ‘UTF-8’... OK ‘index.Rmd’ using ‘UTF-8’... OK ‘mutation.Rmd’ using ‘UTF-8’... OK ‘query.Rmd’ using ‘UTF-8’... OK ‘stemness_score.Rmd’ using ‘UTF-8’... OK ‘subtypes.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... ERROR Error(s) in re-building vignettes: --- re-building ‘analysis.Rmd’ using rmarkdown --- finished re-building ‘analysis.Rmd’ --- re-building ‘casestudy.Rmd’ using rmarkdown --- finished re-building ‘casestudy.Rmd’ --- re-building ‘classifiers.Rmd’ using rmarkdown --- finished re-building ‘classifiers.Rmd’ --- re-building ‘clinical.Rmd’ using rmarkdown --- finished re-building ‘clinical.Rmd’ --- re-building ‘download_prepare.Rmd’ using rmarkdown --- finished re-building ‘download_prepare.Rmd’ --- re-building ‘extension.Rmd’ using rmarkdown --- finished re-building ‘extension.Rmd’ --- re-building ‘index.Rmd’ using rmarkdown --- finished re-building ‘index.Rmd’ --- re-building ‘mutation.Rmd’ using rmarkdown --- finished re-building ‘mutation.Rmd’ --- re-building ‘query.Rmd’ using rmarkdown --- finished re-building ‘query.Rmd’ --- re-building ‘stemness_score.Rmd’ using rmarkdown --- finished re-building ‘stemness_score.Rmd’ --- re-building ‘subtypes.Rmd’ using rmarkdown Quitting from lines 114-121 (subtypes.Rmd) Error: processing vignette 'subtypes.Rmd' failed with diagnostics: object 'lgg.gbm.subtype' not found --- failed re-building ‘subtypes.Rmd’ SUMMARY: processing the following file failed: ‘subtypes.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 1 WARNING, 3 NOTEs See ‘/home/biocbuild/bbs-3.17-bioc/meat/TCGAbiolinks.Rcheck/00check.log’ for details.