############################################################################## ############################################################################## ### ### 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_2.35.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/TCGAbiolinks.Rcheck’ * using R Under development (unstable) (2024-11-14 r87333) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * 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 ‘2.35.0’ * 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 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’ 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 ... 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 ... ERROR Running examples in ‘TCGAbiolinks-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: GDCquery_ATAC_seq > ### Title: Retrieve open access ATAC-seq files from GDC server > ### Aliases: GDCquery_ATAC_seq > > ### ** Examples > > query <- GDCquery_ATAC_seq(file.type = "txt") Warning: Failed to open 'https://gdc.cancer.gov/files/public/file/ATACseq-AWG_Open_GDC-Manifest.txt': The requested URL returned error: 404 Error in open.connection(3L, "rb") : cannot open the connection Calls: GDCquery_ATAC_seq ... -> vroom_ -> -> open.connection Execution halted Examples with CPU (user + system) or elapsed time > 5s user system elapsed GDCprepare_clinic 1.671 0.125 31.218 GDCquery 0.642 0.051 7.487 * 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 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 Quitting from lines 313-320 [unnamed-chunk-9] (query.Rmd) Error: processing vignette 'query.Rmd' failed with diagnostics: cannot open the connection --- failed re-building ‘query.Rmd’ --- re-building ‘stemness_score.Rmd’ using rmarkdown --- finished re-building ‘stemness_score.Rmd’ --- re-building ‘subtypes.Rmd’ using rmarkdown --- finished re-building ‘subtypes.Rmd’ SUMMARY: processing the following file failed: ‘query.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 2 ERRORs, 2 WARNINGs, 1 NOTE See ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/TCGAbiolinks.Rcheck/00check.log’ for details.