############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:ELMER.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings ELMER_2.23.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/ELMER.Rcheck’ * using R Under development (unstable) (2023-02-14 r83833) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0 GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0 * running under: Ubuntu 20.04.6 LTS * using session charset: UTF-8 * checking for file ‘ELMER/DESCRIPTION’ ... OK * this is package ‘ELMER’ version ‘2.23.0’ * 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 ‘ELMER’ can be installed ... OK * checking installed package size ... OK * 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 loading without being on the library search path ... OK * checking dependencies in R code ... WARNING Missing or unexported object: 'TCGAbiolinks::GDCquery_Maf' * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE TCGA.pipe: warning in render_report(genome = genome, mode = mode, title = paste0(disease, " report"), minSubgroupFrac = ifelse(mode == "supervised", 1, 0.2), mae = mae.path, direction = direction, group.col = group.col, group1 = group1, group2 = group2, dir.out = results.path, out_file = file.path(results.path, paste0(disease, "_report.html"))): partial argument match of 'mae' to 'mae.file' Stat.nonpara: no visible global function definition for 'head' Stat.nonpara: no visible global function definition for 'tail' Stat.nonpara.permu: no visible global function definition for 'head' Stat.nonpara.permu: no visible global function definition for 'tail' TFsurvival.plot: no visible global function definition for 'head' TFsurvival.plot: no visible global function definition for 'tail' addMutCol: no visible binding for global variable 'Hugo_Symbol' calcDistNearestTSS: no visible binding for global variable 'DistanceTSS' get.top.tf.by.pval: no visible global function definition for 'head' getRegionNearGenes : f: no visible binding for global variable 'Side' getRegionNearGenes: no visible binding for global variable 'ID' getTFtargets: no visible binding for global variable 'TF' Undefined global functions or variables: DistanceTSS Hugo_Symbol ID Side TF head tail Consider adding importFrom("utils", "head", "tail") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... WARNING Codoc mismatches from documentation object 'render_report': render_report Code: function(title = "Report", mae.file, group.col, group1, group2, direction, dir.out, genome = "hg38", mode = "supervised", minSubgroupFrac = 0.2, minMetdiff = 0.3, metfdr = 0.01, permu = 10000, rawpval = 0.01, pe = 0.01, nprobes = 10, lower.OR = 1.1, out_file = file.path(getwd(), "report.html"), funcivar = FALSE) Docs: function(title = "Report", mae.file, group.col, group1, group2, direction, dir.out, genome = "hg38", mode = "supervised", minSubgroupFrac = "20%", minMetdiff = "0.3", metfdr = "0.01", permu = "10000", rawpval = "0.01", pe = "0.01", nprobes = "10", lower.OR = "1.1", out_file = file.path(getwd(), "report.html"), funcivar = FALSE) Mismatches in argument default values: Name: 'minSubgroupFrac' Code: 0.2 Docs: "20%" * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed TCGA.pipe 77.982 3.351 83.257 getRandomPairs 27.404 1.648 29.620 createMAE 21.782 1.965 24.867 schematic.plot 19.706 0.987 24.961 get.enriched.motif 17.862 1.218 22.265 scatter.plot 12.718 0.356 13.075 get.feature.probe 11.010 0.944 12.270 get.pair 10.433 0.504 10.933 GetNearGenes 8.996 0.300 9.296 getRegionNearGenes 8.618 0.348 8.967 preAssociationProbeFiltering 6.947 0.513 7.772 getTCGA 1.916 0.181 8.113 * 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_data_input.Rmd’ using ‘UTF-8’... OK ‘analysis_diff_meth.Rmd’ using ‘UTF-8’... OK ‘analysis_get_pair.Rmd’ using ‘UTF-8’... OK ‘analysis_gui.Rmd’ using ‘UTF-8’... OK ‘analysis_motif_enrichment.Rmd’ using ‘UTF-8’... OK ‘analysis_regulatory_tf.Rmd’ using ‘UTF-8’... OK ‘index.Rmd’ using ‘UTF-8’... OK ‘input.Rmd’ using ‘UTF-8’... OK ‘pipe.Rmd’ using ‘UTF-8’... OK ‘plots_TF.Rmd’ using ‘UTF-8’... OK ‘plots_heatmap.Rmd’ using ‘UTF-8’... OK ‘plots_motif_enrichment.Rmd’ using ‘UTF-8’... OK ‘plots_scatter.Rmd’ using ‘UTF-8’... OK ‘plots_schematic.Rmd’ using ‘UTF-8’... OK ‘usecase.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 WARNINGs, 1 NOTE See ‘/home/biocbuild/bbs-3.17-bioc/meat/ELMER.Rcheck/00check.log’ for details.