############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:ELMER.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings ELMER_2.26.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/ELMER.Rcheck’ * using R version 4.3.3 (2024-02-29) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘ELMER/DESCRIPTION’ ... OK * this is package ‘ELMER’ version ‘2.26.0’ * 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE addMutCol: no visible binding for global variable 'Hugo_Symbol' calcDistNearestTSS: no visible binding for global variable 'DistanceTSS' 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 * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed TCGA.pipe 74.253 2.671 78.537 createMAE 23.328 2.112 26.411 getRandomPairs 22.521 1.788 24.790 schematic.plot 21.002 1.959 32.987 get.enriched.motif 18.325 1.020 21.596 scatter.plot 11.933 0.388 12.321 get.feature.probe 10.005 0.975 11.317 preAssociationProbeFiltering 8.539 0.861 9.749 get.pair 8.134 0.564 8.696 GetNearGenes 8.252 0.308 8.561 getRegionNearGenes 6.051 0.236 6.287 getTCGA 2.208 0.297 7.029 * 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’... failed ‘analysis_get_pair.Rmd’ using ‘UTF-8’... failed ‘analysis_gui.Rmd’ using ‘UTF-8’... OK ‘analysis_motif_enrichment.Rmd’ using ‘UTF-8’... failed ‘analysis_regulatory_tf.Rmd’ using ‘UTF-8’... failed ‘index.Rmd’ using ‘UTF-8’... OK ‘input.Rmd’ using ‘UTF-8’... OK ‘pipe.Rmd’ using ‘UTF-8’... OK ‘plots_TF.Rmd’ using ‘UTF-8’... failed ‘plots_heatmap.Rmd’ using ‘UTF-8’... failed ‘plots_motif_enrichment.Rmd’ using ‘UTF-8’... failed ‘plots_scatter.Rmd’ using ‘UTF-8’... failed ‘plots_schematic.Rmd’ using ‘UTF-8’... failed ‘usecase.Rmd’ using ‘UTF-8’... OK ERROR Errors in running code in vignettes: when running code in ‘analysis_diff_meth.Rmd’ ... > library(BiocStyle) > mae <- get(load("mae.rda")) Warning in readChar(con, 5L, useBytes = TRUE) : cannot open compressed file 'mae.rda', probable reason 'No such file or directory' When sourcing 'analysis_diff_meth.R': Error: cannot open the connection Execution halted when running code in ‘analysis_get_pair.Rmd’ ... > library(BiocStyle) > mae <- get(load("mae.rda")) Warning in readChar(con, 5L, useBytes = TRUE) : cannot open compressed file 'mae.rda', probable reason 'No such file or directory' When sourcing 'analysis_get_pair.R': Error: cannot open the connection Execution halted when running code in ‘analysis_motif_enrichment.Rmd’ ... > library(BiocStyle) > mae <- get(load("mae.rda")) Warning in readChar(con, 5L, useBytes = TRUE) : cannot open compressed file 'mae.rda', probable reason 'No such file or directory' When sourcing 'analysis_motif_enrichment.R': Error: cannot open the connection Execution halted when running code in ‘analysis_regulatory_tf.Rmd’ ... > library(BiocStyle) > mae <- get(load("mae.rda")) Warning in readChar(con, 5L, useBytes = TRUE) : cannot open compressed file 'mae.rda', probable reason 'No such file or directory' When sourcing 'analysis_regulatory_tf.R': Error: cannot open the connection Execution halted when running code in ‘plots_TF.Rmd’ ... > library(BiocStyle) > load("result/getTF.hypo.TFs.with.motif.pvalue.rda") Warning in readChar(con, 5L, useBytes = TRUE) : cannot open compressed file 'result/getTF.hypo.TFs.with.motif.pvalue.rda', probable reason 'No such file or directory' When sourcing 'plots_TF.R': Error: cannot open the connection Execution halted when running code in ‘plots_heatmap.Rmd’ ... > library(BiocStyle) > mae <- get(load("mae.rda")) Warning in readChar(con, 5L, useBytes = TRUE) : cannot open compressed file 'mae.rda', probable reason 'No such file or directory' When sourcing 'plots_heatmap.R': Error: cannot open the connection Execution halted when running code in ‘plots_motif_enrichment.Rmd’ ... > library(BiocStyle) > motif.enrichment.plot(motif.enrichment = "result/getMotif.hypo.motif.enrichment.csv", + significant = list(OR = 1.5, lowerOR = 1.3), label = "h ..." ... [TRUNCATED] Warning in file(file, "rt") : cannot open file 'result/getMotif.hypo.motif.enrichment.csv': No such file or directory When sourcing 'plots_motif_enrichment.R': Error: cannot open the connection Execution halted when running code in ‘plots_scatter.Rmd’ ... > library(BiocStyle) > mae <- get(load("mae.rda")) Warning in readChar(con, 5L, useBytes = TRUE) : cannot open compressed file 'mae.rda', probable reason 'No such file or directory' When sourcing 'plots_scatter.R': Error: cannot open the connection Execution halted when running code in ‘plots_schematic.Rmd’ ... > library(BiocStyle) > mae <- get(load("mae.rda")) Warning in readChar(con, 5L, useBytes = TRUE) : cannot open compressed file 'mae.rda', probable reason 'No such file or directory' When sourcing 'plots_schematic.R': Error: cannot open the connection Execution halted * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 1 NOTE See ‘/home/biocbuild/bbs-3.18-bioc/meat/ELMER.Rcheck/00check.log’ for details.