############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:CoSIAdata.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings CoSIAdata_1.9.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-data-experiment/meat/CoSIAdata.Rcheck’ * using R version 4.5.1 (2025-06-13) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.3 LTS * using session charset: UTF-8 * checking for file ‘CoSIAdata/DESCRIPTION’ ... OK * this is package ‘CoSIAdata’ version ‘1.9.0’ * 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 ‘CoSIAdata’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF. * 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * 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 ... ERROR Running examples in ‘CoSIAdata-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: CoSIAdata > ### Title: CoSIAdata: VST normalized RNA-Sequencing data with annotations > ### for multiple species samples from Bgee > ### Aliases: CoSIAdata _PACKAGE > ### Keywords: internal > > ### ** Examples > > library(ExperimentHub) > eh <- ExperimentHub() > query(eh, "CoSIAdata") ExperimentHub with 6 records # snapshotDate(): 2025-07-17 # $dataprovider: Bgee # $species: Rattus norvegicus, Mus musculus, Homo sapiens, Drosophila melano... # $rdataclass: data.frame # additional mcols(): taxonomyid, genome, description, # coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags, # rdatapath, sourceurl, sourcetype # retrieve records with, e.g., 'object[["EH7858"]]' title EH7858 | VST normalized RNA-Sequencing data with annotations for 362,533,... EH7859 | VST normalized RNA-Sequencing data with annotations for 31,405,6... EH7860 | VST normalized RNA-Sequencing data with annotations for 3,814,42... EH7861 | VST normalized RNA-Sequencing data with annotations for 5,235,72... EH7862 | VST normalized RNA-Sequencing data with annotations for 4,576,39... EH7863 | VST normalized RNA-Sequencing data with annotations for 1,923,06... > eh[["EH7863"]] see ?CoSIAdata and browseVignettes('CoSIAdata') for documentation loading from cache Warning: namespace ‘ggplot2’ is not available and has been replaced by .GlobalEnv when processing object ‘celegans_data’ Error loading resource. attempting to re-download downloading 1 resources retrieving 1 resource loading from cache Warning: namespace ‘ggplot2’ is not available and has been replaced by .GlobalEnv when processing object ‘celegans_data’ Error: failed to load resource name: EH7863 title: VST normalized RNA-Sequencing data with annotations for 1,923,064 Caenorhabditis elegans samples from Bgee reason: C stack usage 7969316 is too close to the limit Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 1 NOTE See ‘/home/biocbuild/bbs-3.22-data-experiment/meat/CoSIAdata.Rcheck/00check.log’ for details.