############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:ViSEAGO.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings ViSEAGO_1.20.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/ViSEAGO.Rcheck’ * using R version 4.4.2 (2024-10-31) * 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 ‘ViSEAGO/DESCRIPTION’ ... OK * this is package ‘ViSEAGO’ version ‘1.20.0’ * 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 ‘ViSEAGO’ can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import ‘data.table::set’ by ‘dendextend::set’ when loading ‘ViSEAGO’ See ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/ViSEAGO.Rcheck/00install.out’ for details. * checking installed package size ... NOTE installed size is 12.3Mb sub-directories of 1Mb or more: extdata 10.6Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... WARNING Non-standard license specification: GPL-3 bioconductor.org Standardizable: FALSE * 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 dependencies in R code ... WARNING 'library' or 'require' call not declared from: ‘topGO’ 'library' or 'require' call to ‘topGO’ in package code. Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Namespace in Imports field not imported from: ‘processx’ All declared Imports should be used. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE annotate,character-genomic_ressource: warning in getBM(attributes = c("ensembl_gene_id", "go_id", "go_linkage_type", "namespace_1003"), filters = unlist(go_filter[grep("with GO ID", ignore.case = TRUE, go_filter$description), "name", with = FALSE]), value = TRUE, mart = myspecies): partial argument match of 'value' to 'values' compute_SS_distances,ANY-character: warning in select(GO.db, keys = onto$values, column = "TERM"): partial argument match of 'column' to 'columns' merge_enrich_terms,list : genes_symbols_add: warning in getBM(attributes = c("ensembl_gene_id", "external_gene_name"), value = TRUE, mart = myspecies): partial argument match of 'value' to 'values' GOterms_heatmap,GO_SS: no visible binding for global variable ‘GO.ID’ MDSplot,ANY: no visible binding for global variable ‘text’ MDSplot,ANY: no visible binding for global variable ‘GO.cluster’ Upset,ANY: no visible global function definition for ‘png’ Upset,ANY: no visible global function definition for ‘dev.off’ annotate,character-genomic_ressource: no visible global function definition for ‘.’ annotate,character-genomic_ressource: no visible binding for global variable ‘ENTREZID’ annotate,character-genomic_ressource: no visible binding for global variable ‘GO’ annotate,character-genomic_ressource: no visible binding for global variable ‘EVIDENCE’ annotate,character-genomic_ressource: no visible binding for global variable ‘ONTOLOGY’ compute_SS_distances,ANY-character: no visible binding for global variable ‘N’ compute_SS_distances,ANY-character: no visible binding for global variable ‘IC’ merge_enrich_terms,list : genes_symbols_add : esummary : : no visible binding for global variable ‘start’ merge_enrich_terms,list : genes_symbols_add : esummary : : no visible binding for global variable ‘end’ merge_enrich_terms,list : : no visible binding for global variable ‘pval’ merge_enrich_terms,list : : no visible binding for global variable ‘pathway’ merge_enrich_terms,list : : no visible binding for global variable ‘Id’ merge_enrich_terms,list : : no visible global function definition for ‘.’ merge_enrich_terms,list : : no visible binding for global variable ‘padj’ merge_enrich_terms,list : : no visible binding for global variable ‘nMoreExtreme’ merge_enrich_terms,list : : no visible binding for global variable ‘ES’ merge_enrich_terms,list : : no visible binding for global variable ‘NES’ merge_enrich_terms,list : : no visible binding for global variable ‘size’ merge_enrich_terms,list : : no visible binding for global variable ‘genes_frequency’ merge_enrich_terms,list : : no visible binding for global variable ‘log2err’ merge_enrich_terms,list : : no visible binding for global variable ‘leadingEdge’ merge_enrich_terms,list : : no visible binding for global variable ‘Significant_genes’ merge_enrich_terms,list : : no visible binding for global variable ‘GO.ID’ runfgsea,ANY-gene2GO-character: no visible binding for global variable ‘genes_frequency’ runfgsea,ANY-gene2GO-character: no visible binding for global variable ‘leadingEdge’ runfgsea,ANY-gene2GO-character: no visible binding for global variable ‘size’ runfgsea,ANY-gene2GO-character: no visible binding for global variable ‘pathway’ Undefined global functions or variables: . ENTREZID ES EVIDENCE GO GO.ID GO.cluster IC Id N NES ONTOLOGY Significant_genes dev.off end genes_frequency leadingEdge log2err nMoreExtreme padj pathway png pval size start text Consider adding importFrom("grDevices", "dev.off", "png") importFrom("graphics", "text") importFrom("stats", "end", "start") 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 ... 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 data for ASCII and uncompressed saves ... WARNING Note: significantly better compression could be obtained by using R CMD build --resave-data old_size new_size compress myGOs.RData 876Kb 517Kb xz * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘ViSEAGO-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: Custom2GO > ### Title: Store organisms GO annotations from custom database file. > ### Aliases: Custom2GO > > ### ** Examples > > # Download custom GO annotations > Custom<-ViSEAGO::Custom2GO( + system.file( + "extdata/customfile.txt", + package = "ViSEAGO" + ) + ) Error in ViSEAGO::Custom2GO(system.file("extdata/customfile.txt", package = "ViSEAGO")) : GOID must be a valid identifiant. see select(GO.db,columns=columns(GO.db),keys=keys(GO.db) 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, 4 WARNINGs, 2 NOTEs See ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/ViSEAGO.Rcheck/00check.log’ for details.