############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ViSEAGO.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ViSEAGO_1.16.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/ViSEAGO.Rcheck’ * using R version 4.3.3 (2024-02-29) * using platform: x86_64-apple-darwin20 (64-bit) * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ViSEAGO/DESCRIPTION’ ... OK * this is package ‘ViSEAGO’ version ‘1.16.0’ * 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 ‘/Users/biocbuild/bbs-3.18-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 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 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 ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed taxonomy 0.035 0.007 6.188 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 4 WARNINGs, 2 NOTEs See ‘/Users/biocbuild/bbs-3.18-bioc/meat/ViSEAGO.Rcheck/00check.log’ for details.