############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:psygenet2r.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings psygenet2r_1.37.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/psygenet2r.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-apple-darwin20 * 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 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘psygenet2r/DESCRIPTION’ ... OK * this is package ‘psygenet2r’ version ‘1.37.1’ * checking package namespace information ... NOTE Found export directives that require package ‘methods’: ‘exportClasses’ ‘exportMethods’ Remove all such namespace directives (if obsolete) or ensure that the DESCRIPTION Depends or Imports field contains ‘methods’. * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 ‘psygenet2r’ 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 whether startup messages can be suppressed ... OK * checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘GO.db’ All declared Imports should be used. package 'methods' is used but not declared * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .category_plot: no visible binding for global variable ‘category’ .category_plot: no visible binding for global variable ‘value’ .category_plot: no visible binding for global variable ‘variable’ .gene_plot: no visible binding for global variable ‘gene’ .gene_plot: no visible binding for global variable ‘value’ .gene_plot: no visible binding for global variable ‘variable’ .index_plot: no visible binding for global variable ‘Category’ .index_plot: no visible binding for global variable ‘value’ .index_plot: no visible binding for global variable ‘variable’ .pie_plot: no visible global function definition for ‘pie’ ListPsyGeNETIds: no visible global function definition for ‘read.csv’ disGenetCurated: no visible global function definition for ‘read.csv’ enrichedPD : : no visible global function definition for ‘phyper’ getUMLs: no visible global function definition for ‘read.csv’ jaccardEstimation: no visible binding for global variable ‘universe’ multipleInput: no visible global function definition for ‘new’ pantherGraphic: no visible binding for global variable ‘Var1’ pantherGraphic: no visible binding for global variable ‘perc’ pantherGraphic: no visible binding for global variable ‘diseases’ plot_pmids_barplot: no visible binding for global variable ‘c2.DiseaseName’ plot_pmids_barplot: no visible binding for global variable ‘c0.Number_of_Abstracts’ plot_pmids_barplot: no visible binding for global variable ‘c1.Gene_Symbol’ plot_psy_heatmap: no visible binding for global variable ‘c2.PsychiatricDisorder’ plot_psy_heatmap: no visible binding for global variable ‘c1.Gene_Symbol’ plot_psy_heatmap: no visible binding for global variable ‘value’ plot_psy_heatmapDisease: no visible binding for global variable ‘c2.DiseaseName’ plot_psy_heatmapDisease: no visible binding for global variable ‘c1.Gene_Symbol’ plot_psy_heatmapDisease: no visible binding for global variable ‘c0.Score’ plot_psy_heatmapGenes: no visible binding for global variable ‘c1.Gene_Symbol’ plot_psy_heatmapGenes: no visible binding for global variable ‘c2.DiseaseName’ plot_psy_heatmapGenes: no visible binding for global variable ‘c0.Score’ psyGenDisId: no visible global function definition for ‘read.csv’ psyPanther: no visible global function definition for ‘read.csv’ psygenetAll: no visible global function definition for ‘read.csv’ psygenetDisease: no visible global function definition for ‘read.csv’ psygenetDisease: no visible global function definition for ‘new’ psygenetDiseaseSentences: no visible global function definition for ‘read.csv’ psygenetDiseaseSentences: no visible global function definition for ‘new’ psygenetGene: no visible global function definition for ‘read.csv’ psygenetGene: no visible global function definition for ‘new’ psygenetGeneSentences: no visible global function definition for ‘read.csv’ psygenetGeneSentences: no visible global function definition for ‘new’ singleInput: no visible global function definition for ‘combn’ singleInput: no visible global function definition for ‘new’ singleInput.genes: no visible global function definition for ‘new’ topAnatEnrichment: no visible binding for global variable ‘database’ topAnatEnrichment: no visible global function definition for ‘read.delim’ plot,JaccardIndexPsy-ANY: no visible binding for global variable ‘Disease1’ plot,JaccardIndexPsy-ANY: no visible binding for global variable ‘Disease2’ plot,JaccardIndexPsy-ANY: no visible binding for global variable ‘JaccardIndex’ plot,JaccardIndexPsy-ANY: no visible binding for global variable ‘value’ plot,JaccardIndexPsy-ANY: no visible binding for global variable ‘variable’ Undefined global functions or variables: Category Disease1 Disease2 JaccardIndex Var1 c0.Number_of_Abstracts c0.Score c1.Gene_Symbol c2.DiseaseName c2.PsychiatricDisorder category combn database diseases gene new perc phyper pie read.csv read.delim universe value variable Consider adding importFrom("graphics", "pie") importFrom("methods", "new") importFrom("stats", "phyper") importFrom("utils", "combn", "read.csv", "read.delim") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * 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 LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed pantherGraphic-methods 0.201 0.009 5.328 psygenetGeneSentences 0.175 0.021 28.777 enrichedPD-methods 0.051 0.007 6.661 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 4 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/psygenet2r.Rcheck/00check.log’ for details.