############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:fobitools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings fobitools_1.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/fobitools.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 ‘fobitools/DESCRIPTION’ ... OK * this is package ‘fobitools’ version ‘1.12.0’ * 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 ‘fobitools’ 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 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 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 annotate_foods: no visible binding for global variable ‘FOOD_NAME’ annotate_foods: no visible binding for global variable ‘FOOD_ID’ annotate_foods: no visible binding for global variable ‘words’ annotate_foods: no visible binding for global variable ‘words_joint’ annotate_foods: no visible binding for global variable ‘id_code’ annotate_foods: no visible binding for global variable ‘name’ annotate_foods: no visible binding for global variable ‘ref’ annotate_foods: no visible binding for global variable ‘detect’ annotate_foods: no visible binding for global variable ‘.’ annotate_foods: no visible binding for global variable ‘match_score’ fobi_graph: no visible binding for global variable ‘is_a_code’ fobi_graph: no visible binding for global variable ‘id_code’ fobi_graph: no visible binding for global variable ‘Contains’ fobi_graph: no visible binding for global variable ‘Property’ fobi_graph: no visible binding for global variable ‘name’ fobi_graph: no visible binding for global variable ‘BiomarkerOf’ fobi_graph: no visible binding for global variable ‘is_a_name’ fobi_graph: no visible binding for global variable ‘subOntology’ id_convert: no visible binding for global variable ‘BiomarkerOf’ id_convert: no visible binding for global variable ‘name’ id_convert: no visible binding for global variable ‘FOBI’ id_convert: no visible binding for global variable ‘HMDB’ id_convert: no visible binding for global variable ‘KEGG’ id_convert: no visible binding for global variable ‘PubChemCID’ id_convert: no visible binding for global variable ‘InChIKey’ id_convert: no visible binding for global variable ‘InChICode’ id_convert: no visible binding for global variable ‘ChemSpider’ id_convert: no visible binding for global variable ‘metaboliteNames’ id_convert: no visible binding for global variable ‘presence’ id_convert: no visible binding for global variable ‘.’ msea: no visible binding for global variable ‘BiomarkerOf’ msea: no visible binding for global variable ‘id_BiomarkerOf’ msea: no visible binding for global variable ‘name’ msea: no visible binding for global variable ‘FOBI’ msea: no visible binding for global variable ‘is_a_code’ msea: no visible binding for global variable ‘is_a_name’ msea: no visible binding for global variable ‘.’ msea: no visible global function definition for ‘unstack’ msea: no visible binding for global variable ‘pathway’ msea: no visible binding for global variable ‘size’ msea: no visible binding for global variable ‘className’ msea: no visible binding for global variable ‘classSize’ msea: no visible binding for global variable ‘log2err’ msea: no visible binding for global variable ‘ES’ msea: no visible binding for global variable ‘NES’ msea: no visible binding for global variable ‘pval’ msea: no visible binding for global variable ‘padj’ msea: no visible binding for global variable ‘leadingEdge’ ora: no visible binding for global variable ‘BiomarkerOf’ ora: no visible binding for global variable ‘id_BiomarkerOf’ ora: no visible binding for global variable ‘name’ ora: no visible binding for global variable ‘FOBI’ ora: no visible binding for global variable ‘is_a_code’ ora: no visible binding for global variable ‘is_a_name’ ora: no visible binding for global variable ‘.’ ora: no visible global function definition for ‘unstack’ ora: no visible binding for global variable ‘pathway’ ora: no visible binding for global variable ‘size’ ora: no visible binding for global variable ‘overlapGenes’ ora: no visible binding for global variable ‘className’ ora: no visible binding for global variable ‘classSize’ ora: no visible binding for global variable ‘overlap’ ora: no visible binding for global variable ‘pval’ ora: no visible binding for global variable ‘padj’ ora: no visible binding for global variable ‘overlapMetabolites’ parse_fobi: no visible binding for global variable ‘V2’ parse_fobi: no visible binding for global variable ‘V1’ parse_fobi: no visible binding for global variable ‘gf’ parse_fobi: no visible binding for global variable ‘name’ parse_fobi: no visible binding for global variable ‘id_code’ parse_fobi: no visible binding for global variable ‘Contains’ parse_fobi: no visible binding for global variable ‘disjoint_from’ parse_fobi: no visible binding for global variable ‘FOBI:050339’ parse_fobi: no visible binding for global variable ‘ChemSpider’ parse_fobi: no visible binding for global variable ‘KEGG’ parse_fobi: no visible binding for global variable ‘is_a_code’ parse_fobi: no visible binding for global variable ‘id_BiomarkerOf’ parse_fobi: no visible binding for global variable ‘id_Contains’ Undefined global functions or variables: . BiomarkerOf ChemSpider Contains ES FOBI FOBI:050339 FOOD_ID FOOD_NAME HMDB InChICode InChIKey KEGG NES Property PubChemCID V1 V2 className classSize detect disjoint_from gf id_BiomarkerOf id_Contains id_code is_a_code is_a_name leadingEdge log2err match_score metaboliteNames name overlap overlapGenes overlapMetabolites padj pathway presence pval ref size subOntology unstack words words_joint Consider adding importFrom("methods", "className") importFrom("utils", "unstack") 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 ... NOTE Note: found 199 marked UTF-8 strings * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... NOTE The following directory looks like a leftover from 'knitr': ‘figure’ Please remove from your package. * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed parse_fobi 55.631 2.114 70.423 * 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: 3 NOTEs See ‘/Users/biocbuild/bbs-3.19-bioc/meat/fobitools.Rcheck/00check.log’ for details.