############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:sparrow.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings sparrow_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/sparrow.Rcheck’ * using R version 4.5.0 RC (2025-04-04 r88126) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘sparrow/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘sparrow’ version ‘1.14.0’ * 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 ‘sparrow’ 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .map_ids_orthogene: no visible binding for global variable ‘gspecies’ .map_ids_orthogene: no visible binding for global variable ‘species’ .map_ids_orthogene: no visible binding for global variable ‘input_ensg’ .map_ids_orthogene: no visible binding for global variable ‘ortholog_ensg’ .map_ids_orthogene: no visible binding for global variable ‘ortholog_gene’ .map_ids_orthogene: no visible binding for global variable ‘symbol’ .map_ids_orthogene: no visible binding for global variable ‘input_id’ .map_ids_orthogene: no visible global function definition for ‘starts_with’ .map_ids_orthogene: no visible global function definition for ‘last_col’ .map_ids_orthogene: no visible binding for global variable ‘rm_na’ geneSetsStats: no visible binding for global variable ‘direction’ getMSigGeneSetDb: no visible binding for global variable ‘ncbi_gene’ getMSigGeneSetDb: no visible binding for global variable ‘db_species’ getMSigGeneSetDb: no visible binding for global variable ‘msigdb_collection’ getMSigGeneSetDb: no visible binding for global variable ‘gene_symbol’ getMSigGeneSetDb: no visible binding for global variable ‘gs_collection_name’ getMSigGeneSetDb: no visible binding for global variable ‘gs_url’ convertIdentifiers,GeneSetDb: no visible binding for global variable ‘.convert_ids_with_babelgene’ convertIdentifiers,GeneSetDb: no visible global function definition for ‘.map_ids_babelgene’ Undefined global functions or variables: .convert_ids_with_babelgene .map_ids_babelgene db_species direction gene_symbol gs_collection_name gs_url gspecies input_ensg input_id last_col msigdb_collection ncbi_gene ortholog_ensg ortholog_gene rm_na species starts_with symbol * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Non-topic package-anchored link(s) in Rd file 'GeneSetDb-class.Rd': ‘[GSEABase:GeneIdentifierType-constructors]{GSEABase::EntrezIdentifier()}’ Non-topic package-anchored link(s) in Rd file 'calculateIndividualLogFC.Rd': ‘[limma:ebayes]{limma::eBayes()}’ Non-topic package-anchored link(s) in Rd file 'collectionMetadata.Rd': ‘[GSEABase:GeneIdentifierType-constructors]{GSEABase::EntrezIdentifier()}’ Non-topic package-anchored link(s) in Rd file 'seas.Rd': ‘[limma:toptable]{limma::topTable()}’ ‘[limma:dupcor]{limma::duplicateCorrelation()}’ See section 'Cross-references' in the 'Writing R Extensions' manual. Found the following Rd file(s) with Rd \link{} targets missing package anchors: seas.Rd: BiocParallel Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 line endings in Makefiles ... OK * checking for GNU extensions in Makefiles ... OK * checking include directives in Makefiles ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed goseq 6.320 0.459 6.818 scoreSingleSamples 6.295 0.302 6.635 * 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-3.21-bioc/meat/sparrow.Rcheck/00check.log’ for details.