############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BgeeCall.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BgeeCall_1.22.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/BgeeCall.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: aarch64-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 Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘BgeeCall/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘BgeeCall’ version ‘1.22.0’ * 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 ‘BgeeCall’ can be installed ... OK * checking installed package size ... NOTE installed size is 9.1Mb sub-directories of 1Mb or more: extdata 8.6Mb * 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 ... NOTE Namespace in Imports field not imported from: ‘txdbmaker’ 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 approachesMerging : : no visible global function definition for ‘p.adjust’ generate_calls_workflow: no visible binding for global variable ‘myUserMetadata’ generate_qValue: no visible global function definition for ‘approxfun’ generate_qValue: no visible global function definition for ‘integrate’ generate_qValue : calculate_qValue: no visible global function definition for ‘integrate’ generate_theoretical_pValue: no visible binding for global variable ‘abundance’ generate_theoretical_pValue: no visible binding for global variable ‘type’ generate_theoretical_pValue: no visible global function definition for ‘pnorm’ merging_libraries: no visible binding for global variable ‘read.delim’ should_ignore_tx_version: no visible global function definition for ‘complete.cases’ Undefined global functions or variables: abundance approxfun complete.cases integrate myUserMetadata p.adjust pnorm read.delim type Consider adding importFrom("stats", "approxfun", "complete.cases", "integrate", "p.adjust", "pnorm") importFrom("utils", "read.delim") to your NAMESPACE file. * checking Rd files ... NOTE checkRd: (-1) list_bgee_ref_intergenic_species.Rd:22: Lost braces in \itemize; meant \describe ? checkRd: (-1) list_bgee_ref_intergenic_species.Rd:23: Lost braces in \itemize; meant \describe ? checkRd: (-1) list_bgee_ref_intergenic_species.Rd:24-25: Lost braces in \itemize; meant \describe ? checkRd: (-1) list_bgee_ref_intergenic_species.Rd:26: Lost braces in \itemize; meant \describe ? * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed generate_presence_absence 4.547 0.196 5.592 * 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/BgeeCall.Rcheck/00check.log’ for details.