############################################################################## ############################################################################## ### ### 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_1.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/BgeeCall.Rcheck’ * using R version 4.1.3 (2022-03-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘BgeeCall/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘BgeeCall’ version ‘1.10.0’ * 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 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 ... OK * 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 ... 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed generate_presence_absence 5.687 0.281 11.432 setAnnotationFromFile 3.382 0.728 6.754 merge_transcriptome_and_intergenic 0.459 0.202 7.289 list_bgee_ref_intergenic_species 0.019 0.012 8.116 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * 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: 2 NOTEs See ‘/Users/biocbuild/bbs-3.14-bioc/meat/BgeeCall.Rcheck/00check.log’ for details.