############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:cnvGSA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings cnvGSA_1.47.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/cnvGSA.Rcheck’ * using R Under development (unstable) (2024-03-18 r86148) * 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 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘cnvGSA/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘cnvGSA’ version ‘1.47.0’ * 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 ‘cnvGSA’ 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 ... NOTE Packages in Depends field not imported from: ‘brglm’ ‘doParallel’ ‘foreach’ ‘splitstackshape’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE cnvGSAgsTables: no visible global function definition for ‘detectCores’ cnvGSAgsTables: no visible binding for global variable ‘SID’ cnvGSAgsTables: no visible binding for global variable ‘geneID_TYPE’ cnvGSAgsTables: no visible binding for global variable ‘SubjCnvKey’ cnvGSAgsTables: no visible global function definition for ‘registerDoParallel’ cnvGSAgsTables: no visible global function definition for ‘%dopar%’ cnvGSAgsTables: no visible global function definition for ‘foreach’ cnvGSAgsTables: no visible binding for global variable ‘i’ cnvGSAgsTables: no visible binding for global variable ‘CHR’ cnvGSAgsTables: no visible binding for global variable ‘BP1’ cnvGSAgsTables: no visible binding for global variable ‘BP2’ cnvGSAgsTables: no visible binding for global variable ‘TYPE’ cnvGSAgsTables: no visible binding for global variable ‘geneID’ cnvGSAgsTables: no visible binding for global variable ‘Symbol’ cnvGSAgsTables: no visible binding for global variable ‘Symbol_TYPE’ cnvGSAgsTables: no visible binding for global variable ‘GsKey’ cnvGSAlogRegTest: no visible binding for global variable ‘GsID’ cnvGSAlogRegTest: no visible binding for global variable ‘GsKey’ cnvGSAlogRegTest: no visible binding for global variable ‘OlpKL_SID’ cnvGSAlogRegTest : f.testGLM_wrap: no visible binding for global variable ‘Condition’ cnvGSAlogRegTest : f.testGLM_wrap: no visible global function definition for ‘detectCores’ cnvGSAlogRegTest : f.testGLM_wrap: no visible global function definition for ‘registerDoParallel’ cnvGSAlogRegTest : f.testGLM_wrap: no visible global function definition for ‘%dopar%’ cnvGSAlogRegTest : f.testGLM_wrap: no visible global function definition for ‘foreach’ cnvGSAlogRegTest : f.testGLM_wrap: no visible binding for global variable ‘i’ cnvGSAlogRegTest : f.testGLM_unit: no visible global function definition for ‘glm’ cnvGSAlogRegTest : f.testGLM_unit: no visible global function definition for ‘as.formula’ cnvGSAlogRegTest : f.testGLM_unit: no visible global function definition for ‘binomial’ cnvGSAlogRegTest : f.testGLM_unit: no visible binding for global variable ‘logit’ cnvGSAlogRegTest : f.testGLM_unit: no visible global function definition for ‘anova’ cnvGSAlogRegTest: no visible global function definition for ‘p.adjust’ cnvGSAlogRegTest: no visible global function definition for ‘write.table’ f.enrProcess: no visible global function definition for ‘write.table’ f.makeViz: no visible global function definition for ‘write.table’ f.makeViz: no visible global function definition for ‘pdf’ f.makeViz: no visible global function definition for ‘par’ f.makeViz: no visible global function definition for ‘barplot’ f.makeViz: no visible global function definition for ‘dev.off’ f.readConfig: no visible global function definition for ‘read.table’ f.readData: no visible global function definition for ‘read.table’ f.readData: no visible binding for global variable ‘IID’ f.readData: no visible binding for global variable ‘FID’ f.readData: no visible binding for global variable ‘AFF’ f.readData: no visible binding for global variable ‘SID’ f.readData: no visible binding for global variable ‘gs_all.ls’ f.readData: no visible binding for global variable ‘gsid2name.chv’ f.readData: no visible global function definition for ‘GRanges’ f.readData: no visible global function definition for ‘Rle’ f.readData: no visible global function definition for ‘IRanges’ f.readData: no visible global function definition for ‘strand’ f.readData: no visible global function definition for ‘start’ f.readData: no visible global function definition for ‘ranges’ f.readData: no visible global function definition for ‘end’ f.readData: no visible global function definition for ‘mcols’ f.readData: no visible binding for global variable ‘OlpKL_CNV’ f.readData: no visible global function definition for ‘stack’ f.readData: no visible binding for global variable ‘geneID_type’ f.readData: no visible binding for global variable ‘CnvKey’ f.readData: no visible binding for global variable ‘OlpKL_SID’ f.readData: no visible binding for global variable ‘geneID_TYPE’ f.readData: no visible binding for global variable ‘SubjCnvKey’ f.readData: no visible binding for global variable ‘GsKey’ f.readData: no visible binding for global variable ‘GsID’ f.readData: no visible binding for global variable ‘GsName’ f.readData: no visible global function definition for ‘cSplit’ f.readData: no visible binding for global variable ‘Symbol’ f.readData: no visible global function definition for ‘aggregate’ Undefined global functions or variables: %dopar% AFF BP1 BP2 CHR CnvKey Condition FID GRanges GsID GsKey GsName IID IRanges OlpKL_CNV OlpKL_SID Rle SID SubjCnvKey Symbol Symbol_TYPE TYPE aggregate anova as.formula barplot binomial cSplit detectCores dev.off end foreach geneID geneID_TYPE geneID_type glm gs_all.ls gsid2name.chv i logit mcols p.adjust par pdf ranges read.table registerDoParallel stack start strand write.table Consider adding importFrom("grDevices", "dev.off", "pdf") importFrom("graphics", "barplot", "par") importFrom("stats", "aggregate", "anova", "as.formula", "binomial", "end", "glm", "p.adjust", "start") importFrom("utils", "read.table", "stack", "write.table") 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 sizes of PDF files under ‘inst/doc’ ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... 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: 2 NOTEs See ‘/Users/biocbuild/bbs-3.19-bioc/meat/cnvGSA.Rcheck/00check.log’ for details.