############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:cnvGSA.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings cnvGSA_1.48.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/cnvGSA.Rcheck’ * using R version 4.4.0 beta (2024-04-15 r86425) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘cnvGSA/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘cnvGSA’ version ‘1.48.0’ * 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 loading without being on the library search path ... 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 aggregate anova as.formula barplot binomial BP1 BP2 CHR CnvKey Condition cSplit detectCores dev.off end FID foreach geneID geneID_type geneID_TYPE glm GRanges gs_all.ls GsID gsid2name.chv GsKey GsName i IID IRanges logit mcols OlpKL_CNV OlpKL_SID p.adjust par pdf ranges read.table registerDoParallel Rle SID stack start strand SubjCnvKey Symbol Symbol_TYPE TYPE write.table Consider adding importFrom("graphics", "barplot", "par") importFrom("grDevices", "dev.off", "pdf") 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 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/home/biocbuild/bbs-3.19-bioc/meat/cnvGSA.Rcheck/00check.log’ for details.