############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GRENITS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GRENITS_1.48.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/GRENITS.Rcheck’ * using R version 4.2.1 (2022-06-23) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘GRENITS/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘GRENITS’ 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 ‘GRENITS’ 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 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 ... NOTE Packages in Depends field not imported from: ‘Rcpp’ ‘RcppArmadillo’ ‘ggplot2’ 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 .heatMap.ggplot: no visible global function definition for ‘ggplot’ .heatMap.ggplot: no visible global function definition for ‘aes’ .heatMap.ggplot: no visible binding for global variable ‘Var2’ .heatMap.ggplot: no visible binding for global variable ‘Var1’ .heatMap.ggplot: no visible global function definition for ‘geom_tile’ .heatMap.ggplot: no visible binding for global variable ‘value’ .heatMap.ggplot: no visible global function definition for ‘scale_fill_gradient’ .heatMap.ggplot: no visible global function definition for ‘theme’ .heatMap.ggplot: no visible global function definition for ‘element_blank’ .heatMap.ggplot: no visible global function definition for ‘element_text’ .heatMap.ggplot: no visible global function definition for ‘ggtitle’ .heatMap.ggplot: no visible global function definition for ‘labs’ .heatMap.ggplot: no visible global function definition for ‘scale_x_discrete’ .heatMap.ggplot: no visible global function definition for ‘scale_y_discrete’ .plotDistribParents.LargeMat: no visible global function definition for ‘ggplot’ .plotDistribParents.LargeMat: no visible global function definition for ‘aes’ .plotDistribParents.LargeMat: no visible binding for global variable ‘variable’ .plotDistribParents.LargeMat: no visible binding for global variable ‘GeneNames’ .plotDistribParents.LargeMat: no visible global function definition for ‘geom_tile’ .plotDistribParents.LargeMat: no visible binding for global variable ‘value’ .plotDistribParents.LargeMat: no visible global function definition for ‘scale_fill_gradient’ .plotDistribParents.LargeMat: no visible global function definition for ‘theme’ .plotDistribParents.LargeMat: no visible global function definition for ‘element_blank’ .plotDistribParents.LargeMat: no visible global function definition for ‘element_text’ .plotDistribParents.LargeMat: no visible global function definition for ‘ggtitle’ .plotDistribParents.LargeMat: no visible global function definition for ‘labs’ .plotDistribParents.LargeMat: no visible global function definition for ‘scale_x_discrete’ .plotDistribParents.LargeMat: no visible global function definition for ‘scale_y_discrete’ .plotDistribParents.LargeMat: no visible global function definition for ‘facet_wrap’ Undefined global functions or variables: GeneNames Var1 Var2 aes element_blank element_text facet_wrap geom_tile ggplot ggtitle labs scale_fill_gradient scale_x_discrete scale_y_discrete theme value variable * 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed function_NonLinearNet 113.498 0.339 114.044 function_ReplicatesNet_student 54.563 0.340 57.759 function_ReplicatesNet_gauss 44.257 0.338 61.043 function_LinearNet 23.800 0.147 24.024 analyse.output 23.287 0.155 23.470 readChains 12.372 0.108 18.623 * 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: 3 NOTEs See ‘/Users/biocbuild/bbs-3.15-bioc/meat/GRENITS.Rcheck/00check.log’ for details.