############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scMultiSim.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scMultiSim_1.2.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/scMultiSim.Rcheck’ * using R version 4.4.1 (2024-06-14) * 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 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘scMultiSim/DESCRIPTION’ ... OK * this is package ‘scMultiSim’ version ‘1.2.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... NOTE Found the following hidden files and directories: inst/shiny-app/www/.prettierrc These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘scMultiSim’ 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .SpatialGrid: no visible global function definition for ‘new’ .amplifyOneCell: no visible binding for global variable ‘len2nfrag’ .atacSeq: no visible binding for global variable ‘dens_nonzero’ .check_opt: no visible binding for global variable ‘val’ .check_opt: no visible binding for global variable ‘checker’ .check_opt: no visible binding for global variable ‘desc’ .check_opt: no visible binding for global variable ‘check’ .check_opt: no visible binding for global variable ‘err_msg’ .check_opt: no visible global function definition for ‘check’ .continuousCIFParamNormal : : no visible binding for global variable ‘.’ .continuousCIFParamNormal : : no visible binding for global variable ‘tips’ .continuousCIFParamNormal : : no visible binding for global variable ‘internal’ .continuousCIFParamNormal : : : no visible global function definition for ‘Impulsecifpertip’ .continuousCIFParamNormal : : : no visible binding for global variable ‘tips’ .continuousCIFParamNormal : : : no visible binding for global variable ‘internal’ .continuousCIFParamSpatial: no visible binding for global variable ‘max_layers’ .continuousCIFParamSpatial: no visible binding for global variable ‘paths’ .continuousCIFParamSpatial: no visible binding for global variable ‘cell_path’ .continuousCIFParamSpatial: no visible binding for global variable ‘path_len’ .continuousCIFParamSpatial: no visible binding for global variable ‘i_cell’ .continuousCIFParamSpatial : : no visible binding for global variable ‘.’ .continuousCIFParamSpatial : : no visible binding for global variable ‘i_cell’ .continuousCIFParamSpatial : : no visible binding for global variable ‘tips’ .continuousCIFParamSpatial : : no visible binding for global variable ‘internal’ .continuousCIFParamSpatial : : : no visible global function definition for ‘Impulsecifpertip’ .continuousCIFParamSpatial : : : no visible binding for global variable ‘tips’ .continuousCIFParamSpatial : : : no visible binding for global variable ‘internal’ .continuousCIFParamSpatial : : no visible binding for global variable ‘max_layers’ .continuousCIFParamSpatial : : no visible binding for global variable ‘paths’ .continuousCIFParamSpatial: no visible binding for global variable ‘id’ .continuousCIFParamSpatial: no visible binding for global variable ‘from’ .continuousCIFParamSpatial: no visible binding for global variable ‘to’ .continuousCIFParamSpatial: no visible binding for global variable ‘len’ .discreteCIF : : no visible binding for global variable ‘.’ .discreteCIFSpatial : : no visible binding for global variable ‘.’ .dynGRN: no visible global function definition for ‘new’ .geneEffectsByRegulator: no visible binding for global variable ‘target’ .geneEffectsByRegulator: no visible binding for global variable ‘regulator’ .geneEffectsByRegulator: no visible binding for global variable ‘effect’ .getPaths: no visible binding for global variable ‘tips’ .getPaths: no visible binding for global variable ‘internal’ .identityVectors: no visible binding for global variable ‘.’ .print_opt: no visible binding for global variable ‘val’ .print_opt: no visible binding for global variable ‘checker’ .print_opt: no visible binding for global variable ‘desc’ .processVelocity : get_velo: no visible binding for global variable ‘vx_normalized’ .processVelocity : get_velo: no visible binding for global variable ‘vy_normalized’ .processVelocity : get_velo: no visible binding for global variable ‘vx_knn_normalized’ .processVelocity : get_velo: no visible binding for global variable ‘vy_knn_normalized’ .regionToGeneMatrix: no visible binding for global variable ‘.’ .rnaSeq: no visible binding for global variable ‘tips’ .rnaSeq: no visible binding for global variable ‘internal’ .rnaSeq: no visible binding for global variable ‘.’ .rnaSeq: no visible binding for global variable ‘parent’ .rnaSeq: no visible binding for global variable ‘child’ .rnaSeqSpatial: no visible binding for global variable ‘tips’ .rnaSeqSpatial: no visible binding for global variable ‘internal’ .rnaVelocityCosine: no visible binding for global variable ‘current_counts_s_tsne’ .rnaVelocityCosine: no visible binding for global variable ‘future_counts_s_tsne’ .rnaVelocityCosine: no visible binding for global variable ‘vx_raw’ .rnaVelocityCosine: no visible binding for global variable ‘vy_raw’ .rnaVelocityCosine: no visible binding for global variable ‘vx_normalized’ .rnaVelocityCosine: no visible binding for global variable ‘vy_normalized’ .rnaVelocityCosine: no visible binding for global variable ‘vx_knn’ .rnaVelocityCosine: no visible binding for global variable ‘vy_knn’ .rnaVelocityCosine: no visible binding for global variable ‘vx_knn_normalized’ .rnaVelocityCosine: no visible binding for global variable ‘vy_knn_normalized’ .rnaVelocityCosine: no visible binding for global variable ‘future_counts_s_tsne2’ .rnaVelocityCosine: no visible binding for global variable ‘vx_raw2’ .rnaVelocityCosine: no visible binding for global variable ‘vy_raw2’ .rnaVelocityCosine: no visible binding for global variable ‘vx_normalized2’ .rnaVelocityCosine: no visible binding for global variable ‘vy_normalized2’ .rnaVelocityCosine: no visible binding for global variable ‘vx_knn2’ .rnaVelocityCosine: no visible binding for global variable ‘vy_knn2’ .rnaVelocityCosine: no visible binding for global variable ‘vx_knn_normalized2’ .rnaVelocityCosine: no visible binding for global variable ‘vy_knn_normalized2’ .rnaVelocityCosine : : no visible binding for global variable ‘vx_knn_normalized’ .rnaVelocityCosine : : no visible binding for global variable ‘vy_knn_normalized’ .rnaVelocityCosine : : no visible binding for global variable ‘vx_knn_normalized2’ .rnaVelocityCosine : : no visible binding for global variable ‘vy_knn_normalized2’ .rnaVelocityCosine: no visible binding for global variable ‘x’ .rnaVelocityCosine: no visible binding for global variable ‘y’ .summarizeExp: no visible global function definition for ‘metadata<-’ SampleDen: no visible global function definition for ‘rmultinom’ add_expr_noise: no visible binding for global variable ‘gene_len_pool’ add_outliers: no visible global function definition for ‘rowVars’ cci_cell_type_params: no visible binding for global variable ‘tips’ cci_cell_type_params: no visible binding for global variable ‘internal’ gene_coexpr_cci: no visible binding for global variable ‘name’ gene_coexpr_cci: no visible binding for global variable ‘value’ gene_corr_cci: no visible binding for global variable ‘name’ gene_corr_cci: no visible binding for global variable ‘value’ gene_corr_regulator: no visible binding for global variable ‘.’ generateSpatialLoc: no visible binding for global variable ‘paths’ generateSpatialLoc: no visible binding for global variable ‘max_layers’ generateSpatialLoc: no visible binding for global variable ‘id’ generateSpatialLoc: no visible binding for global variable ‘from’ generateSpatialLoc: no visible binding for global variable ‘to’ generateSpatialLoc: no visible binding for global variable ‘len’ generateSpatialLoc: no visible binding for global variable ‘meta’ plot_cell_loc: no visible binding for global variable ‘x’ plot_cell_loc: no visible binding for global variable ‘y’ plot_cell_loc: no visible binding for global variable ‘cell_type’ plot_cell_loc: no visible binding for global variable ‘xend’ plot_cell_loc: no visible binding for global variable ‘yend’ plot_grid: no visible binding for global variable ‘x’ plot_grid: no visible binding for global variable ‘y’ plot_grid: no visible binding for global variable ‘index’ plot_rna_velocity: no visible binding for global variable ‘current_counts_s_tsne’ plot_rna_velocity: no visible binding for global variable ‘future_counts_s_tsne’ plot_rna_velocity: no visible binding for global variable ‘vx_raw’ plot_rna_velocity: no visible binding for global variable ‘vy_raw’ plot_rna_velocity: no visible binding for global variable ‘vx_normalized’ plot_rna_velocity: no visible binding for global variable ‘vy_normalized’ plot_rna_velocity: no visible binding for global variable ‘vx_knn’ plot_rna_velocity: no visible binding for global variable ‘vy_knn’ plot_rna_velocity: no visible binding for global variable ‘vx_knn_normalized’ plot_rna_velocity: no visible binding for global variable ‘vy_knn_normalized’ plot_rna_velocity: no visible binding for global variable ‘index’ plot_tsne: no visible global function definition for ‘prcomp’ plot_tsne: no visible binding for global variable ‘x’ plot_tsne: no visible binding for global variable ‘y’ plot_tsne: no visible binding for global variable ‘index’ rna_velo_knn: no visible global function definition for ‘paired_simil’ rna_velo_knn : : no visible global function definition for ‘distMat.KernelKnn’ sim_example: no visible binding for global variable ‘GRN_params_100’ sim_example_spatial: no visible binding for global variable ‘GRN_params_100’ sim_true_counts: no visible binding for global variable ‘.rn_sp’ sim_true_counts: no visible binding for global variable ‘paths’ sim_true_counts: no visible binding for global variable ‘total_ncell’ Undefined global functions or variables: . .rn_sp GRN_params_100 Impulsecifpertip cell_path cell_type check checker child current_counts_s_tsne dens_nonzero desc distMat.KernelKnn effect err_msg from future_counts_s_tsne future_counts_s_tsne2 gene_len_pool i_cell id index internal len len2nfrag max_layers meta metadata<- name new paired_simil parent path_len paths prcomp regulator rmultinom rowVars target tips to total_ncell val value vx_knn vx_knn2 vx_knn_normalized vx_knn_normalized2 vx_normalized vx_normalized2 vx_raw vx_raw2 vy_knn vy_knn2 vy_knn_normalized vy_knn_normalized2 vy_normalized vy_normalized2 vy_raw vy_raw2 x xend y yend Consider adding importFrom("methods", "new") importFrom("stats", "prcomp", "rmultinom") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * 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 files in ‘vignettes’ ... OK * checking examples ... OK * 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: 2 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/scMultiSim.Rcheck/00check.log’ for details.