* using log directory ‘/srv/hornik/tmp/CRAN_pretest/gedi.Rcheck’ * using R Under development (unstable) (2026-02-08 r89382) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 21.1.8 (1+b1) Debian flang version 21.1.8 (1+b1) * running under: Debian GNU/Linux forky/sid * using session charset: UTF-8 * current time: 2026-02-09 03:26:05 UTC * checking for file ‘gedi/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘gedi’ version ‘2.3.1’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [2s/3s] ERROR Maintainer: ‘Arsham Mikaeili Namini ’ New submission Conflicting package names (submitted: gedi, existing: GeDi [file:///data/Repositories/Bioconductor/3.22/bioc/src/contrib]) * 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 executable files ... OK * checking for hidden files and directories ... NOTE Found the following hidden files and directories: .claude These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. CRAN-pack does not know about .claude * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘gedi’ can be installed ... [68s/68s] NOTE Found the following notes/warnings: SystemRequirements specified C++14: support has been removed See ‘/srv/hornik/tmp/CRAN_pretest/gedi.Rcheck/00install.out’ for details. * used C++ compiler: ‘Debian clang version 21.1.8 (1+b1)’ * checking C++ specification ... NOTE Obsolete C++14 standard request will be ignored * checking package directory ... OK * checking for future file timestamps ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... NOTE Non-standard file/directory found at top level: ‘Logo.svg’ * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... WARNING Found the following files with non-ASCII characters: R/gedi_class.R R/gedi_dynamics.R R/gedi_projections.R R/seurat_integration.R Portable packages must use only ASCII characters in their R code and NAMESPACE directives, except perhaps in comments. Use \uxxxx escapes for other characters. Function ‘tools::showNonASCIIfile’ can help in finding non-ASCII characters in files. * checking R files for syntax errors ... OK * checking whether the package can be loaded ... [1s/1s] OK * checking whether the package can be loaded with stated dependencies ... [1s/1s] OK * checking whether the package can be unloaded cleanly ... [1s/1s] OK * checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK * checking whether the namespace can be unloaded cleanly ... [1s/1s] OK * checking loading without being on the library search path ... [1s/1s] OK * checking whether startup messages can be suppressed ... [1s/1s] OK * checking use of S3 registration ... OK * checking dependencies in R code ... WARNING '::' or ':::' import not declared from: ‘glmnet’ 'loadNamespace' or 'requireNamespace' call not declared from: ‘glmnet’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [9s/9s] NOTE .plot_embedding_base: no visible binding for global variable ‘Dim1’ .plot_embedding_base: no visible binding for global variable ‘Dim2’ .plot_embedding_base: no visible binding for global variable ‘Color’ compute_Y_variance: no visible global function definition for ‘txtProgressBar’ compute_Y_variance: no visible global function definition for ‘setTxtProgressBar’ compute_dispersion: no visible global function definition for ‘txtProgressBar’ compute_dispersion: no visible global function definition for ‘setTxtProgressBar’ compute_sparse_A: no visible global function definition for ‘coef’ compute_sparse_A: no visible global function definition for ‘median’ create_progress_bar: no visible global function definition for ‘txtProgressBar’ get_cache_memory: no visible global function definition for ‘object.size’ get_dimred_cache_memory: no visible global function definition for ‘object.size’ get_imputation_cache_memory : : no visible global function definition for ‘object.size’ get_imputation_cache_memory: no visible global function definition for ‘object.size’ get_imputed_Y: no visible global function definition for ‘txtProgressBar’ get_imputed_Y: no visible global function definition for ‘setTxtProgressBar’ plot_convergence: no visible binding for global variable ‘Iteration’ plot_convergence: no visible binding for global variable ‘RMSD’ plot_convergence: no visible binding for global variable ‘Parameter’ plot_convergence: no visible binding for global variable ‘Sample’ plot_convergence: no visible binding for global variable ‘Factor’ plot_convergence: no visible binding for global variable ‘sigma2’ plot_convergence: no visible binding for global variable ‘Group’ plot_dispersion: no visible binding for global variable ‘Expected_Var’ plot_dispersion: no visible binding for global variable ‘Observed_Var’ plot_dispersion: no visible binding for global variable ‘Sample’ plot_embedding: no visible binding for global variable ‘Dim1’ plot_embedding: no visible binding for global variable ‘Dim2’ plot_embedding: no visible binding for global variable ‘Color’ plot_features: no visible binding for global variable ‘Dim1’ plot_features: no visible binding for global variable ‘Dim2’ plot_features: no visible binding for global variable ‘Value’ plot_vector_field: no visible binding for global variable ‘Alpha’ plot_vector_field: no visible binding for global variable ‘Color’ run_gradient_svd: no visible global function definition for ‘var’ run_joint_svd: no visible global function definition for ‘var’ update_progress_bar: no visible global function definition for ‘setTxtProgressBar’ Undefined global functions or variables: Alpha Color Dim1 Dim2 Expected_Var Factor Group Iteration Observed_Var Parameter RMSD Sample Value coef median object.size setTxtProgressBar sigma2 txtProgressBar var Consider adding importFrom("stats", "coef", "median", "var") importFrom("utils", "object.size", "setTxtProgressBar", "txtProgressBar") to your NAMESPACE file. * checking Rd files ... [0s/0s] OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... WARNING Missing link(s) in Rd file 'gedi-package.Rd': ‘GEDI’ Missing link(s) in Rd file 'plot_feature_ratio.Rd': ‘gene1,’ ‘gene2,’ See section 'Cross-references' in the 'Writing R Extensions' manual. Found the following Rd file(s) with Rd \link{} targets missing package anchors: gedi-package.Rd: GEDI plot_feature_ratio.Rd: gene1,, gene2, Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... NOTE S3 methods shown with full name in Rd file 'print.gedi_dynamics.Rd': ‘print.gedi_dynamics’ S3 methods shown with full name in Rd file 'print.gedi_dynamics_svd.Rd': ‘print.gedi_dynamics_svd’ S3 methods shown with full name in Rd file 'print.gedi_imputation.Rd': ‘print.gedi_imputation’ S3 methods shown with full name in Rd file 'print.gedi_pathway_associations.Rd': ‘print.gedi_pathway_associations’ The \usage entries for S3 methods should use the \method markup and not their full name. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... WARNING Non-portable flags in variable 'PKG_CXXFLAGS': -Wno-unused-parameter -Wno-ignored-attributes * 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 use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK * checking pragmas in C/C++ headers and code ... OK * checking compilation flags used ... WARNING Compilation used the following non-portable flag(s): ‘-Wno-ignored-attributes’ ‘-Wno-unused-parameter’ including flag(s) suppressing warnings * checking compiled code ... OK * checking examples ... [3s/3s] OK * checking PDF version of manual ... [3s/3s] OK * checking HTML version of manual ... [1s/1s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR, 5 WARNINGs, 6 NOTEs