* using log directory 'd:/RCompile/CRANincoming/R-devel/funMoDisco.Rcheck' * using R Under development (unstable) (2025-09-19 r88859 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * checking for file 'funMoDisco/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'funMoDisco' version '1.2.0' * package encoding: UTF-8 * checking CRAN incoming feasibility ... NOTE Maintainer: 'Jacopo Di Iorio ' The Date field is over a month old. Size of tarball: 5021075 bytes * 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 whether package 'funMoDisco' can be installed ... WARNING Found the following significant warnings: SobolDiss.cpp:16:17: warning: 'bool arma::is_finite(const Base&) [with T1 = subview; typename T1::elem_type = double]' is deprecated: change arma::is_finite(X) to X.is_finite() [-Wdeprecated-declarations] probKMAImpl.cpp:791:28: warning: 'bool arma::is_finite(eT, const typename arma_scalar_only::result*) [with eT = double; typename arma_scalar_only::result = double]' is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations] See 'd:/RCompile/CRANincoming/R-devel/funMoDisco.Rcheck/00install.out' for details. * used C++ compiler: 'g++.exe (GCC) 14.2.0' * checking C++ specification ... OK Not all R platforms support C++20 * checking installed package size ... OK * checking package directory ... OK * checking for future file timestamps ... 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 use of S3 registration ... OK * checking dependencies in R code ... NOTE Package in Depends field not imported from: 'shiny' 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 ... [20s] OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... WARNING Functions or methods with usage in Rd file 'motifSimulationApp.Rd' but not in code: 'motifSimulationApp' Codoc mismatches from Rd file 'dot-generate_coefficients.Rd': .generate_coefficients Code: function(motif_i, distrib, dist_knots, norder, coeff_min, coeff_max, motif_seed) Docs: function(motif_i, distrib, dist_knots, norder, coeff_min, coeff_max) Argument names in code not in docs: motif_seed Codoc mismatches from Rd file 'generateCurves-motifSimulation-method.Rd': \S4method{generateCurves}{motifSimulation} Code: function(object, noise_type = NULL, noise_str = NULL, seed_background = NULL, only_der = FALSE, coeff_min_shift = -10, coeff_max_shift = 10) Docs: function(object, noise_type = NULL, noise_str = NULL, seed_background = 777, seed_motif = 43213, only_der = TRUE, coeff_min_shift = -10, coeff_max_shift = 10) Argument names in docs not in code: seed_motif Mismatches in argument names: Position: 5 Code: only_der Docs: seed_motif Position: 6 Code: coeff_min_shift Docs: only_der Position: 7 Code: coeff_max_shift Docs: coeff_min_shift Mismatches in argument default values: Name: 'seed_background' Code: NULL Docs: 777 Name: 'only_der' Code: FALSE Docs: TRUE Codoc mismatches from Rd file 'generateCurves.Rd': generateCurves Code: function(object, noise_type = NULL, noise_str = NULL, seed_background = NULL, only_der = FALSE, coeff_min_shift = -10, coeff_max_shift = 10) Docs: function(object, noise_type = NULL, noise_str = NULL, seed_background = 777, seed_motif = 43213, only_der = TRUE, coeff_min_shift = -10, coeff_max_shift = 10) Argument names in docs not in code: seed_motif Mismatches in argument names: Position: 5 Code: only_der Docs: seed_motif Position: 6 Code: coeff_min_shift Docs: only_der Position: 7 Code: coeff_max_shift Docs: coeff_min_shift Mismatches in argument default values: Name: 'seed_background' Code: NULL Docs: 777 Name: 'only_der' Code: FALSE Docs: TRUE Codoc mismatches from Rd file 'motifSimulationBuilder.Rd': motifSimulationBuilder Code: function(N, len, mot_details, norder = 3, coeff_min = -15, coeff_max = 15, dist_knots = 10, min_dist_motifs = NULL, distribution = "beta", motif_seed = NULL) Docs: function(N, len, mot_details, norder = 3, coeff_min = -15, coeff_max = 15, dist_knots = 10, min_dist_motifs = NULL, distribution = "unif") Argument names in code not in docs: motif_seed Mismatches in argument default values: Name: 'distribution' Code: "beta" Docs: "unif" * 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 LazyData ... 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 ... WARNING Variables overriding user/site settings: CXXFLAGS: -o /dev/null -std=c++20 * checking for GNU extensions in Makefiles ... WARNING Found the following file(s) containing GNU extensions: src/Makevars Portable Makefiles do not use GNU extensions such as +=, :=, $(shell), $(wildcard), ifeq ... endif, .NOTPARALLEL See section 'Writing portable packages' in the 'Writing R Extensions' manual. * 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 ... OK * checking compiled code ... 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 'tests' ... OK * checking tests ... OK Running 'tinytest.R' * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... [14s] OK * checking HTML version of manual ... OK * DONE Status: 4 WARNINGs, 2 NOTEs