############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MEIGOR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MEIGOR_1.40.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/MEIGOR.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 ‘MEIGOR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MEIGOR’ version ‘1.40.0’ * 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 ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘MEIGOR’ 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 CeSSR: no visible global function definition for ‘sd’ CeSSR: no visible binding for global variable ‘sd’ between_chain_variances: no visible global function definition for ‘var’ essR: no visible global function definition for ‘combn’ essR: no visible global function definition for ‘runif’ essR_multistart: no visible global function definition for ‘runif’ essR_multistart: no visible global function definition for ‘hist’ estimate: no visible global function definition for ‘runif’ generate_new_position: no visible global function definition for ‘rnorm’ initialize: no visible global function definition for ‘runif’ initialize_and_pool: no visible binding for global variable ‘mulichain’ nls_fobj: no visible binding for global variable ‘fobj_global’ nls_fobj: no visible binding for '<<-' assignment to ‘n_fun_eval’ nls_fobj: no visible binding for global variable ‘n_fun_eval’ optim_fobj: no visible binding for global variable ‘fobj_global’ optim_fobj: no visible binding for '<<-' assignment to ‘n_fun_eval’ optim_fobj: no visible binding for global variable ‘n_fun_eval’ runBayesFit : prior: no visible binding for global variable ‘prior_mean’ runBayesFit : prior: no visible binding for global variable ‘prior_var’ rvnds_hamming: no visible global function definition for ‘runif’ solnp_eq: no visible binding for global variable ‘fobj_global’ solnp_eq: no visible binding for '<<-' assignment to ‘n_fun_eval’ solnp_eq: no visible binding for global variable ‘n_fun_eval’ solnp_eq: no visible binding for global variable ‘neq_global’ solnp_fobj: no visible binding for global variable ‘fobj_global’ solnp_fobj: no visible binding for '<<-' assignment to ‘n_fun_eval’ solnp_fobj: no visible binding for global variable ‘n_fun_eval’ solnp_ineq: no visible binding for global variable ‘fobj_global’ solnp_ineq: no visible binding for '<<-' assignment to ‘n_fun_eval’ solnp_ineq: no visible binding for global variable ‘n_fun_eval’ solnp_ineq: no visible binding for global variable ‘neq_global’ solnp_ineq: no visible binding for global variable ‘nconst_global’ ssm_beyond: no visible global function definition for ‘runif’ ssm_localsolver: no visible binding for '<<-' assignment to ‘n_fun_eval’ ssm_localsolver: no visible binding for '<<-' assignment to ‘fobj_global’ ssm_localsolver: no visible binding for '<<-' assignment to ‘neq_global’ ssm_localsolver: no visible binding for '<<-' assignment to ‘nconst_global’ ssm_localsolver: no visible binding for '<<-' assignment to ‘extra_args’ ssm_localsolver: no visible global function definition for ‘optim’ ssm_localsolver: no visible binding for global variable ‘n_fun_eval’ ssm_localsolver: no visible global function definition for ‘nls’ ssm_localsolver: no visible binding for global variable ‘extra_args’ ssm_localsolver: no visible global function definition for ‘coef’ within_chain_variances: no visible global function definition for ‘var’ Undefined global functions or variables: coef combn extra_args fobj_global hist mulichain n_fun_eval nconst_global neq_global nls optim prior_mean prior_var rnorm runif sd var Consider adding importFrom("graphics", "hist") importFrom("stats", "coef", "nls", "optim", "rnorm", "runif", "sd", "var") importFrom("utils", "combn") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... NOTE Invalid package aliases in Rd file 'BayesFit.Rd': ‘BayesFit-package’ Invalid package aliases in Rd file 'essR-MEIGOR.Rd': ‘essR-package’ * 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 ... NOTE Argument items with no description in Rd file 'vns_defaults.Rd': ‘\dots’ * 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 Examples with CPU (user + system) or elapsed time > 5s user system elapsed essR 9.004 0.147 9.162 cur_params 6.215 0.308 6.532 runBayesFit 6.126 0.307 6.479 * 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: 3 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/MEIGOR.Rcheck/00check.log’ for details.