############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:MEIGOR.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings MEIGOR_1.36.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/MEIGOR.Rcheck’ * using R version 4.3.3 (2024-02-29) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘MEIGOR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MEIGOR’ version ‘1.36.2’ * package encoding: UTF-8 * 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 ‘MEIGOR’ can be installed ... WARNING Found the following significant warnings: Note: possible error in 'runif(seed = options$seed)': unused argument (seed = options$seed) See ‘/home/biocbuild/bbs-3.18-bioc/meat/MEIGOR.Rcheck/00install.out’ for details. Information on the location(s) of code generating the ‘Note’s can be obtained by re-running with environment variable R_KEEP_PKG_SOURCE set to ‘yes’. * 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 loading without being on the library search path ... 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 ... 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 Examples with CPU (user + system) or elapsed time > 5s user system elapsed essR 9.129 0.124 9.253 cur_params 7.271 0.131 7.403 runBayesFit 6.827 0.092 6.920 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘MEIGOR-vignette.Rmd’ using ‘UTF-8’... OK OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 1 NOTE See ‘/home/biocbuild/bbs-3.18-bioc/meat/MEIGOR.Rcheck/00check.log’ for details.