############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:MEIGOR.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings MEIGOR_1.32.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/MEIGOR.Rcheck’ * using R version 4.2.3 (2023-03-15) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * checking for file ‘MEIGOR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MEIGOR’ version ‘1.32.0’ * 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-3.16-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 ... NOTE Malformed Description field: should contain one or more complete sentences. * checking top-level files ... NOTE File LICENSE is not mentioned in the DESCRIPTION file. * 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 installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... NOTE The following files look like leftovers/mistakes: ‘MEIGOR-vignette.bbl’ Please remove them from your package. The following directory looks like a leftover from 'knitr': ‘figure’ Please remove from your package. * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed essR 9.126 0.123 9.249 cur_params 7.171 0.132 7.303 runBayesFit 7.018 0.104 7.123 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘MEIGOR-vignette.Rnw’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... ERROR Error(s) in re-building vignettes: --- re-building ‘MEIGOR-vignette.Rnw’ using knitr ----------- FAILURE REPORT -------------- --- failure: length > 1 in coercion to logical --- --- srcref --- : --- package (from environment) --- MEIGOR --- call from context --- doTryCatch(return(expr), name, parentenv, handler) --- call from argument --- !is.null(n_elements) && n_elements > 1 --- R stacktrace --- where 1: doTryCatch(return(expr), name, parentenv, handler) where 2: tryCatchOne(expr, names, parentenv, handlers[[1L]]) where 3: tryCatchList(expr, classes, parentenv, handlers) where 4: tryCatch({ libpaths = .libPaths() res = sfClusterEval(.libPaths(.libPaths())) res = sfClusterEval(getwd()) sfClusterEval(library("MEIGOR")) cpu_time_0 = proc.time()[3] res = sfLapply(1:n_nodes, ith_VNSR, problem, opts, ...) results$time = c() results$fbest = c() results$xbest = list() results$f_mean = c() results$numeval = c() results$iteration_res = list() results$iteration_res[[1]] = res matF_0 = c() matX_0 = c() for (j in 1:n_nodes) { matX_0 = rbind(matX_0, res[[j]]$xbest) matF_0 = c(matF_0, res[[j]]$fbest) total_evals = total_evals + res[[j]]$numeval if (res[[j]]$fbest <= fbest) { fbest = res[[j]]$fbest xbest = res[[j]]$xbest } } index_duplicated = which(duplicated(matX_0)) if (length(index_duplicated) > 0) { matX_0 = matX_0[-index_duplicated, ] matF_0 = matF_0[-index_duplicated] } min_index = which(matF_0 == min(matF_0)) for (j in 1:n_nodes) { n_elements = dim(matX_0) if (!is.null(n_elements) && n_elements > 1) { problem[[j]]$x_0 = matX_0[min_index, ] problem[[j]]$f_0 = matF_0[min_index] } else { problem[[j]]$x_0 = matX_0 problem[[j]]$f_0 = matF_0 } } cpu_time_1 = proc.time()[3] results$numeval[1] = total_evals results$time[1] = cpu_time_1 - cpu_time_0 results$fbest[1] = fbest results$xbest[[1]] = xbest results$f_mean[1] = mean(matF_0) results$iteration_res[[1]] = res print(paste("iteration:", 0, "cputime:", results$time[1], "num_evals;", results$numeval[1], "best", results$fbest[1], "mean", results$f_mean[1], sep = " ")) save(file = "Results_iter_0", results) if (n_iter > 0) { for (i in 1:n_iter) { f_0 = list() x_0 = list() count = 0 if (total_evals > max_eval) return(results) res = sfLapply(1:n_nodes, ith_VNSR, problem, opts, ...) matF_0 = c() matX_0 = c() for (j in 1:n_nodes) { matX_0 = rbind(matX_0, res[[j]]$xbest) matF_0 = c(matF_0, res[[j]]$fbest) total_evals = total_evals + res[[j]]$numeval if (res[[j]]$fbest <= fbest) { fbest = res[[j]]$fbest xbest = res[[j]]$xbest } } index_duplicated = which(duplicated(matX_0)) if (length(index_duplicated) > 0) { matX_0 = matX_0[-index_duplicated, ] matF_0 = matF_0[-index_duplicated] } min_index = which(matF_0 == min(matF_0)) for (j in 1:n_nodes) { n_elements = dim(matX_0) if (!is.null(n_elements) && n_elements > 1) { problem[[j]]$x_0 = matX_0[min_index, ] problem[[j]]$f_0 = matF_0[min_index] } else { problem[[j]]$x_0 = matX_0 problem[[j]]$f_0 = matF_0 } } results$numeval[i + 1] = total_evals cpu_time_1 = proc.time()[3] results$time[i + 1] = cpu_time_1 - cpu_time_0 results$fbest[i + 1] = fbest results$xbest[[i + 1]] = xbest results$f_mean[i + 1] = mean(matF_0) results$iteration_res[[i + 1]] = res print(paste("iteration:", i, "cputime:", results$time[i + 1], "num_evals;", results$numeval[i + 1], "best_f", results$fbest[i + 1], "mean", results$f_mean[i + 1], sep = " ")) save(file = paste("Results_iter_", i, sep = ""), results) } } }, error = function(e) { print("something happened") }, finally = { sfStop() }) where 5: CeVNSR(problem, opts, max_eval, max_time, n_iter, is_parallel, type, ...) where 6: MEIGO(problem, opts, algorithm = "CeVNSR") where 7: eval(expr, envir, enclos) where 8: eval(expr, envir, enclos) where 9: eval_with_user_handlers(expr, envir, enclos, user_handlers) where 10: withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)) where 11: withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler) where 12: handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler)) where 13: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler))) where 14: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, debug = debug, last = i == length(out), use_try = stop_on_error != 2L, keep_warning = keep_warning, keep_message = keep_message, output_handler = output_handler, include_timing = include_timing) where 15: evaluate::evaluate(...) where 16: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options)) where 17: in_dir(input_dir(), expr) where 18: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options))) where 19: eng_r(options) where 20: block_exec(params) where 21: call_block(x) where 22: process_group.block(group) where 23: process_group(group) where 24: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { setwd(wd) cat(res, sep = "\n", file = output %n% "") message("Quitting from lines ", paste(current_lines(i), collapse = "-"), " (", knit_concord$get("infile"), ") ") }) where 25: process_file(text, output) where 26: (if (grepl("\\.[Rr]md$", file)) knit2html else if (grepl("\\.[Rr]rst$", file)) knit2pandoc else knit)(file, encoding = encoding, quiet = quiet, envir = globalenv(), ...) where 27: engine$weave(file, quiet = quiet, encoding = enc) where 28: doTryCatch(return(expr), name, parentenv, handler) where 29: tryCatchOne(expr, names, parentenv, handlers[[1L]]) where 30: tryCatchList(expr, classes, parentenv, handlers) where 31: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) } outputs <- c(outputs, output) }, error = function(e) { thisOK <<- FALSE fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e))) }) where 32: tools::buildVignettes(dir = "/home/biocbuild/bbs-3.16-bioc/meat/MEIGOR.Rcheck/vign_test/MEIGOR", ser_elibs = "/tmp/Rtmpiocwu0/file37e84f5881221c.rds") --- value of length: 2 type: logical --- [1] TRUE TRUE --- function from context --- function (expr, name, parentenv, handler) { .Internal(.addCondHands(name, list(handler), parentenv, environment(), FALSE)) expr } --- function search by body --- ----------- END OF FAILURE REPORT -------------- Fatal error: length > 1 in coercion to logical * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 1 WARNING, 4 NOTEs See ‘/home/biocbuild/bbs-3.16-bioc/meat/MEIGOR.Rcheck/00check.log’ for details.