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###
### 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
###
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* 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
}
<bytecode: 0x5628572891f8>
<environment: 0x56285e42a770>
 --- 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.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL MEIGOR
###
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* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’
* installing *source* package ‘MEIGOR’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Note: possible error in 'runif(seed = options$seed)': unused argument (seed = options$seed) 
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (MEIGOR)