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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:GeneAccord.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings GeneAccord_1.16.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/GeneAccord.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 ‘GeneAccord/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GeneAccord’ version ‘1.16.0’
* 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 ‘GeneAccord’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 10.0Mb
  sub-directories of 1Mb or more:
    data      3.0Mb
    extdata   6.6Mb
* 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 ... OK
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘GeneAccord.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘GeneAccord.Rmd’ using rmarkdown
 ----------- FAILURE REPORT -------------- 
 --- failure: length > 1 in coercion to logical ---
 --- srcref --- 
: 
 --- package (from environment) --- 
GeneAccord
 --- call from context --- 
FUN(X[[i]], ...)
 --- call from argument --- 
this_beta_distored_rate == 0 && num_clon_excl_this_pair[cnt] == 
    num_trees_this_pair[cnt]
 --- R stacktrace ---
where 1: FUN(X[[i]], ...)
where 2: vapply(these_rate_this_pair, function(this_rate) {
    cnt <- which(these_rate_this_pair == this_rate)
    this_alpha <- this_rate * beta_distortion
    this_beta <- (1 - this_rate) * beta_distortion
    this_beta_distored_rate <- rbeta(1, shape1 = this_alpha, 
        shape2 = this_beta)
    stopifnot(this_beta_distored_rate >= 0 && this_beta_distored_rate <= 
        1)
    if (this_beta_distored_rate == 0 && num_clon_excl_this_pair[cnt] == 
        num_trees_this_pair[cnt]) {
        stop("[Function: build_null_test_statistic]: The beta", 
            " distorted rate is 0,", "\nbut there is a pair which is clonally ", 
            "exclusive across ALL trees,\ni.e. num_clon_excl", 
            " == num_trees_pair, which is == ", num_trees_this_pair[cnt], 
            ". The computation of the delta\nwill not be", " possible since the likelihood is zero. ", 
            "Make sure that the rates\nare not distorted too", 
            " much by the beta distribution.", "The original rate of\nthe current simulated pair ", 
            "was ", this_rate)
    }
    else if (this_beta_distored_rate == 1 && num_clon_excl_this_pair[cnt] == 
        0) {
        stop("[Function: build_null_test_statistic]: ", " The beta distorted rate is 1,", 
            ",\nbut there is a pair which is clonally ", "exclusive across ALL trees,\ni.e. num_clon_excl", 
            " == num_trees_pair, which is == ", num_trees_this_pair[cnt], 
            ". The computation of the delta\nwill not be", " possible since the likelihood is zero. ", 
            "Make sure that the rates\nare not distorted too", 
            " much by the beta distribution.", "The original rate of\nthe current simulated pair ", 
            "was ", this_rate)
    }
    return(this_beta_distored_rate)
}, numeric(1))
where 3: FUN(newX[, i], ...)
where 4: apply(pairs_indices_pats_list, 2, function(x) {
    this_num_pat_this_pair <- length(x)
    these_rate_this_pair <- avg_rates_m[x]
    this_hist_sample <- vapply(x, function(y) {
        num_pairs_this_pat <- length(list_of_clon_excl_frac_trees_all_pats[[1]][[y]])
        hist_entry <- sample(num_pairs_this_pat, 1)
        num_trees_this_pair <- list_of_clon_excl_frac_trees_all_pats[[1]][[y]][hist_entry]
        num_clon_excl_this_pair <- list_of_clon_excl_frac_trees_all_pats[[2]][[y]][hist_entry]
        return(c(num_trees_this_pair, num_clon_excl_this_pair))
    }, numeric(2))
    stopifnot(is.matrix(this_hist_sample))
    stopifnot(dim(this_hist_sample)[1] == 2)
    stopifnot(dim(this_hist_sample)[2] == this_num_pat_this_pair)
    num_trees_this_pair <- this_hist_sample[1, ]
    num_clon_excl_this_pair <- this_hist_sample[2, ]
    beta_distorted_rates <- vapply(these_rate_this_pair, function(this_rate) {
        cnt <- which(these_rate_this_pair == this_rate)
        this_alpha <- this_rate * beta_distortion
        this_beta <- (1 - this_rate) * beta_distortion
        this_beta_distored_rate <- rbeta(1, shape1 = this_alpha, 
            shape2 = this_beta)
        stopifnot(this_beta_distored_rate >= 0 && this_beta_distored_rate <= 
            1)
        if (this_beta_distored_rate == 0 && num_clon_excl_this_pair[cnt] == 
            num_trees_this_pair[cnt]) {
            stop("[Function: build_null_test_statistic]: The beta", 
                " distorted rate is 0,", "\nbut there is a pair which is clonally ", 
                "exclusive across ALL trees,\ni.e. num_clon_excl", 
                " == num_trees_pair, which is == ", num_trees_this_pair[cnt], 
                ". The computation of the delta\nwill not be", 
                " possible since the likelihood is zero. ", "Make sure that the rates\nare not distorted too", 
                " much by the beta distribution.", "The original rate of\nthe current simulated pair ", 
                "was ", this_rate)
        }
        else if (this_beta_distored_rate == 1 && num_clon_excl_this_pair[cnt] == 
            0) {
            stop("[Function: build_null_test_statistic]: ", " The beta distorted rate is 1,", 
                ",\nbut there is a pair which is clonally ", 
                "exclusive across ALL trees,\ni.e. num_clon_excl", 
                " == num_trees_pair, which is == ", num_trees_this_pair[cnt], 
                ". The computation of the delta\nwill not be", 
                " possible since the likelihood is zero. ", "Make sure that the rates\nare not distorted too", 
                " much by the beta distribution.", "The original rate of\nthe current simulated pair ", 
                "was ", this_rate)
        }
        return(this_beta_distored_rate)
    }, numeric(1))
    this_lr_test_res <- suppressMessages(compute_test_stat_avg_rate(beta_distorted_rates, 
        num_trees_this_pair, num_clon_excl_this_pair))
    this_test_statistic <- this_lr_test_res[[1]]
    this_delta <- this_lr_test_res[[2]]
    return(list(this_test_statistic, this_delta, this_num_pat_this_pair, 
        these_rate_this_pair, num_trees_this_pair, num_clon_excl_this_pair, 
        beta_distorted_rates))
})
where 5: build_null_test_statistic(avg_rates_m, list_of_clon_excl_frac_trees_all_pats, 
    num_pat_pair = i, num_pairs_sim = num_pairs_sim, beta_distortion = beta_distortion)
where 6: withCallingHandlers(expr, message = function(c) if (inherits(c, 
    classes)) tryInvokeRestart("muffleMessage"))
where 7: suppressMessages(build_null_test_statistic(avg_rates_m, list_of_clon_excl_frac_trees_all_pats, 
    num_pat_pair = i, num_pairs_sim = num_pairs_sim, beta_distortion = beta_distortion))
where 8: generate_ecdf_test_stat(avg_rates_m, list_of_num_trees_all_pats, 
    list_of_clon_excl_all_pats, num_pat_pair_max, num_pairs_sim = 100)
where 9: eval(expr, envir, enclos)
where 10: eval(expr, envir, enclos)
where 11: eval_with_user_handlers(expr, envir, enclos, user_handlers)
where 12: withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers))
where 13: withCallingHandlers(withVisible(eval_with_user_handlers(expr, 
    envir, enclos, user_handlers)), warning = wHandler, error = eHandler, 
    message = mHandler)
where 14: handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, 
    envir, enclos, user_handlers)), warning = wHandler, error = eHandler, 
    message = mHandler))
where 15: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, 
    envir, enclos, user_handlers)), warning = wHandler, error = eHandler, 
    message = mHandler)))
where 16: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, 
    debug = debug, last = i == length(out), use_try = stop_on_error != 
        2L, keep_warning = keep_warning, keep_message = keep_message, 
    output_handler = output_handler, include_timing = include_timing)
where 17: evaluate::evaluate(...)
where 18: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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: in_dir(input_dir(), expr)
where 20: 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$render, options)))
where 21: eng_r(options)
where 22: block_exec(params)
where 23: call_block(x)
where 24: process_group.block(group)
where 25: process_group(group)
where 26: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 
    error = function(e) {
        setwd(wd)
        cat(res, sep = "\n", file = output %n% "")
        message("Quitting from lines ", paste(current_lines(i), 
            collapse = "-"), " (", knit_concord$get("infile"), 
            ") ")
    })
where 27: process_file(text, output)
where 28: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
where 29: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), 
    output_dir = getwd(), ...)
where 30: vweave_rmarkdown(...)
where 31: engine$weave(file, quiet = quiet, encoding = enc)
where 32: doTryCatch(return(expr), name, parentenv, handler)
where 33: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 34: tryCatchList(expr, classes, parentenv, handlers)
where 35: tryCatch({
    engine$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 36: tools::buildVignettes(dir = "/home/biocbuild/bbs-3.16-bioc/meat/GeneAccord.Rcheck/vign_test/GeneAccord", 
    ser_elibs = "/tmp/Rtmpjc2nDu/file226bfe8e6e9d7.rds")

 --- value of length: 2 type: logical ---
[1] FALSE FALSE
 --- function from context --- 
function (this_rate) 
{
    cnt <- which(these_rate_this_pair == this_rate)
    this_alpha <- this_rate * beta_distortion
    this_beta <- (1 - this_rate) * beta_distortion
    this_beta_distored_rate <- rbeta(1, shape1 = this_alpha, 
        shape2 = this_beta)
    stopifnot(this_beta_distored_rate >= 0 && this_beta_distored_rate <= 
        1)
    if (this_beta_distored_rate == 0 && num_clon_excl_this_pair[cnt] == 
        num_trees_this_pair[cnt]) {
        stop("[Function: build_null_test_statistic]: The beta", 
            " distorted rate is 0,", "\nbut there is a pair which is clonally ", 
            "exclusive across ALL trees,\ni.e. num_clon_excl", 
            " == num_trees_pair, which is == ", num_trees_this_pair[cnt], 
            ". The computation of the delta\nwill not be", " possible since the likelihood is zero. ", 
            "Make sure that the rates\nare not distorted too", 
            " much by the beta distribution.", "The original rate of\nthe current simulated pair ", 
            "was ", this_rate)
    }
    else if (this_beta_distored_rate == 1 && num_clon_excl_this_pair[cnt] == 
        0) {
        stop("[Function: build_null_test_statistic]: ", " The beta distorted rate is 1,", 
            ",\nbut there is a pair which is clonally ", "exclusive across ALL trees,\ni.e. num_clon_excl", 
            " == num_trees_pair, which is == ", num_trees_this_pair[cnt], 
            ". The computation of the delta\nwill not be", " possible since the likelihood is zero. ", 
            "Make sure that the rates\nare not distorted too", 
            " much by the beta distribution.", "The original rate of\nthe current simulated pair ", 
            "was ", this_rate)
    }
    return(this_beta_distored_rate)
}
<bytecode: 0x55b4a2cce6b0>
<environment: 0x55b4a0888fb0>
 --- 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 NOTE
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/GeneAccord.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL GeneAccord
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’
* installing *source* package ‘GeneAccord’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** 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 (GeneAccord)

R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library("testthat")
> library("assertthat")
> 
> library("GeneAccord")
> # "When R CMD check runs tests, it sets R_TESTS. When the tests
> # themeselves run R CMD xxxx, as is the case with the tests in
> # devtools, having R_TESTS set causes errors because it confuses
> # the R subprocesses. Unsetting it here avoids those problems.
> #"R_TESTS" = "" "
> Sys.setenv("R_TESTS" = "")
> 
> test_check("GeneAccord")
[ FAIL 0 | WARN 9 | SKIP 15 | PASS 27 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (15)

[ FAIL 0 | WARN 9 | SKIP 15 | PASS 27 ]
> 
> 
> proc.time()
   user  system elapsed 
 13.682   0.465  14.131