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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data mina
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* checking for file ‘mina/DESCRIPTION’ ... OK
* preparing ‘mina’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘mina.Rmd’ using rmarkdown
norm_tab_method_list           package:mina            R Documentation

_L_i_s_t _o_f _n_o_r_m_a_l_i_z_a_t_i_o_n _m_e_t_h_o_d_s _s_u_p_p_o_r_t_e_d _i_n '_n_o_r_m__t_a_b'

_D_e_s_c_r_i_p_t_i_o_n:

     Normalization methods should be specified by exact string match.

_U_s_a_g_e:

     norm_tab_method_list
     
_F_o_r_m_a_t:

     A list of character vectors.

     'raref' By downsampling all samples to specific depth.

     'total' Devided by the total read of each sample.

_S_e_e _A_l_s_o:

     'norm_tab'

_E_x_a_m_p_l_e_s:

     ? norm_tab_method_list
     

com_dis_list               package:mina                R Documentation

_L_i_s_t _o_f _d_i_s_s_i_m_i_l_a_r_i_t_y / _d_i_s_t_a_n_c_e _s_u_p_p_o_r_t_e_d _i_n '_c_o_m__d_i_s'. _D_i_s_s_i_m_i_l_a_r_i_t_y
/ _d_i_s_t_a_n_c_e _s_h_o_u_l_d _b_e _s_p_e_c_i_f_i_e_d _b_y _e_x_a_c_t _s_t_r_i_n_g _m_a_t_c_h.

_D_e_s_c_r_i_p_t_i_o_n:

     List of dissimilarity / distance supported in 'com_dis'.
     Dissimilarity / distance should be specified by exact string
     match.

_U_s_a_g_e:

     com_dis_list
     
_F_o_r_m_a_t:

     A list of character vectors indicate the dissimilarity / distance
     method used.

     'tina' TINA from Schmidt_et_al_2016

     'Jaccard' Jaccard defined by 'vegdist'

     weighted Dissimilarity / distance method for weighted matrix:

     'bhjattacharyya' from 'parDist'

     'canberra' from 'parDist'

     'bray' from 'parDist'

     'chord' from 'parDist'

     'divergence' from 'parDist'

     'euclidean' from 'parDist'

     'fJaccard' from 'parDist'

     'geodesic' from 'parDist'

     'hellinger' from 'parDist'

     'kullback' from 'parDist'

     'manhattan' from 'parDist'

     'maximum' from 'parDist'

     'minkowski' from 'parDist'

     'podani' from 'parDist'

     'soergel' from 'parDist'

     'wave' from 'parDist'

     'whittaker' from 'parDist'

     unweighted Dissimilarity / Distance for unweighted matrix:

     'binary' from 'parDist'

     'braun-blanquet' from 'parDist'

     'consine' from 'parDist'

     'dice' from 'parDist'

     'fager' from 'parDist'

     'faith' from 'parDist'

     'hamman' from 'parDist'

     'hamming' from 'parDist'

     'kulczynski1' from 'parDist'

     'kulczynski2' from 'parDist'

     'michael' from 'parDist'

     'mountford' from 'parDist'

     'mozley' from 'parDist'

     'ochiai' from 'parDist'

     'phi' from 'parDist'

     'russel' from 'parDist'

     'simple matching' from 'parDist'

     'simpson' from 'parDist'

     'stiles' from 'parDist'

     'tanimoto' from 'parDist'

     'yule' from 'parDist'

     'yule2' from 'parDist'

_E_x_a_m_p_l_e_s:

     ? com_dis_list
     


 *** caught bus error ***
address 0x11, cause 'invalid alignment'

Traceback:
 1: parDist(x, method = method)
 2: as.matrix(parDist(x, method = method))
 3: .local(x, method, ...)
 4: com_dis(norm(x), method = method, threads = threads, nblocks = nblocks)
 5: com_dis(norm(x), method = method, threads = threads, nblocks = nblocks)
 6: .local(x, method, ...)
 7: com_dis(maize, method = "bray")
 8: com_dis(maize, method = "bray")
 9: eval(expr, envir)
10: eval(expr, envir)
11: withVisible(eval(expr, envir))
12: withCallingHandlers(code, message = function (cnd) {    watcher$capture_plot_and_output()    if (on_message$capture) {        watcher$push(cnd)    }    if (on_message$silence) {        invokeRestart("muffleMessage")    }}, warning = function (cnd) {    if (getOption("warn") >= 2 || getOption("warn") < 0) {        return()    }    watcher$capture_plot_and_output()    if (on_warning$capture) {        cnd <- sanitize_call(cnd)        watcher$push(cnd)    }    if (on_warning$silence) {        invokeRestart("muffleWarning")    }}, error = function (cnd) {    watcher$capture_plot_and_output()    cnd <- sanitize_call(cnd)    watcher$push(cnd)    switch(on_error, continue = invokeRestart("eval_continue"),         stop = invokeRestart("eval_stop"), error = NULL)})
13: eval(call)
14: eval(call)
15: with_handlers({    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)    }    TRUE}, handlers)
16: doWithOneRestart(return(expr), restart)
17: withOneRestart(expr, restarts[[1L]])
18: withRestartList(expr, restarts[-nr])
19: doWithOneRestart(return(expr), restart)
20: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
21: withRestartList(expr, restarts)
22: withRestarts(with_handlers({    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)    }    TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
23: evaluate::evaluate(...)
24: 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$render, options))
25: in_dir(input_dir(), expr)
26: in_input_dir(evaluate(code, envir = env, new_device = FALSE,     keep_warning = if (is.numeric(options$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)))
27: eng_r(options)
28: block_exec(params)
29: call_block(x)
30: process_group(group)
31: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e))
32: xfun:::handle_error(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e)),     function(loc) {        setwd(wd)        write_utf8(res, output %n% stdout())        paste0("\nQuitting from lines ", loc)    }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
33: process_file(text, output)
34: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
35: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),     output_dir = getwd(), ...)
36: vweave_rmarkdown(...)
37: engine$weave(file, quiet = quiet, encoding = enc)
38: doTryCatch(return(expr), name, parentenv, handler)
39: tryCatchOne(expr, names, parentenv, handlers[[1L]])
40: tryCatchList(expr, classes, parentenv, handlers)
41: tryCatch({    engine$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)))})
42: tools::buildVignettes(dir = ".", tangle = TRUE)
An irrecoverable exception occurred. R is aborting now ...