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###
### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data APL
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* checking for file ‘APL/DESCRIPTION’ ... OK
* preparing ‘APL’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ...sh: line 1: 21848 Abort trap: 6           '/Library/Frameworks/R.framework/Resources/bin/Rscript' --vanilla --default-packages= -e "tools::buildVignettes(dir = '.', tangle = TRUE)" > '/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpzms4ct/xshell4f249f2c0cb' 2>&1
 ERROR
--- re-building ‘APL.Rmd’ using rmarkdown
2024-10-09 15:47:25.452 R[21848:59342168] XType: Using static font registry.

 *** caught segfault ***
address 0x540, cause 'invalid permissions'

Traceback:
 1: py_call_impl(callable, call_args$unnamed, call_args$named)
 2: svd_torch(pear_res)
 3: fun(...)
 4: basilisk::basiliskRun(proc, function(pear_res) {    reticulate::source_python(system.file("python/python_svd.py",         package = "APL"))    SVD <- svd_torch(pear_res)    return(SVD)}, pear_res = S)
 5: run_cacomp(obj = obj, coords = coords, princ_coords = princ_coords,     python = python, dims = dims, top = top, inertia = inertia,     rm_zeros = rm_zeros, residuals = residuals, cutoff = cutoff,     clip = clip, ...)
 6: cacomp(obj = obj, coords = TRUE, top = top, princ_coords = 3,     dims = dims, python = python, residuals = "pearson", clip = clip)
 7: cacomp(obj = obj, coords = TRUE, top = top, princ_coords = 3,     dims = dims, python = python, residuals = "pearson", clip = clip)
 8: run_APL(obj = mat, caobj = caobj, dims = dims, group = group,     mark_rows = mark_rows, mark_cols = mark_cols, nrow = nrow,     top = top, clip = clip, score = score, score_method = score_method,     reps = reps, python = python, row_labs = row_labs, col_labs = col_labs,     type = type, show_cols = show_cols, show_rows = show_rows,     score_cutoff = score_cutoff, score_color = score_color, pd_method = pd_method,     pd_reps = pd_reps, pd_use = pd_use)
 9: .local(obj, group, caobj, dims, nrow, top, clip, score, score_method,     mark_rows, mark_cols, reps, python, row_labs, col_labs, type,     show_cols, show_rows, score_cutoff, score_color, pd_method,     pd_reps, pd_use, ...)
10: runAPL(darmanis, assay = "logcounts", top = 5000, group = which(darmanis$cell.type ==     "oligodendrocytes"), type = "ggplot", python = TRUE)
11: runAPL(darmanis, assay = "logcounts", top = 5000, group = which(darmanis$cell.type ==     "oligodendrocytes"), type = "ggplot", python = TRUE)
12: eval(expr, envir)
13: eval(expr, envir)
14: withVisible(eval(expr, envir))
15: 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 = invokeRestart("eval_error",             cnd))})
16: eval(call)
17: eval(call)
18: with_handlers({    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)    }    TRUE}, handlers)
19: doWithOneRestart(return(expr), restart)
20: withOneRestart(expr, restarts[[1L]])
21: withRestartList(expr, restarts[-nr])
22: doWithOneRestart(return(expr), restart)
23: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
24: withRestartList(expr, restarts[-nr])
25: doWithOneRestart(return(expr), restart)
26: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
27: withRestartList(expr, restarts)
28: withRestarts(with_handlers({    for (expr in tle$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,     eval_error = function(cnd) signalCondition(cnd))
29: evaluate::evaluate(...)
30: 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$render, options))
31: in_dir(input_dir(), expr)
32: in_input_dir(evaluate(code, envir = env, new_device = FALSE,     keep_warning = if (is.numeric(options$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)))
33: eng_r(options)
34: block_exec(params)
35: call_block(x)
36: process_group(group)
37: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e))
38: 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)
39: process_file(text, output)
40: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
41: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),     output_dir = getwd(), ...)
42: vweave_rmarkdown(...)
43: engine$weave(file, quiet = quiet, encoding = enc)
44: doTryCatch(return(expr), name, parentenv, handler)
45: tryCatchOne(expr, names, parentenv, handlers[[1L]])
46: tryCatchList(expr, classes, parentenv, handlers)
47: tryCatch({    engine$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)))})
48: tools::buildVignettes(dir = ".", tangle = TRUE)
An irrecoverable exception occurred. R is aborting now ...
OMP: Error #179: Function pthread_mutex_init failed:
OMP: System error #22: Invalid argument