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clustra

Clustering Longitudinal Trajectories

v0.2.1 · Jan 10, 2024 · BSD 2-clause License + file LICENSE
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Description

Clusters longitudinal trajectories over time (can be unequally spaced, unequal length time series and/or partially overlapping series) on a common time axis. Performs k-means clustering on a single continuous variable measured over time, where each mean is defined by a thin plate spline fit to all points in a cluster. Distance is MSE across trajectory points to cluster spline. Provides graphs of derived cluster splines, silhouette plots, and Adjusted Rand Index evaluations of the number of clusters. Scales well to large data with multicore parallelism available to speed computation.

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re-building of vignette outputs

              
Error(s) in re-building vignettes:
--- re-building ‘clustra_bp_vignette.Rmd’ using rmarkdown

 *** caught segfault ***
address 0x110, cause 'invalid permissions'

 *** caught segfault ***
address 0x110, cause 'invalid permissions'

Traceback:
 1: Predict.matrix.tprs.smooth(object, dk$data)

Traceback:
 1: Predict.matrix.tprs.smooth(object, dk$data)
 2:  2: Predict.matrix(object, dk$data)
 3: Predict.matrix3(object, data)
 4: PredictMat(object$smooth[[i]], dk$mf, n = dk$nr[termk])
 5: predict.bamd(object, newdata, type, se.fit, terms, exclude, block.size,     newdata.guaranteed, na.action, n.threads, gc.level = gc.level,     ...)
 6: Predict.matrix(object, dk$data)
 3: Predict.matrix3(object, data)mgcv::predict.bam(object = tps, newdata = newdata, type = "response",     newdata.guaranteed = TRUE)
 7: as.vector(mgcv::predict.bam(object = tps, newdata = newdata,     type = "response", newdata.guaranteed = TRUE))
 8: FUN(X[[i]], ...)
 9: 
 4: PredictMat(object$smooth[[i]], dk$mf, n = dk$nr[termk])
lapply(X = S, FUN = FUN, ...)
10: doTryCatch(return(expr), name, parentenv, handler)
11: tryCatchOne(expr, names, parentenv, handlers[[1L]])
12: tryCatchList(expr, classes, parentenv, handlers)
 5: predict.bamd(object, newdata, type, se.fit, terms, exclude, block.size,     newdata.guaranteed, na.action, n.threads, gc.level = gc.level,     ...)13: tryCatch(expr, error = function(e) {    call <- conditionCall(e)    if (!is.null(call)) {
 6: mgcv::predict.bam(object = tps, newdata = newdata, type = "response",     newdata.guaranteed = TRUE)        if (identical(call[[1L]], quote(doTryCatch)))             call <- sys.call(-4L)        dcall <- deparse(call, nlines = 1L)        prefix <- paste("Error in", dcall, ": ")        LONG <- 75L        sm <- strsplit(conditionMessage(e), "\n")[[1L]]        w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")        if (is.na(w))             w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],                 type = "b")        if (w > LONG) 
 7: as.vector(mgcv::predict.bam(object = tps, newdata = newdata,     type = "response", newdata.guaranteed = TRUE))
 8: FUN(X[[i]], ...)
 9: lapply(X = S, FUN = FUN, ...)
            prefix <- paste0(prefix, "\n  ")    }    else prefix <- "Error : "    msg <- paste0(prefix, conditionMessage(e), "\n")    .Internal(seterrmessage(msg[1L]))    if (!silent && isTRUE(getOption("show.error.messages"))) {        cat(msg, file = outFile)        .Internal(printDeferredWarnings())    }    invisible(structure(msg, class = "try-error", condition = e))})
14: 10: doTryCatch(return(expr), name, parentenv, handler)
11: tryCatchOne(expr, names, parentenv, handlers[[1L]])
12: tryCatchList(expr, classes, parentenv, handlers)
try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
15: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
16: FUN(X[[i]], ...)
17: 13: tryCatch(expr, error = function(e) {lapply(seq_len(cores), inner.do)
    call <- conditionCall(e)    if (!is.null(call)) {        if (identical(call[[1L]], quote(doTryCatch)))             call <- sys.call(-4L)        dcall <- deparse(call, nlines = 1L)        prefix <- paste("Error in", dcall, ": ")        LONG <- 75L        sm <- strsplit(conditionMessage(e), "\n")[[1L]]        w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")        if (is.na(w))             w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], 18: parallel::mclapply(tps, pred_g, newdata = newdata, mc.cores = mccores)
19: trajectories(data, k, group, maxdf, conv, mccores, verbose = verbose,     ...)
20: clustra(data, k = 5, maxdf = 30, conv = c(20, 0.5), mccores = mc,     verbose = TRUE)
                type = "b")        if (w > LONG)             prefix <- paste0(prefix, "\n  ")    }    else prefix <- "Error : "    msg <- paste0(prefix, conditionMessage(e), "\n")    .Internal(seterrmessage(msg[1L]))    if (!silent && isTRUE(getOption("show.error.messages"))) {        cat(msg, file = outFile)        .Internal(printDeferredWarnings())    }21: eval(expr, envir)
22: eval(expr, envir)
23: withVisible(eval(expr, envir))
24: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) {    watcher$capture_plot_and_output()    if (on_message$capture) {        watcher$push(cnd)    }    if (on_message$silence) {        invokeRestart("muffleMessage")    }}, warning = function (cnd) {    if (getOption("warn") >= 2 || getOption("warn") < 0) {    invisible(structure(msg, class = "try-error", condition = e))})
14:         return()    }    watcher$capture_plot_and_output()    if (on_warning$capture) {        cnd <- sanitize_call(cnd)        watcher$push(cnd)    }    if (on_warning$silence) {        invokeRestart("muffleWarning")    }}, error = function (cnd) {try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
15: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
16:     watcher$capture_plot_and_output()    cnd <- sanitize_call(cnd)    watcher$push(cnd)FUN(X[[i]], ...)
17:     switch(on_error, continue = invokeRestart("eval_continue"),         stop = invokeRestart("eval_stop"), error = NULL)})lapply(seq_len(cores), inner.do)
18: 
25: eval(call)parallel::mclapply(tps, pred_g, newdata = newdata, mc.cores = mccores)
19: 
26: eval(call)trajectories(data, k, group, maxdf, conv, mccores, verbose = verbose,     ...)
20: clustra(data, k = 5, maxdf = 30, conv = c(20, 0.5), mccores = mc,     verbose = TRUE)
27: with_handlers({    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)    }    TRUE
21: eval(expr, envir)}, handlers)
28: 
22: eval(expr, envir)doWithOneRestart(return(expr), restart)
29: 
23: withVisible(eval(expr, envir))withOneRestart(expr, restarts[[1L]])
30: 
24: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) {    watcher$capture_plot_and_output()withRestartList(expr, restarts[-nr])
31:     if (on_message$capture) {        watcher$push(cnd)    }doWithOneRestart(return(expr), restart)
32:     if (on_message$silence) {        invokeRestart("muffleMessage")    }withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
33: }, warning = function (cnd) {    if (getOption("warn") >= 2 || getOption("warn") < 0) {        return()    }    watcher$capture_plot_and_output()withRestartList(expr, restarts)
34:     if (on_warning$capture) {        cnd <- sanitize_call(cnd)        watcher$push(cnd)withRestarts(with_handlers({    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)    }    }    if (on_warning$silence) {        invokeRestart("muffleWarning")    TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
    }}, error = function (cnd) {    watcher$capture_plot_and_output()    cnd <- sanitize_call(cnd)    watcher$push(cnd)35: evaluate::evaluate(...)
36: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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$include)             0L    switch(on_error, continue = invokeRestart("eval_continue"),         stop = invokeRestart("eval_stop"), error = NULL)})        else 2L    }, output_handler = knit_handlers(options$render, options))

25: eval(call)37: in_dir(input_dir(), expr)

26: eval(call)38: 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) 
27: with_handlers({    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)    }    TRUE            0L        else 2L    }, output_handler = knit_handlers(options$render, options)))
39: eng_r(options)
40: block_exec(params)
41: }, handlers)
28: doWithOneRestart(return(expr), restart)
29: call_block(x)
42: process_group(group)
43: withOneRestart(expr, restarts[[1L]])
30: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        if (progress && is.function(pb$interrupt)) withRestartList(expr, restarts[-nr])
31: doWithOneRestart(return(expr), restart)
32:             pb$interrupt()        if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)    })
44: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
33: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        if (progress && is.function(pb$interrupt)) withRestartList(expr, restarts)
34:             pb$interrupt()        if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)withRestarts(with_handlers({    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)    }    }), list(rlang_trace_top_env = knit_global()))
45:     TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        if (progress && is.function(pb$interrupt)) 35: evaluate::evaluate(...)
            pb$interrupt()        if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)36: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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$include)             0L    }), list(rlang_trace_top_env = knit_global())), function(loc) {    setwd(wd)    write_utf8(res, output %n% stdout())        else 2L    }, output_handler = knit_handlers(options$render, options))
    paste0("\nQuitting from ", loc, if (!is.null(error))         paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)37: in_dir(input_dir(), expr)

46: process_file(text, output)38: 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) 
47: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)            0L        else 2L    }, output_handler = knit_handlers(options$render, options)))
48: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), 
39: eng_r(options)    output_dir = getwd(), ...)
49: 
40: block_exec(params)vweave_rmarkdown(...)
50: 
41: call_block(x)
42: process_group(group)engine$weave(file, quiet = quiet, encoding = enc)
51: doTryCatch(return(expr), name, parentenv, handler)
52: 
43: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        if (progress && is.function(pb$interrupt))             pb$interrupt()tryCatchOne(expr, names, parentenv, handlers[[1L]])
53:         if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)    })tryCatchList(expr, classes, parentenv, handlers)
54: 
44: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), tryCatch({    engine$weave(file, quiet = quiet, encoding = enc)    setwd(startdir)    output <- find_vignette_product(name, by = "weave", engine = engine)    if (!have.makefile && vignette_is_tex(output)) {        texi2pdf(file = output, clean = FALSE, quiet = quiet)    error = function(e) {        if (progress && is.function(pb$interrupt))             pb$interrupt()        output <- find_vignette_product(name, by = "texi2pdf",             engine = engine)    }}, error = function(e) {    OK <<- FALSE    message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",         file, conditionMessage(e)))})
        if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)    }), list(rlang_trace_top_env = knit_global()))
45: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        if (progress && is.function(pb$interrupt))             pb$interrupt()55: tools:::.buildOneVignette("clustra_bp_vignette.Rmd", "/Volumes/Builds/packages/sonoma-arm64/results/4.6/clustra.Rcheck/vign_test/clustra",     TRUE, FALSE, "clustra_bp_vignette", "UTF-8", "/Volumes/Temp/tmp/RtmphL3YLn/file1a353971c7f0.rds")
An irrecoverable exception occurred. R is aborting now ...
        if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)    }), list(rlang_trace_top_env = knit_global())), function(loc) {    setwd(wd)    write_utf8(res, output %n% stdout())    paste0("\nQuitting from ", loc, if (!is.null(error))         paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
46: process_file(text, output)
47: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
48: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),     output_dir = getwd(), ...)
49: vweave_rmarkdown(...)
50: engine$weave(file, quiet = quiet, encoding = enc)
51: doTryCatch(return(expr), name, parentenv, handler)
52: tryCatchOne(expr, names, parentenv, handlers[[1L]])
53: tryCatchList(expr, classes, parentenv, handlers)
54: 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)    }}, error = function(e) {    OK <<- FALSE    message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",         file, conditionMessage(e)))})
55: tools:::.buildOneVignette("clustra_bp_vignette.Rmd", "/Volumes/Builds/packages/sonoma-arm64/results/4.6/clustra.Rcheck/vign_test/clustra",     TRUE, FALSE, "clustra_bp_vignette", "UTF-8", "/Volumes/Temp/tmp/RtmphL3YLn/file1a353971c7f0.rds")
An irrecoverable exception occurred. R is aborting now ...

Quitting from clustra_bp_vignette.Rmd:71-74 [run5]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `apply()`:
! dim(X) must have a positive length
---
Backtrace:
    ▆
 1. └─clustra::clustra(...)
 2.   └─clustra::trajectories(...)
 3.     └─base::apply(loss, 1, which.min)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'clustra_bp_vignette.Rmd' failed with diagnostics:
dim(X) must have a positive length
--- failed re-building ‘clustra_bp_vignette.Rmd’

--- re-building ‘clustra_vignette.Rmd’ using rmarkdown

 *** caught segfault ***
address 0x110, cause 'invalid permissions'

 *** caught segfault ***
address 0x110, cause 'invalid permissions'

Traceback:
 1: predict.gam(object, newdata = newdata, type = type, se.fit = se.fit,     terms = terms, exclude = exclude, block.size = block.size,     newdata.guaranteed = newdata.guaranteed, na.action = na.action,     ...)
 2: mgcv::predict.bam(object = tps, newdata = newdata, type = "response",     newdata.guaranteed = TRUE)
 3: as.vector(mgcv::predict.bam(object = tps, newdata = newdata,     type = "response", newdata.guaranteed = TRUE))
 4: FUN(X[[i]], ...)
 5: lapply(X = S, FUN = FUN, ...)
 6: doTryCatch(return(expr), name, parentenv, handler)
 7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 8: tryCatchList(expr, classes, parentenv, handlers)
 9: tryCatch(expr, error = function(e) {    call <- conditionCall(e)    if (!is.null(call)) {        if (identical(call[[1L]], quote(doTryCatch)))             call <- sys.call(-4L)        dcall <- deparse(call, nlines = 1L)        prefix <- paste("Error in", dcall, ": ")        LONG <- 75L        sm <- strsplit(conditionMessage(e), "\n")[[1L]]        w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")        if (is.na(w))             w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],                 type = "b")        if (w > LONG)             prefix <- paste0(prefix, "\n  ")    }    else prefix <- "Error : "    msg <- paste0(prefix, conditionMessage(e), "\n")    .Internal(seterrmessage(msg[1L]))    if (!silent && isTRUE(getOption("show.error.messages"))) {        cat(msg, file = outFile)        .Internal(printDeferredWarnings())    }    invisible(structure(msg, class = "try-error", condition = e))})
10: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
11: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
12: FUN(X[[i]], ...)
13: lapply(seq_len(cores), inner.do)
14: parallel::mclapply(sfit, pred_g, newdata = newdata, mc.cores = mccores)
15: start_groups(k, data, starts, maxdf, conv, mccores, verbose = verbose)
16: clustra(data, k = 40, starts = "distant", maxdf = 10, conv = c(10,     0), mccores = mc, verbose = TRUE)
17: eval(expr, envir)
18: eval(expr, envir)
19: withVisible(eval(expr, envir))
20: withCallingHandlers(code, error = function (e) rlang::entrace(e), 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)})
21: eval(call)
22: eval(call)
23: with_handlers({    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)    }    TRUE}, handlers)
24: doWithOneRestart(return(expr), restart)
25: withOneRestart(expr, restarts[[1L]])
26: withRestartList(expr, restarts[-nr])
27: doWithOneRestart(return(expr), restart)
28: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
29: withRestartList(expr, restarts)
30: withRestarts(with_handlers({    for (expr in tle$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)
31: evaluate::evaluate(...)
32: 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$render, options))
33: in_dir(input_dir(), expr)
34: in_input_dir(evaluate(code, envir = env, new_device = FALSE,     keep_warning = if (is.numeric(options$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)))
35: eng_r(options)
36: block_exec(params)
37: call_block(x)
38: process_group(group)
39: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        if (progress && is.function(pb$interrupt))             pb$interrupt()        if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)    })
40: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        if (progress && is.function(pb$interrupt))             pb$interrupt()        if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)    }), list(rlang_trace_top_env = knit_global()))
41: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        if (progress && is.function(pb$interrupt))             pb$interrupt()        if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)    }), list(rlang_trace_top_env = knit_global())), function(loc) {    setwd(wd)    write_utf8(res, output %n% stdout())    paste0("\nQuitting from ", loc, if (!is.null(error))         paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
42: process_file(text, output)
43: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
44: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),     output_dir = getwd(), ...)
45: vweave_rmarkdown(...)
46: engine$weave(file, quiet = quiet, encoding = enc)
47: doTryCatch(return(expr), name, parentenv, handler)
48: tryCatchOne(expr, names, parentenv, handlers[[1L]])
49: tryCatchList(expr, classes, parentenv, handlers)
50: tryCatch({    engine$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)    }}, error = function(e) {    OK <<- FALSE    message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",         file, conditionMessage(e)))})
51: tools:::.buildOneVignette("clustra_vignette.Rmd", "/Volumes/Builds/packages/sonoma-arm64/results/4.6/clustra.Rcheck/vign_test/clustra",     TRUE, FALSE, "clustra_vignette", "UTF-8", "/Volumes/Temp/tmp/RtmphL3YLn/file1a353bbf7ea2.rds")
An irrecoverable exception occurred. R is aborting now ...

Traceback:
 1: predict.gam(object, newdata = newdata, type = type, se.fit = se.fit,     terms = terms, exclude = exclude, block.size = block.size,     newdata.guaranteed = newdata.guaranteed, na.action = na.action,     ...)
 2: mgcv::predict.bam(object = tps, newdata = newdata, type = "response",     newdata.guaranteed = TRUE)
 3: as.vector(mgcv::predict.bam(object = tps, newdata = newdata,     type = "response", newdata.guaranteed = TRUE))
 4: FUN(X[[i]], ...)
 5: lapply(X = S, FUN = FUN, ...)
 6: doTryCatch(return(expr), name, parentenv, handler)
 7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 8: tryCatchList(expr, classes, parentenv, handlers)
 9: tryCatch(expr, error = function(e) {    call <- conditionCall(e)    if (!is.null(call)) {        if (identical(call[[1L]], quote(doTryCatch)))             call <- sys.call(-4L)        dcall <- deparse(call, nlines = 1L)        prefix <- paste("Error in", dcall, ": ")        LONG <- 75L        sm <- strsplit(conditionMessage(e), "\n")[[1L]]        w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")        if (is.na(w))             w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],                 type = "b")        if (w > LONG)             prefix <- paste0(prefix, "\n  ")    }    else prefix <- "Error : "    msg <- paste0(prefix, conditionMessage(e), "\n")    .Internal(seterrmessage(msg[1L]))    if (!silent && isTRUE(getOption("show.error.messages"))) {        cat(msg, file = outFile)        .Internal(printDeferredWarnings())    }    invisible(structure(msg, class = "try-error", condition = e))})
10: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
11: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
12: FUN(X[[i]], ...)
13: lapply(seq_len(cores), inner.do)
14: parallel::mclapply(sfit, pred_g, newdata = newdata, mc.cores = mccores)
15: start_groups(k, data, starts, maxdf, conv, mccores, verbose = verbose)
16: clustra(data, k = 40, starts = "distant", maxdf = 10, conv = c(10,     0), mccores = mc, verbose = TRUE)
17: eval(expr, envir)
18: eval(expr, envir)
19: withVisible(eval(expr, envir))
20: withCallingHandlers(code, error = function (e) rlang::entrace(e), 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)})
21: eval(call)
22: eval(call)
23: with_handlers({    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)    }    TRUE}, handlers)
24: doWithOneRestart(return(expr), restart)
25: withOneRestart(expr, restarts[[1L]])
26: withRestartList(expr, restarts[-nr])
27: doWithOneRestart(return(expr), restart)
28: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
29: withRestartList(expr, restarts)
30: withRestarts(with_handlers({    for (expr in tle$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)
31: evaluate::evaluate(...)
32: 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$render, options))
33: in_dir(input_dir(), expr)
34: in_input_dir(evaluate(code, envir = env, new_device = FALSE,     keep_warning = if (is.numeric(options$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)))
35: eng_r(options)
36: block_exec(params)
37: call_block(x)
38: process_group(group)
39: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        if (progress && is.function(pb$interrupt))             pb$interrupt()        if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)    })
40: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        if (progress && is.function(pb$interrupt))             pb$interrupt()        if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)    }), list(rlang_trace_top_env = knit_global()))
41: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        if (progress && is.function(pb$interrupt))             pb$interrupt()        if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)    }), list(rlang_trace_top_env = knit_global())), function(loc) {    setwd(wd)    write_utf8(res, output %n% stdout())    paste0("\nQuitting from ", loc, if (!is.null(error))         paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
42: process_file(text, output)
43: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
44: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),     output_dir = getwd(), ...)
45: vweave_rmarkdown(...)
46: engine$weave(file, quiet = quiet, encoding = enc)
47: doTryCatch(return(expr), name, parentenv, handler)
48: tryCatchOne(expr, names, parentenv, handlers[[1L]])
49: tryCatchList(expr, classes, parentenv, handlers)
50: tryCatch({    engine$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)    }}, error = function(e) {    OK <<- FALSE    message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",         file, conditionMessage(e)))})
51: tools:::.buildOneVignette("clustra_vignette.Rmd", "/Volumes/Builds/packages/sonoma-arm64/results/4.6/clustra.Rcheck/vign_test/clustra",     TRUE, FALSE, "clustra_vignette", "UTF-8", "/Volumes/Temp/tmp/RtmphL3YLn/file1a353bbf7ea2.rds")
An irrecoverable exception occurred. R is aborting now ...

Quitting from clustra_vignette.Rmd:129-139 [hclust_d]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `apply()`:
! dim(X) must have a positive length
---
Backtrace:
    ▆
 1. └─clustra::clustra(...)
 2.   └─clustra:::start_groups(...)
 3.     └─base::apply(loss, 1, which.min)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'clustra_vignette.Rmd' failed with diagnostics:
dim(X) must have a positive length
--- failed re-building ‘clustra_vignette.Rmd’

SUMMARY: processing the following files failed:
  ‘clustra_bp_vignette.Rmd’ ‘clustra_vignette.Rmd’

Error: Vignette re-building failed.
Execution halted

            

            

              

                OK
                r-devel-windows-x86_64
              

              
*

              

            

            

              

                OK
                r-oldrel-macos-arm64
              

              
*

              

            

            

              

                OK
                r-oldrel-macos-x86_64
              

              
*

              

            

            

              

                OK
                r-oldrel-windows-x86_64
              

              
*

              

            

            

              

                OK
                r-patched-linux-x86_64
              

              
*

              

            

            

              

                OK
                r-release-linux-x86_64
              

              
*

              

            

            

              

                OK
                r-release-macos-arm64
              

              
*

              

            

            

              

                OK
                r-release-macos-x86_64
              

              
*

              

            

            

              

                OK
                r-release-windows-x86_64
              

              
*

              

            

          

        

      



      

      
      

        
Check History

        

          

            
              ERROR
              
                13 OK ·                 0 NOTE ·                 0 WARNING ·                 1 ERROR ·                 0 FAILURE              
              Mar 9, 2026
            
            

              

                

                  ERROR
                  r-devel-macos-arm64
                

                
re-building of vignette outputs

                
Error(s) in re-building vignettes:
--- re-building ‘clustra_bp_vignette.Rmd’ using rmarkdown

 *** caught segfault ***
address 0x110, cause 'invalid permissions'

 *** caught segfault ***
address 0x110, cause 'invalid permissions'

Traceback:
 1: Predict.matrix.tprs.smooth(object, dk$data)

Traceback:
 1: Predict.matrix.tprs.smooth(object, dk$data)
 2:  2: Predict.matrix(object, dk$data)
 3: Predict.matrix3(object, data)
 4: PredictMat(object$smooth[[i]], dk$mf, n = dk$nr[termk])
 5: predict.bam

              

            

          

        

      


      

      
      

        
Dependency Network

        

          
            

            
            
            Dependencies
            
            Reverse dependencies

            
            
            
            

            

            
            
              
              data.table
            
            
              
              mgcv
            
            
              
              MixSim
            

            

            
            
            clustra
          
        

      


      
      

        
Version History

        

          

            new
            0.2.1
            Mar 9, 2026