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SOHPIE

Statistical Approach via Pseudo-Value Information and Estimation

v1.0.6 · Oct 23, 2023 · GPL-3
CRAN GitHub Mirror

Description

'SOHPIE' (pronounced as SOFIE) is a novel pseudo-value regression approach for differential co-abundance network analysis of microbiome data, which can include additional clinical covariate in the model. The full methodological details can be found in Ahn S and Datta S (2023) <arXiv:2303.13702v1>.

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r-devel-linux-x86_64-debian-clang NOTE
r-devel-linux-x86_64-debian-gcc NOTE
r-devel-linux-x86_64-fedora-clang OK
r-devel-linux-x86_64-fedora-gcc OK
r-devel-macos-arm64 ERROR
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
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NOTE r-devel-linux-x86_64-debian-clang

CRAN incoming feasibility

Maintainer: ‘Seungjun Ahn <seungjun.ahn@mountsinai.org>’

The Description field contains
  <arXiv:2303.13702v1>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
NOTE r-devel-linux-x86_64-debian-gcc

CRAN incoming feasibility

Maintainer: ‘Seungjun Ahn <seungjun.ahn@mountsinai.org>’

The Description field contains
  <arXiv:2303.13702v1>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
OK r-devel-linux-x86_64-fedora-clang

*


            

            

              

                OK
                r-devel-linux-x86_64-fedora-gcc
              

              
*

              

            

            

              

                ERROR
                r-devel-macos-arm64
              

              
re-building of vignette outputs

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

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

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

Traceback:
 1: solve.default(Lmat[cp, cp], rowSums(T02[cp, cp]))
 2: solve(Lmat[cp, cp], rowSums(T02[cp, cp]))
 3: SparCC.frac(x = y, kmax = kmax, alpha = alpha, Vmin = Vmin)
 4: sparcc(OTUtab[-j, ])
 5: FUN(X[[i]], ...)
 6: lapply(X = S, FUN = FUN, ...)
 7: doTryCatch(return(expr), name, parentenv, handler)
 8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 9: tryCatchList(expr, classes, parentenv, handlers)
10: 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))})
11: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
12: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
13: FUN(X[[i]], ...)

Traceback:
 1: solve.default(Lmat[cp, cp], rowSums(T02[cp, cp]))
 2: solve(Lmat[cp, cp], rowSums(T02[cp, cp]))
 3: SparCC.frac(x = y, kmax = kmax, alpha = alpha, Vmin = Vmin)14: lapply(seq_len(cores), inner.do)
15: mclapply(group, function(j) sparcc(OTUtab[-j, ])$cor.w)
16: asso_mat(OTUdat = OTUtab, group = newindex_A1)
17: eval(expr, envir)
18: eval(expr, envir)
19: withVisible(eval(expr, envir))
20: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) {    watcher$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"), 
 4: sparcc(OTUtab[-j, ])
 5: FUN(X[[i]], ...)
 6: lapply(X = S, FUN = FUN, ...)
 7: doTryCatch(return(expr), name, parentenv, handler)
 8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 9: tryCatchList(expr, classes, parentenv, handlers)
10:         stop = invokeRestart("eval_stop"), error = NULL)})
21: 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))eval(call)
22: eval(call)})
11: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
12: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))

23: with_handlers({    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)    }    TRUE}, handlers)
24: doWithOneRestart(return(expr), restart)
25: 13: FUN(X[[i]], ...)
withOneRestart(expr, restarts[[1L]])
26: 14: lapply(seq_len(cores), inner.do)
withRestartList(expr, restarts[-nr])
27: 15: mclapply(group, function(j) sparcc(OTUtab[-j, ])$cor.w)
doWithOneRestart(return(expr), restart)
28: 16: asso_mat(OTUdat = OTUtab, group = newindex_A1)
withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
29: 17: eval(expr, envir)
withRestartList(expr, restarts)
30: 18: eval(expr, envir)
withRestarts(with_handlers({    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)    }    TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
31: evaluate::evaluate(...)
19: withVisible(eval(expr, envir))
32: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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))
20: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) 33: in_dir(input_dir(), expr)
{    watcher$capture_plot_and_output()    if (on_message$capture) {        watcher$push(cnd)    }    if (on_message$silence) {        invokeRestart("muffleMessage")    }}, warning = function (cnd) 34: in_input_dir(evaluate(code, envir = env, new_device = FALSE,     keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, {    if (getOption("warn") >= 2 || getOption("warn") < 0) {        return()    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$render, options)))    }    watcher$capture_plot_and_output()    if (on_warning$capture) {
35: eng_r(options)
36: block_exec(params)        cnd <- sanitize_call(cnd)        watcher$push(cnd)    }    if (on_warning$silence) {        invokeRestart("muffleWarning")    }
37: call_block(x)
38: process_group(group)
39: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        if (progress && is.function(pb$interrupt))             pb$interrupt()        if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)    })
40: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), }, error = function (cnd) {    watcher$capture_plot_and_output()    error = function(e) {        if (progress && is.function(pb$interrupt))             pb$interrupt()    cnd <- sanitize_call(cnd)    watcher$push(cnd)    switch(on_error, continue = invokeRestart("eval_continue"),         if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)    }), list(rlang_trace_top_env = knit_global()))        stop = invokeRestart("eval_stop"), error = NULL)})

41: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 21: eval(call)
    error = function(e) {        if (progress && is.function(pb$interrupt))             pb$interrupt()22: eval(call)
        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)) 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)        paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
42: process_file(text, output)

25: withOneRestart(expr, restarts[[1L]])43: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)

26: withRestartList(expr, restarts[-nr])44: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),     output_dir = getwd(), ...)
27: doWithOneRestart(return(expr), restart)
45: vweave_rmarkdown(...)
28: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
46: engine$weave(file, quiet = quiet, encoding = enc)
47: doTryCatch(return(expr), name, parentenv, handler)
48: tryCatchOne(expr, names, parentenv, handlers[[1L]])
29: withRestartList(expr, restarts)
49: tryCatchList(expr, classes, parentenv, handlers)
30: withRestarts(with_handlers({    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()
50: tryCatch({        watcher$print_value(ev$value, ev$visible, envir)    }    TRUE    engine$weave(file, quiet = quiet, encoding = enc)    setwd(startdir)    output <- find_vignette_product(name, by = "weave", engine = engine)    if (!have.makefile && vignette_is_tex(output)) {        texi2pdf(file = output, clean = FALSE, quiet = quiet)        output <- find_vignette_product(name, by = "texi2pdf",             engine = engine)    }    outputs <- c(outputs, output)}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
31: }, error = function(e) {    thisOK <<- FALSE    fails <<- c(fails, file)evaluate::evaluate(...)
32:     message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",         file, conditionMessage(e)))})evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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$error else {
51: tools::buildVignettes(dir = "/Volumes/Builds/packages/sonoma-arm64/results/4.6/SOHPIE.Rcheck/vign_test/SOHPIE",         if (options$error && options$include)             0L        else 2L    skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpDNNoM1/file101e15acc12ee.rds")
An irrecoverable exception occurred. R is aborting now ...
    }, output_handler = knit_handlers(options$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)    }    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)))})
51: tools::buildVignettes(dir = "/Volumes/Builds/packages/sonoma-arm64/results/4.6/SOHPIE.Rcheck/vign_test/SOHPIE",     skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpDNNoM1/file101e15acc12ee.rds")
An irrecoverable exception occurred. R is aborting now ...

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

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

Traceback:
 1: solve.default(Lmat[cp, cp], rowSums(T02[cp, cp]))
 2: solve(Lmat[cp, cp], rowSums(T02[cp, cp]))
 3: SparCC.frac(x = y, kmax = kmax, alpha = alpha, Vmin = Vmin)
 4: sparcc(OTUtab[-j, ])
 5: FUN(X[[i]], ...)
 6: lapply(X = S, FUN = FUN, ...)
 7: doTryCatch(return(expr), name, parentenv, handler)
 8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 9: tryCatchList(expr, classes, parentenv, handlers)
10: 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))})
11: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
12: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
13: FUN(X[[i]], ...)
14: lapply(seq_len(cores), inner.do)
15: mclapply(group, function(j) sparcc(OTUtab[-j, ])$cor.w)
16: asso_mat(OTUdat = OTUtab, group = newindex_A6)
17: eval(expr, envir)
18: eval(expr, envir)
19: withVisible(eval(expr, envir))
20: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) {    watcher$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$interrupt()        if (is_R_CMD_build() || is_R_CMD_check()) 
Traceback:
 1: solve.default(Lmat[cp, cp], rowSums(T02[cp, cp]))
 2: solve(Lmat[cp, cp], rowSums(T02[cp, cp]))
 3: SparCC.frac(x = y, kmax = kmax, alpha = alpha, Vmin = Vmin)
 4: sparcc(OTUtab[-j, ])
            error <<- format(e)    }), list(rlang_trace_top_env = knit_global())), function(loc) {    setwd(wd)    write_utf8(res, output %n% stdout())    paste0("\nQuitting from ", loc, if (!is.null(error))         paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
42: process_file(text, output)
43: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
44: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),     output_dir = getwd(), ...)
45: vweave_rmarkdown(...)
 5: FUN(X[[i]], ...)
 6: lapply(X = S, FUN = FUN, ...)
 7: 46: engine$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)doTryCatch(return(expr), name, parentenv, handler)
 8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 9: tryCatchList(expr, classes, parentenv, handlers)    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
10: 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],     fails <<- c(fails, file)    message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",         file, conditionMessage(e)))})
51: tools::buildVignettes(dir = "/Volumes/Builds/packages/sonoma-arm64/results/4.6/SOHPIE.Rcheck/vign_test/SOHPIE",     skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpDNNoM1/file101e15acc12ee.rds")
An irrecoverable exception occurred. R is aborting now ...
                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))})
11: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
12: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
13: FUN(X[[i]], ...)
14: lapply(seq_len(cores), inner.do)
15: mclapply(group, function(j) sparcc(OTUtab[-j, ])$cor.w)
16: asso_mat(OTUdat = OTUtab, group = newindex_A6)
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)    }    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)))})
51: tools::buildVignettes(dir = "/Volumes/Builds/packages/sonoma-arm64/results/4.6/SOHPIE.Rcheck/vign_test/SOHPIE",     skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpDNNoM1/file101e15acc12ee.rds")
An irrecoverable exception occurred. R is aborting now ...

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

Traceback:
 1: solve.default(Lmat[cp, cp], rowSums(T02[cp, cp]))
 2: solve(Lmat[cp, cp], rowSums(T02[cp, cp]))
 3: SparCC.frac(x = y, kmax = kmax, alpha = alpha, Vmin = Vmin)
 4: sparcc(OTUtab[-j, ])
 5: FUN(X[[i]], ...)
 6: lapply(X = S, FUN = FUN, ...)
 7: doTryCatch(return(expr), name, parentenv, handler)
 8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 9: tryCatchList(expr, classes, parentenv, handlers)
10: 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))})
11: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
12: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
13: FUN(X[[i]], ...)
14: lapply(seq_len(cores), inner.do)
15: mclapply(group, function(j) sparcc(OTUtab[-j, ])$cor.w)
16: asso_mat(OTUdat = OTUtab, group = newindex_B1)
17: eval(expr, envir)
18: eval(expr, envir)
19: withVisible(eval(expr, envir))
20: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) {    watcher$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)    }    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)))})
51: tools::buildVignettes(dir = "/Volumes/Builds/packages/sonoma-arm64/results/4.6/SOHPIE.Rcheck/vign_test/SOHPIE",     skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpDNNoM1/file101e15acc12ee.rds")
 *** caught segfault ***
address 0x110, cause 'invalid permissions'

An irrecoverable exception occurred. R is aborting now ...

Traceback:
 1: solve.default(Lmat[cp, cp], rowSums(T02[cp, cp]))
 2: solve(Lmat[cp, cp], rowSums(T02[cp, cp]))
 3: SparCC.frac(x = y, kmax = kmax, alpha = alpha, Vmin = Vmin)
 4: sparcc(OTUtab[-j, ])
 5: FUN(X[[i]], ...)
 6: lapply(X = S, FUN = FUN, ...)
 7: doTryCatch(return(expr), name, parentenv, handler)
 8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 9: tryCatchList(expr, classes, parentenv, handlers)
10: 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))})
11: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
12: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
13: FUN(X[[i]], ...)
14: lapply(seq_len(cores), inner.do)
15: mclapply(group, function(j) sparcc(OTUtab[-j, ])$cor.w)
16: asso_mat(OTUdat = OTUtab, group = newindex_B1)
17: eval(expr, envir)
18: eval(expr, envir)
19: withVisible(eval(expr, envir))
20: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) {    watcher$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)    }    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)))})
51: tools::buildVignettes(dir = "/Volumes/Builds/packages/sonoma-arm64/results/4.6/SOHPIE.Rcheck/vign_test/SOHPIE",     skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpDNNoM1/file101e15acc12ee.rds")
An irrecoverable exception occurred. R is aborting now ...

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

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

Traceback:
 1: solve.default(Lmat[cp, cp], rowSums(T02[cp, cp]))
 2: solve(Lmat[cp, cp], rowSums(T02[cp, cp]))
 3: SparCC.frac(x = y, kmax = kmax, alpha = alpha, Vmin = Vmin)
 4: sparcc(OTUtab[-j, ])
 5: FUN(X[[i]], ...)
 6: lapply(X = S, FUN = FUN, ...)
 7: doTryCatch(return(expr), name, parentenv, handler)
 8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 9: tryCatchList(expr, classes, parentenv, handlers)
10: 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))})
11: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
12: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
13: FUN(X[[i]], ...)
14: lapply(seq_len(cores), inner.do)
15: mclapply(group, function(j) sparcc(OTUtab[-j, ])$cor.w)
16: asso_mat(OTUdat = OTUtab, group = newindex_B6)
17: eval(expr, envir)
18: eval(expr, envir)
19: withVisible(eval(expr, envir))
Traceback:
 1: solve.default(Lmat[cp, cp], rowSums(T02[cp, cp]))
 2: solve(Lmat[cp, cp], rowSums(T02[cp, cp]))
 3: SparCC.frac(x = y, kmax = kmax, alpha = alpha, Vmin = Vmin)
 4: sparcc(OTUtab[-j, ])
 5: FUN(X[[i]], ...)
 6: lapply(X = S, FUN = FUN, ...)
20: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) {    watcher$capture_plot_and_output()    if (on_message$capture) {        watcher$push(cnd)    }    if (on_message$silence) {        invokeRestart("muffleMessage")    }}, warning = function (cnd) 
 7: doTryCatch(return(expr), name, parentenv, handler)
 8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 9: tryCatchList(expr, classes, parentenv, handlers)
10: tryCatch(expr, error = function(e) {{    if (getOption("warn") >= 2 || getOption("warn") < 0) {        return()    }    watcher$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$push(cnd)    switch(on_error, continue = invokeRestart("eval_continue"),         stop = invokeRestart("eval_stop"), error = NULL)})
21: eval(call)
22: eval(call)
23: with_handlers({    call <- conditionCall(e)    if (!is.null(call)) {        if (identical(call[[1L]], quote(doTryCatch)))             call <- sys.call(-4L)        dcall <- deparse(call, nlines = 1L)        prefix <- paste("Error in", dcall, ": ")        LONG <- 75L        sm <- strsplit(conditionMessage(e), "\n")[[1L]]        w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")        if (is.na(w))             w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],                 type = "b")        if (w > LONG)             prefix <- paste0(prefix, "\n  ")    }    else prefix <- "Error : "    msg <- paste0(prefix, conditionMessage(e), "\n")    .Internal(seterrmessage(msg[1L]))    if (!silent && isTRUE(getOption("show.error.messages"))) {        cat(msg, file = outFile)    for (expr in tle$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({        .Internal(printDeferredWarnings())    }    invisible(structure(msg, class = "try-error", condition = e))})
11: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
12: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
13: FUN(X[[i]], ...)
14:     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, lapply(seq_len(cores), inner.do)
15: mclapply(group, function(j) sparcc(OTUtab[-j, ])$cor.w)
16: asso_mat(OTUdat = OTUtab, group = newindex_B6)
17: eval(expr, envir)
18: eval(expr, envir)
19: withVisible(eval(expr, envir))
20: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) {    watcher$capture_plot_and_output()    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$interrupt()        if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)    if (on_message$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$capture_plot_and_output()    }), list(rlang_trace_top_env = knit_global()))
41: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        if (progress && is.function(pb$interrupt))             pb$interrupt()        if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)    }), list(rlang_trace_top_env = knit_global())), function(loc) {    setwd(wd)    write_utf8(res, output %n% stdout())    paste0("\nQuitting from ", loc, if (!is.null(error))         paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
42: process_file(text, output)
43: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)    cnd <- sanitize_call(cnd)    watcher$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$visible, envir)    }
44: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),     output_dir = getwd(), ...)
45: vweave_rmarkdown(...)
46: engine$weave(file, quiet = quiet, encoding = enc)
47: doTryCatch(return(expr), name, parentenv, handler)
48: tryCatchOne(expr, names, parentenv, handlers[[1L]])
49:     TRUE}, handlers)
24: doWithOneRestart(return(expr), restart)
25: withOneRestart(expr, restarts[[1L]])
26: withRestartList(expr, restarts[-nr])tryCatchList(expr, classes, parentenv, handlers)
50: tryCatch({    engine$weave(file, quiet = quiet, encoding = enc)    setwd(startdir)    output <- find_vignette_product(name, by = "weave", engine = engine)    if (!have.makefile && vignette_is_tex(output)) {        texi2pdf(file = output, clean = FALSE, quiet = quiet)        output <- find_vignette_product(name, by = "texi2pdf",             engine = engine)    }    outputs <- c(outputs, output)
27: doWithOneRestart(return(expr), restart)
28: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
29: withRestartList(expr, restarts)
30: withRestarts(with_handlers({    for (expr in tle$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: }, error = function(e) {    thisOK <<- FALSE    fails <<- c(fails, file)    message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",         file, conditionMessage(e)))})
51: tools::buildVignettes(dir = "/Volumes/Builds/packages/sonoma-arm64/results/4.6/SOHPIE.Rcheck/vign_test/SOHPIE",     skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpDNNoM1/file101e15acc12ee.rds")
An irrecoverable exception occurred. R is aborting now ...
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)    }    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)))})
51: tools::buildVignettes(dir = "/Volumes/Builds/packages/sonoma-arm64/results/4.6/SOHPIE.Rcheck/vign_test/SOHPIE",     skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpDNNoM1/file101e15acc12ee.rds")
An irrecoverable exception occurred. R is aborting now ...
Warning in file("", "w+b") :
  cannot open file '/Volumes/Temp/tmp/Rtmp4D6gRl/Rf105c06a524e05': No such file or directory

Quitting from UserManualSOHPIE.Rmd:150-158 [unnamed-chunk-13]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cannot open the connection
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~


Quitting from UserManualSOHPIE.Rmd:150-158 [unnamed-chunk-13]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
file("", "w+b")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'UserManualSOHPIE.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘UserManualSOHPIE.Rmd’

SUMMARY: processing the following file failed:
  ‘UserManualSOHPIE.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
              
                11 OK ·                 2 NOTE ·                 0 WARNING ·                 1 ERROR ·                 0 FAILURE              
              Mar 9, 2026
            
            

              

                

                  NOTE
                  r-devel-linux-x86_64-debian-clang
                

                
CRAN incoming feasibility

                
Maintainer: ‘Seungjun Ahn <seungjun.ahn@mountsinai.org>’

The Description field contains
  <arXiv:2303.13702v1>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.

              

              

                

                  NOTE
                  r-devel-linux-x86_64-debian-gcc
                

                
CRAN incoming feasibility

                
Maintainer: ‘Seungjun Ahn <seungjun.ahn@mountsinai.org>’

The Description field contains
  <arXiv:2303.13702v1>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.

              

              

                

                  ERROR
                  r-devel-macos-arm64
                

                
re-building of vignette outputs

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

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

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

Traceback:
 1: solve.default(Lmat[cp, cp], rowSums(T02[cp, cp]))
 2: solve(Lmat[cp, cp], rowSums(T02[cp, cp]))
 3: SparCC.frac(x = y, kmax = kmax, alpha = alpha, Vmin = Vmin)
 4: sparcc(OTUtab[-j, ])
 5: FUN(X[[i]], ...)
 6: lapply(X = S, FUN = FUN, ...)
 7: doTryCatch(r

              

            

          

        

      


      

      
      

        
Dependency Network

        

          
            

            
            
            Dependencies
            
            Reverse dependencies

            
            
            
            
            

            

            
            
              
              robustbase
            
            
              
              dplyr
            
            
              
              fdrtool
            
            
              
              gtools
            

            

            
            
            SOHPIE
          
        

      


      
      

        
Version History

        

          

            new
            1.0.6
            Mar 9, 2026