Last updated on 2020-02-19 10:49:01 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.0 | 2.69 | 27.72 | 30.41 | WARN | |
| r-devel-linux-x86_64-debian-gcc | 1.0.0 | 2.13 | 22.03 | 24.16 | WARN | |
| r-devel-linux-x86_64-fedora-clang | 1.0.0 | 38.12 | WARN | |||
| r-devel-linux-x86_64-fedora-gcc | 1.0.0 | 38.32 | WARN | |||
| r-devel-windows-ix86+x86_64 | 1.0.0 | 6.00 | 46.00 | 52.00 | NOTE | |
| r-devel-windows-ix86+x86_64-gcc8 | 1.0.0 | 8.00 | 55.00 | 63.00 | NOTE | |
| r-patched-linux-x86_64 | 1.0.0 | 2.25 | 30.33 | 32.58 | NOTE | |
| r-patched-solaris-x86 | 1.0.0 | 59.90 | NOTE | |||
| r-release-linux-x86_64 | 1.0.0 | 2.33 | 27.45 | 29.78 | NOTE | |
| r-release-windows-ix86+x86_64 | 1.0.0 | 5.00 | 42.00 | 47.00 | NOTE | |
| r-release-osx-x86_64 | 1.0.0 | NOTE | ||||
| r-oldrel-windows-ix86+x86_64 | 1.0.0 | 3.00 | 41.00 | 44.00 | NOTE | |
| r-oldrel-osx-x86_64 | 1.0.0 | NOTE |
Version: 1.0.0
Check: R code for possible problems
Result: NOTE
BoundingRA: no visible global function definition for 'rnorm'
check_y_estimator: no visible global function definition for 'rnorm'
genNORTARA: no visible global function definition for 'rnorm'
genNORTARA: no visible global function definition for 'pnorm'
valid_input_cormat: no visible global function definition for 'rnorm'
valid_input_cormat: no visible global function definition for 'pnorm'
valid_input_cormat: no visible global function definition for 'cor'
y_control_estimator: no visible global function definition for 'pnorm'
y_control_estimator: no visible global function definition for 'cor'
y_control_estimator : <anonymous>: no visible global function
definition for 'cor'
y_control_estimator: no visible global function definition for 'cov'
y_control_estimator: no visible global function definition for 'var'
y_crude_estimator: no visible global function definition for 'pnorm'
y_crude_estimator: no visible global function definition for 'cor'
Undefined global functions or variables:
cor cov pnorm rnorm var
Consider adding
importFrom("stats", "cor", "cov", "pnorm", "rnorm", "var")
to your NAMESPACE file.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-devel-windows-ix86+x86_64-gcc8, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64
Version: 1.0.0
Check: package vignettes
Result: NOTE
Package vignette with placeholder title 'Vignette Title':
'NORTARA.Rmd'
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-windows-ix86+x86_64, r-devel-windows-ix86+x86_64-gcc8
Version: 1.0.0
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building 'NORTARA.Rmd' using rmarkdown
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
NORTARA
--- call from context ---
Perform_chol(r_matrix, w_k_bar, invcdfnames, paramslists)
--- call from argument ---
if (class(chol_decompose_val) == "try-error") {
b <- b + 1
r_adjust_matrix <- r_matrix[1:(ndim - b), 1:(ndim - b)]
} else break
--- R stacktrace ---
where 1: Perform_chol(r_matrix, w_k_bar, invcdfnames, paramslists)
where 2: BoundingRA(cor_matrix, invcdfnames, paramslists, m1, c1, c2,
delta1, sigma0, epsilon, maxit)
where 3: NORTARA::genNORTARA(10000, cor_matrix, invcdfnames, paramslists)
where 4: eval(expr, envir, enclos)
where 5: eval(expr, envir, enclos)
where 6: withVisible(eval(expr, envir, enclos))
where 7: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler,
error = eHandler, message = mHandler)
where 8: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir,
enclos)), warning = wHandler, error = eHandler, message = mHandler))
where 9: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr,
envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
where 10: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos,
debug = debug, last = i == length(out), use_try = stop_on_error !=
2L, keep_warning = keep_warning, keep_message = keep_message,
output_handler = output_handler, include_timing = include_timing)
where 11: evaluate::evaluate(...)
where 12: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning),
keep_message = !isFALSE(options$message), stop_on_error = if (options$error &&
options$include) 0L else 2L, output_handler = knit_handlers(options$render,
options))
where 13: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE,
keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message),
stop_on_error = if (options$error && options$include) 0L else 2L,
output_handler = knit_handlers(options$render, options)))
where 14: block_exec(params)
where 15: call_block(x)
where 16: process_group.block(group)
where 17: process_group(group)
where 18: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
error = function(e) {
setwd(wd)
cat(res, sep = "\n", file = output %n% "")
message("Quitting from lines ", paste(current_lines(i),
collapse = "-"), " (", knit_concord$get("infile"),
") ")
})
where 19: process_file(text, output)
where 20: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
where 21: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),
output_dir = getwd(), ...)
where 22: vweave_rmarkdown(...)
where 23: engine$weave(file, quiet = quiet, encoding = enc)
where 24: doTryCatch(return(expr), name, parentenv, handler)
where 25: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 26: tryCatchList(expr, classes, parentenv, handlers)
where 27: tryCatch({
engine$weave(file, quiet = quiet, encoding = enc)
setwd(startdir)
output <- find_vignette_product(name, by = "weave", engine = engine)
if (!have.makefile && vignette_is_tex(output)) {
texi2pdf(file = output, clean = FALSE, quiet = quiet)
output <- find_vignette_product(name, by = "texi2pdf",
engine = engine)
}
outputs <- c(outputs, output)
}, error = function(e) {
thisOK <<- FALSE
fails <<- c(fails, file)
message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",
file, conditionMessage(e)))
})
where 28: tools:::buildVignettes(dir = "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/NORTARA.Rcheck/vign_test/NORTARA",
ser_elibs = "/tmp/RtmpnovnRy/file24d440ea776.rds")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (r_matrix, w_k_bar, invcdfnames, paramslists)
{
ndim <- ncol(r_matrix)
mk <- nrow(w_k_bar)
tmp_paramslists <- list()
r_matrix[lower.tri(r_matrix)] <- 0
upper_elements <- r_matrix[upper.tri(r_matrix)]
upper_elements[upper_elements == 1] <- 0.999
upper_elements[upper_elements == -1] <- -0.999
r_matrix[upper.tri(r_matrix)] <- upper_elements
r_matrix <- r_matrix + t(r_matrix)
diag(r_matrix) <- 1
r_adjust_matrix <- r_matrix
b <- 0
while (1) {
chol_decompose_val <- try(chol(r_adjust_matrix), silent = TRUE)
if (class(chol_decompose_val) == "try-error") {
b <- b + 1
r_adjust_matrix <- r_matrix[1:(ndim - b), 1:(ndim -
b)]
}
else break
}
mk_correlated_standard_norm <- w_k_bar[, 1:(ndim - b)] %*%
chol_decompose_val
y_estimator <- matrix(rep(0, ndim * ndim), nrow = ndim)
diag(y_estimator) <- 1
if (mk < 60)
y_estimator[1:(ndim - b), 1:(ndim - b)] <- y_crude_estimator(mk_correlated_standard_norm,
invcdfnames[1:(ndim - b)], paramslists[1:(ndim -
b)])
else y_estimator[1:(ndim - b), 1:(ndim - b)] <- y_control_estimator(mk_correlated_standard_norm,
r_matrix[1:(ndim - b), 1:(ndim - b)], invcdfnames[1:(ndim -
b)], paramslists[1:(ndim - b)])
if (b != 0) {
for (i in ndim:(ndim - b + 1)) for (j in 1:(i - 1)) {
r_mat <- matrix(c(1, r_matrix[j, i], r_matrix[j,
i], 1), nrow = 2)
mk_correlated_standard_norm <- w_k_bar[, c(j, i)] %*%
chol(r_mat)
if (mk < 60)
tmp <- y_crude_estimator(mk_correlated_standard_norm,
invcdfnames[c(i, j)], paramslists[c(i, j)])[1,
2]
else tmp <- y_control_estimator(mk_correlated_standard_norm,
r_mat, invcdfnames[c(i, j)], paramslists[c(i,
j)])[1, 2]
y_estimator[j, i] <- y_estimator[i, j] <- tmp
}
}
y_estimator
}
<bytecode: 0x390aaf8>
<environment: namespace:NORTARA>
--- function search by body ---
Function Perform_chol in namespace NORTARA has this body.
----------- END OF FAILURE REPORT --------------
Quitting from lines 86-111 (NORTARA.Rmd)
Error: processing vignette 'NORTARA.Rmd' failed with diagnostics:
the condition has length > 1
--- failed re-building 'NORTARA.Rmd'
SUMMARY: processing the following file failed:
'NORTARA.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.0.0
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building ‘NORTARA.Rmd’ using rmarkdown
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
NORTARA
--- call from context ---
Perform_chol(r_matrix, w_k_bar, invcdfnames, paramslists)
--- call from argument ---
if (class(chol_decompose_val) == "try-error") {
b <- b + 1
r_adjust_matrix <- r_matrix[1:(ndim - b), 1:(ndim - b)]
} else break
--- R stacktrace ---
where 1: Perform_chol(r_matrix, w_k_bar, invcdfnames, paramslists)
where 2: BoundingRA(cor_matrix, invcdfnames, paramslists, m1, c1, c2,
delta1, sigma0, epsilon, maxit)
where 3: NORTARA::genNORTARA(10000, cor_matrix, invcdfnames, paramslists)
where 4: eval(expr, envir, enclos)
where 5: eval(expr, envir, enclos)
where 6: withVisible(eval(expr, envir, enclos))
where 7: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler,
error = eHandler, message = mHandler)
where 8: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir,
enclos)), warning = wHandler, error = eHandler, message = mHandler))
where 9: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr,
envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
where 10: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos,
debug = debug, last = i == length(out), use_try = stop_on_error !=
2L, keep_warning = keep_warning, keep_message = keep_message,
output_handler = output_handler, include_timing = include_timing)
where 11: evaluate::evaluate(...)
where 12: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning),
keep_message = !isFALSE(options$message), stop_on_error = if (options$error &&
options$include) 0L else 2L, output_handler = knit_handlers(options$render,
options))
where 13: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE,
keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message),
stop_on_error = if (options$error && options$include) 0L else 2L,
output_handler = knit_handlers(options$render, options)))
where 14: block_exec(params)
where 15: call_block(x)
where 16: process_group.block(group)
where 17: process_group(group)
where 18: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
error = function(e) {
setwd(wd)
cat(res, sep = "\n", file = output %n% "")
message("Quitting from lines ", paste(current_lines(i),
collapse = "-"), " (", knit_concord$get("infile"),
") ")
})
where 19: process_file(text, output)
where 20: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
where 21: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),
output_dir = getwd(), ...)
where 22: vweave_rmarkdown(...)
where 23: engine$weave(file, quiet = quiet, encoding = enc)
where 24: doTryCatch(return(expr), name, parentenv, handler)
where 25: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 26: tryCatchList(expr, classes, parentenv, handlers)
where 27: tryCatch({
engine$weave(file, quiet = quiet, encoding = enc)
setwd(startdir)
output <- find_vignette_product(name, by = "weave", engine = engine)
if (!have.makefile && vignette_is_tex(output)) {
texi2pdf(file = output, clean = FALSE, quiet = quiet)
output <- find_vignette_product(name, by = "texi2pdf",
engine = engine)
}
outputs <- c(outputs, output)
}, error = function(e) {
thisOK <<- FALSE
fails <<- c(fails, file)
message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",
file, conditionMessage(e)))
})
where 28: tools:::buildVignettes(dir = "/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/NORTARA.Rcheck/vign_test/NORTARA",
ser_elibs = "/home/hornik/tmp/scratch/RtmpH7c585/file52952da288c9.rds")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (r_matrix, w_k_bar, invcdfnames, paramslists)
{
ndim <- ncol(r_matrix)
mk <- nrow(w_k_bar)
tmp_paramslists <- list()
r_matrix[lower.tri(r_matrix)] <- 0
upper_elements <- r_matrix[upper.tri(r_matrix)]
upper_elements[upper_elements == 1] <- 0.999
upper_elements[upper_elements == -1] <- -0.999
r_matrix[upper.tri(r_matrix)] <- upper_elements
r_matrix <- r_matrix + t(r_matrix)
diag(r_matrix) <- 1
r_adjust_matrix <- r_matrix
b <- 0
while (1) {
chol_decompose_val <- try(chol(r_adjust_matrix), silent = TRUE)
if (class(chol_decompose_val) == "try-error") {
b <- b + 1
r_adjust_matrix <- r_matrix[1:(ndim - b), 1:(ndim -
b)]
}
else break
}
mk_correlated_standard_norm <- w_k_bar[, 1:(ndim - b)] %*%
chol_decompose_val
y_estimator <- matrix(rep(0, ndim * ndim), nrow = ndim)
diag(y_estimator) <- 1
if (mk < 60)
y_estimator[1:(ndim - b), 1:(ndim - b)] <- y_crude_estimator(mk_correlated_standard_norm,
invcdfnames[1:(ndim - b)], paramslists[1:(ndim -
b)])
else y_estimator[1:(ndim - b), 1:(ndim - b)] <- y_control_estimator(mk_correlated_standard_norm,
r_matrix[1:(ndim - b), 1:(ndim - b)], invcdfnames[1:(ndim -
b)], paramslists[1:(ndim - b)])
if (b != 0) {
for (i in ndim:(ndim - b + 1)) for (j in 1:(i - 1)) {
r_mat <- matrix(c(1, r_matrix[j, i], r_matrix[j,
i], 1), nrow = 2)
mk_correlated_standard_norm <- w_k_bar[, c(j, i)] %*%
chol(r_mat)
if (mk < 60)
tmp <- y_crude_estimator(mk_correlated_standard_norm,
invcdfnames[c(i, j)], paramslists[c(i, j)])[1,
2]
else tmp <- y_control_estimator(mk_correlated_standard_norm,
r_mat, invcdfnames[c(i, j)], paramslists[c(i,
j)])[1, 2]
y_estimator[j, i] <- y_estimator[i, j] <- tmp
}
}
y_estimator
}
<bytecode: 0x55d42a7131c0>
<environment: namespace:NORTARA>
--- function search by body ---
Function Perform_chol in namespace NORTARA has this body.
----------- END OF FAILURE REPORT --------------
Quitting from lines 86-111 (NORTARA.Rmd)
Error: processing vignette 'NORTARA.Rmd' failed with diagnostics:
the condition has length > 1
--- failed re-building ‘NORTARA.Rmd’
SUMMARY: processing the following file failed:
‘NORTARA.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.0.0
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
--- re-building ‘NORTARA.Rmd’ using rmarkdown
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
NORTARA
--- call from context ---
Perform_chol(r_matrix, w_k_bar, invcdfnames, paramslists)
--- call from argument ---
if (class(chol_decompose_val) == "try-error") {
b <- b + 1
r_adjust_matrix <- r_matrix[1:(ndim - b), 1:(ndim - b)]
} else break
--- R stacktrace ---
where 1: Perform_chol(r_matrix, w_k_bar, invcdfnames, paramslists)
where 2: BoundingRA(cor_matrix, invcdfnames, paramslists, m1, c1, c2,
delta1, sigma0, epsilon, maxit)
where 3: NORTARA::genNORTARA(10000, cor_matrix, invcdfnames, paramslists)
where 4: eval(expr, envir, enclos)
where 5: eval(expr, envir, enclos)
where 6: withVisible(eval(expr, envir, enclos))
where 7: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler,
error = eHandler, message = mHandler)
where 8: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir,
enclos)), warning = wHandler, error = eHandler, message = mHandler))
where 9: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr,
envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
where 10: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos,
debug = debug, last = i == length(out), use_try = stop_on_error !=
2L, keep_warning = keep_warning, keep_message = keep_message,
output_handler = output_handler, include_timing = include_timing)
where 11: evaluate::evaluate(...)
where 12: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning),
keep_message = !isFALSE(options$message), stop_on_error = if (options$error &&
options$include) 0L else 2L, output_handler = knit_handlers(options$render,
options))
where 13: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE,
keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message),
stop_on_error = if (options$error && options$include) 0L else 2L,
output_handler = knit_handlers(options$render, options)))
where 14: block_exec(params)
where 15: call_block(x)
where 16: process_group.block(group)
where 17: process_group(group)
where 18: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
error = function(e) {
setwd(wd)
cat(res, sep = "\n", file = output %n% "")
message("Quitting from lines ", paste(current_lines(i),
collapse = "-"), " (", knit_concord$get("infile"),
") ")
})
where 19: process_file(text, output)
where 20: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
where 21: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),
output_dir = getwd(), ...)
where 22: vweave_rmarkdown(...)
where 23: engine$weave(file, quiet = quiet, encoding = enc)
where 24: doTryCatch(return(expr), name, parentenv, handler)
where 25: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 26: tryCatchList(expr, classes, parentenv, handlers)
where 27: tryCatch({
engine$weave(file, quiet = quiet, encoding = enc)
setwd(startdir)
output <- find_vignette_product(name, by = "weave", engine = engine)
if (!have.makefile && vignette_is_tex(output)) {
texi2pdf(file = output, clean = FALSE, quiet = quiet)
output <- find_vignette_product(name, by = "texi2pdf",
engine = engine)
}
outputs <- c(outputs, output)
}, error = function(e) {
thisOK <<- FALSE
fails <<- c(fails, file)
message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",
file, conditionMessage(e)))
})
where 28: tools:::buildVignettes(dir = "/data/gannet/ripley/R/packages/tests-clang/NORTARA.Rcheck/vign_test/NORTARA",
ser_elibs = "/tmp/Rtmpgg3k6e/fileb1bf7d876c5b.rds")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (r_matrix, w_k_bar, invcdfnames, paramslists)
{
ndim <- ncol(r_matrix)
mk <- nrow(w_k_bar)
tmp_paramslists <- list()
r_matrix[lower.tri(r_matrix)] <- 0
upper_elements <- r_matrix[upper.tri(r_matrix)]
upper_elements[upper_elements == 1] <- 0.999
upper_elements[upper_elements == -1] <- -0.999
r_matrix[upper.tri(r_matrix)] <- upper_elements
r_matrix <- r_matrix + t(r_matrix)
diag(r_matrix) <- 1
r_adjust_matrix <- r_matrix
b <- 0
while (1) {
chol_decompose_val <- try(chol(r_adjust_matrix), silent = TRUE)
if (class(chol_decompose_val) == "try-error") {
b <- b + 1
r_adjust_matrix <- r_matrix[1:(ndim - b), 1:(ndim -
b)]
}
else break
}
mk_correlated_standard_norm <- w_k_bar[, 1:(ndim - b)] %*%
chol_decompose_val
y_estimator <- matrix(rep(0, ndim * ndim), nrow = ndim)
diag(y_estimator) <- 1
if (mk < 60)
y_estimator[1:(ndim - b), 1:(ndim - b)] <- y_crude_estimator(mk_correlated_standard_norm,
invcdfnames[1:(ndim - b)], paramslists[1:(ndim -
b)])
else y_estimator[1:(ndim - b), 1:(ndim - b)] <- y_control_estimator(mk_correlated_standard_norm,
r_matrix[1:(ndim - b), 1:(ndim - b)], invcdfnames[1:(ndim -
b)], paramslists[1:(ndim - b)])
if (b != 0) {
for (i in ndim:(ndim - b + 1)) for (j in 1:(i - 1)) {
r_mat <- matrix(c(1, r_matrix[j, i], r_matrix[j,
i], 1), nrow = 2)
mk_correlated_standard_norm <- w_k_bar[, c(j, i)] %*%
chol(r_mat)
if (mk < 60)
tmp <- y_crude_estimator(mk_correlated_standard_norm,
invcdfnames[c(i, j)], paramslists[c(i, j)])[1,
2]
else tmp <- y_control_estimator(mk_correlated_standard_norm,
r_mat, invcdfnames[c(i, j)], paramslists[c(i,
j)])[1, 2]
y_estimator[j, i] <- y_estimator[i, j] <- tmp
}
}
y_estimator
}
<bytecode: 0x4e48878>
<environment: namespace:NORTARA>
--- function search by body ---
Function Perform_chol in namespace NORTARA has this body.
----------- END OF FAILURE REPORT --------------
Quitting from lines 86-111 (NORTARA.Rmd)
Error: processing vignette 'NORTARA.Rmd' failed with diagnostics:
the condition has length > 1
--- failed re-building ‘NORTARA.Rmd’
SUMMARY: processing the following file failed:
‘NORTARA.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.0.0
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
--- re-building ‘NORTARA.Rmd’ using rmarkdown
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
NORTARA
--- call from context ---
Perform_chol(r_matrix, w_k_bar, invcdfnames, paramslists)
--- call from argument ---
if (class(chol_decompose_val) == "try-error") {
b <- b + 1
r_adjust_matrix <- r_matrix[1:(ndim - b), 1:(ndim - b)]
} else break
--- R stacktrace ---
where 1: Perform_chol(r_matrix, w_k_bar, invcdfnames, paramslists)
where 2: BoundingRA(cor_matrix, invcdfnames, paramslists, m1, c1, c2,
delta1, sigma0, epsilon, maxit)
where 3: NORTARA::genNORTARA(10000, cor_matrix, invcdfnames, paramslists)
where 4: eval(expr, envir, enclos)
where 5: eval(expr, envir, enclos)
where 6: withVisible(eval(expr, envir, enclos))
where 7: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler,
error = eHandler, message = mHandler)
where 8: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir,
enclos)), warning = wHandler, error = eHandler, message = mHandler))
where 9: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr,
envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
where 10: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos,
debug = debug, last = i == length(out), use_try = stop_on_error !=
2L, keep_warning = keep_warning, keep_message = keep_message,
output_handler = output_handler, include_timing = include_timing)
where 11: evaluate::evaluate(...)
where 12: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning),
keep_message = !isFALSE(options$message), stop_on_error = if (options$error &&
options$include) 0L else 2L, output_handler = knit_handlers(options$render,
options))
where 13: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE,
keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message),
stop_on_error = if (options$error && options$include) 0L else 2L,
output_handler = knit_handlers(options$render, options)))
where 14: block_exec(params)
where 15: call_block(x)
where 16: process_group.block(group)
where 17: process_group(group)
where 18: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
error = function(e) {
setwd(wd)
cat(res, sep = "\n", file = output %n% "")
message("Quitting from lines ", paste(current_lines(i),
collapse = "-"), " (", knit_concord$get("infile"),
") ")
})
where 19: process_file(text, output)
where 20: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
where 21: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),
output_dir = getwd(), ...)
where 22: vweave_rmarkdown(...)
where 23: engine$weave(file, quiet = quiet, encoding = enc)
where 24: doTryCatch(return(expr), name, parentenv, handler)
where 25: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 26: tryCatchList(expr, classes, parentenv, handlers)
where 27: tryCatch({
engine$weave(file, quiet = quiet, encoding = enc)
setwd(startdir)
output <- find_vignette_product(name, by = "weave", engine = engine)
if (!have.makefile && vignette_is_tex(output)) {
texi2pdf(file = output, clean = FALSE, quiet = quiet)
output <- find_vignette_product(name, by = "texi2pdf",
engine = engine)
}
outputs <- c(outputs, output)
}, error = function(e) {
thisOK <<- FALSE
fails <<- c(fails, file)
message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",
file, conditionMessage(e)))
})
where 28: tools:::buildVignettes(dir = "/data/gannet/ripley/R/packages/tests-devel/NORTARA.Rcheck/vign_test/NORTARA",
ser_elibs = "/tmp/RtmpukOnhm/file8529af46135.rds")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (r_matrix, w_k_bar, invcdfnames, paramslists)
{
ndim <- ncol(r_matrix)
mk <- nrow(w_k_bar)
tmp_paramslists <- list()
r_matrix[lower.tri(r_matrix)] <- 0
upper_elements <- r_matrix[upper.tri(r_matrix)]
upper_elements[upper_elements == 1] <- 0.999
upper_elements[upper_elements == -1] <- -0.999
r_matrix[upper.tri(r_matrix)] <- upper_elements
r_matrix <- r_matrix + t(r_matrix)
diag(r_matrix) <- 1
r_adjust_matrix <- r_matrix
b <- 0
while (1) {
chol_decompose_val <- try(chol(r_adjust_matrix), silent = TRUE)
if (class(chol_decompose_val) == "try-error") {
b <- b + 1
r_adjust_matrix <- r_matrix[1:(ndim - b), 1:(ndim -
b)]
}
else break
}
mk_correlated_standard_norm <- w_k_bar[, 1:(ndim - b)] %*%
chol_decompose_val
y_estimator <- matrix(rep(0, ndim * ndim), nrow = ndim)
diag(y_estimator) <- 1
if (mk < 60)
y_estimator[1:(ndim - b), 1:(ndim - b)] <- y_crude_estimator(mk_correlated_standard_norm,
invcdfnames[1:(ndim - b)], paramslists[1:(ndim -
b)])
else y_estimator[1:(ndim - b), 1:(ndim - b)] <- y_control_estimator(mk_correlated_standard_norm,
r_matrix[1:(ndim - b), 1:(ndim - b)], invcdfnames[1:(ndim -
b)], paramslists[1:(ndim - b)])
if (b != 0) {
for (i in ndim:(ndim - b + 1)) for (j in 1:(i - 1)) {
r_mat <- matrix(c(1, r_matrix[j, i], r_matrix[j,
i], 1), nrow = 2)
mk_correlated_standard_norm <- w_k_bar[, c(j, i)] %*%
chol(r_mat)
if (mk < 60)
tmp <- y_crude_estimator(mk_correlated_standard_norm,
invcdfnames[c(i, j)], paramslists[c(i, j)])[1,
2]
else tmp <- y_control_estimator(mk_correlated_standard_norm,
r_mat, invcdfnames[c(i, j)], paramslists[c(i,
j)])[1, 2]
y_estimator[j, i] <- y_estimator[i, j] <- tmp
}
}
y_estimator
}
<bytecode: 0x376dff0>
<environment: namespace:NORTARA>
--- function search by body ---
Function Perform_chol in namespace NORTARA has this body.
----------- END OF FAILURE REPORT --------------
Quitting from lines 86-111 (NORTARA.Rmd)
Error: processing vignette 'NORTARA.Rmd' failed with diagnostics:
the condition has length > 1
--- failed re-building ‘NORTARA.Rmd’
SUMMARY: processing the following file failed:
‘NORTARA.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc