Last updated on 2026-09-24 02:52:18 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.2.2 | 4.00 | 65.14 | 69.14 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.2.2 | 3.10 | 50.51 | 53.61 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.2.2 | 36.33 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 1.2.2 | 41.28 | ERROR | |||
| r-devel-windows-x86_64 | 1.2.2 | 7.00 | 129.00 | 136.00 | OK | |
| r-patched-linux-x86_64 | 1.2.2 | 4.14 | 42.17 | 46.31 | ERROR | |
| r-release-linux-x86_64 | 1.2.2 | 3.98 | 60.40 | 64.38 | ERROR | |
| r-release-macos-arm64 | 1.2.2 | 1.00 | 65.00 | 66.00 | OK | |
| r-release-macos-x86_64 | 1.2.2 | 3.00 | 116.00 | 119.00 | OK | |
| r-release-windows-x86_64 | 1.2.2 | 7.00 | 67.00 | 74.00 | ERROR | |
| r-oldrel-macos-arm64 | 1.2.2 | 2.00 | 60.00 | 62.00 | ERROR | |
| r-oldrel-macos-x86_64 | 1.2.2 | 3.00 | 120.00 | 123.00 | OK | |
| r-oldrel-windows-x86_64 | 1.2.2 | 8.00 | 131.00 | 139.00 | OK |
Version: 1.2.2
Check: examples
Result: ERROR
Running examples in ‘isoWater-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: wiDB_data
> ### Title: Obtain data from wiDB using a query
> ### Aliases: wiDB_data
>
> ### ** Examples
>
> #Download data for US precipitation in the 1990s
> vals = wiDB_data(minDate = "1990-01-01", maxDate = "2000-01-01",
+ countries = "US", types = "Precipitation")
Error in wiDB_data(minDate = "1990-01-01", maxDate = "2000-01-01", countries = "US", :
object 'd' not found
Calls: wiDB_data -> message -> paste
Execution halted
Flavors: r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64
Version: 1.2.2
Check: examples
Result: ERROR
Running examples in ‘isoWater-Ex.R’ failed
The error most likely occurred in:
> ### Name: wiDB_data
> ### Title: Obtain data from wiDB using a query
> ### Aliases: wiDB_data
>
> ### ** Examples
>
> #Download data for US precipitation in the 1990s
> vals = wiDB_data(minDate = "1990-01-01", maxDate = "2000-01-01",
+ countries = "US", types = "Precipitation")
Error in wiDB_data(minDate = "1990-01-01", maxDate = "2000-01-01", countries = "US", :
object 'd' not found
Calls: wiDB_data -> message -> paste
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-release-windows-x86_64, r-oldrel-macos-arm64
Version: 1.2.2
Check: tests
Result: ERROR
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(curl)
Using libcurl 8.18.0 with OpenSSL/3.5.8
> library(isoWater)
>
> test_check("isoWater")
Compiling model graph
Resolving undeclared variables
Allocating nodes
Graph information:
Observed stochastic nodes: 1
Unobserved stochastic nodes: 6
Total graph size: 72
Initializing model
Compiling model graph
Resolving undeclared variables
Allocating nodes
Graph information:
Observed stochastic nodes: 1
Unobserved stochastic nodes: 6
Total graph size: 72
Initializing model
Compiling model graph
Resolving undeclared variables
Allocating nodes
Graph information:
Observed stochastic nodes: 1
Unobserved stochastic nodes: 6
Total graph size: 72
Initializing model
Compiling model graph
Resolving undeclared variables
Allocating nodes
Graph information:
Observed stochastic nodes: 1
Unobserved stochastic nodes: 6
Total graph size: 72
Initializing model
Compiling model graph
Resolving undeclared variables
Allocating nodes
Graph information:
Observed stochastic nodes: 1
Unobserved stochastic nodes: 6
Total graph size: 72
Initializing model
Compiling model graph
Resolving undeclared variables
Allocating nodes
Graph information:
Observed stochastic nodes: 1
Unobserved stochastic nodes: 4
Total graph size: 46
Initializing model
Compiling model graph
Resolving undeclared variables
Allocating nodes
Graph information:
Observed stochastic nodes: 1
Unobserved stochastic nodes: 4
Total graph size: 46
Initializing model
Compiling model graph
Resolving undeclared variables
Allocating nodes
Graph information:
Observed stochastic nodes: 1
Unobserved stochastic nodes: 4
Total graph size: 46
Initializing model
Compiling model graph
Resolving undeclared variables
Allocating nodes
Graph information:
Observed stochastic nodes: 1
Unobserved stochastic nodes: 4
Total graph size: 46
Initializing model
Compiling model graph
Resolving undeclared variables
Allocating nodes
Graph information:
Observed stochastic nodes: 1
Unobserved stochastic nodes: 4
Total graph size: 46
Initializing model
Saving _problems/test-wiDB-21.R
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 17 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-wiDB.R:20:3'): (code run outside of `test_that()`) ─────────────
<objectNotFoundError/error/condition>
Error in `wiDB_data(minDate = "1990-01-01", maxDate = "1990-02-01", countries = "US", types = "Precipitation")`: object 'd' not found
Backtrace:
▆
1. └─isoWater::wiDB_data(...) at test-wiDB.R:20:3
2. ├─base::message(paste("Request returned error code", d$status_code))
3. └─base::paste("Request returned error code", d$status_code)
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 17 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.2.2
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘isoWater.Rmd’ using rmarkdown
Quitting from isoWater.Rmd:52-55 [query2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `wiDB_data()`:
! object 'd' not found
---
Backtrace:
▆
1. └─isoWater::wiDB_data(...)
2. ├─base::message(paste("Request returned error code", d$status_code))
3. └─base::paste("Request returned error code", d$status_code)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'isoWater.Rmd' failed with diagnostics:
object 'd' not found
--- failed re-building ‘isoWater.Rmd’
SUMMARY: processing the following file failed:
‘isoWater.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-release-windows-x86_64
Version: 1.2.2
Check: tests
Result: ERROR
Running ‘testthat.R’ [3s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(curl)
Using libcurl 8.21.0 with GnuTLS/3.8.13
> library(isoWater)
>
> test_check("isoWater")
Compiling model graph
Resolving undeclared variables
Allocating nodes
Graph information:
Observed stochastic nodes: 1
Unobserved stochastic nodes: 6
Total graph size: 72
Initializing model
Compiling model graph
Resolving undeclared variables
Allocating nodes
Graph information:
Observed stochastic nodes: 1
Unobserved stochastic nodes: 6
Total graph size: 72
Initializing model
Compiling model graph
Resolving undeclared variables
Allocating nodes
Graph information:
Observed stochastic nodes: 1
Unobserved stochastic nodes: 6
Total graph size: 72
Initializing model
Compiling model graph
Resolving undeclared variables
Allocating nodes
Graph information:
Observed stochastic nodes: 1
Unobserved stochastic nodes: 6
Total graph size: 72
Initializing model
Compiling model graph
Resolving undeclared variables
Allocating nodes
Graph information:
Observed stochastic nodes: 1
Unobserved stochastic nodes: 6
Total graph size: 72
Initializing model
Compiling model graph
Resolving undeclared variables
Allocating nodes
Graph information:
Observed stochastic nodes: 1
Unobserved stochastic nodes: 4
Total graph size: 46
Initializing model
Compiling model graph
Resolving undeclared variables
Allocating nodes
Graph information:
Observed stochastic nodes: 1
Unobserved stochastic nodes: 4
Total graph size: 46
Initializing model
Compiling model graph
Resolving undeclared variables
Allocating nodes
Graph information:
Observed stochastic nodes: 1
Unobserved stochastic nodes: 4
Total graph size: 46
Initializing model
Compiling model graph
Resolving undeclared variables
Allocating nodes
Graph information:
Observed stochastic nodes: 1
Unobserved stochastic nodes: 4
Total graph size: 46
Initializing model
Compiling model graph
Resolving undeclared variables
Allocating nodes
Graph information:
Observed stochastic nodes: 1
Unobserved stochastic nodes: 4
Total graph size: 46
Initializing model
Saving _problems/test-wiDB-21.R
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 17 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-wiDB.R:20:3'): (code run outside of `test_that()`) ─────────────
Error in `wiDB_data(minDate = "1990-01-01", maxDate = "1990-02-01", countries = "US", types = "Precipitation")`: object 'd' not found
Backtrace:
▆
1. └─isoWater::wiDB_data(...) at test-wiDB.R:20:3
2. ├─base::message(paste("Request returned error code", d$status_code))
3. └─base::paste("Request returned error code", d$status_code)
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 17 ]
Error:
! Test failures.
Execution halted
Flavor: r-patched-linux-x86_64
Version: 1.2.2
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘isoWater.Rmd’ using rmarkdown
Quitting from isoWater.Rmd:52-55 [query2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `wiDB_data()`:
! object 'd' not found
---
Backtrace:
▆
1. └─isoWater::wiDB_data(...)
2. ├─base::message(paste("Request returned error code", d$status_code))
3. └─base::paste("Request returned error code", d$status_code)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'isoWater.Rmd' failed with diagnostics:
object 'd' not found
--- failed re-building ‘isoWater.Rmd’
SUMMARY: processing the following file failed:
‘isoWater.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-patched-linux-x86_64
Version: 1.2.2
Check: tests
Result: ERROR
Running 'testthat.R' [5s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(curl)
Using libcurl 8.14.1 with Schannel
> library(isoWater)
>
> test_check("isoWater")
Compiling model graph
Resolving undeclared variables
Allocating nodes
Graph information:
Observed stochastic nodes: 1
Unobserved stochastic nodes: 6
Total graph size: 72
Initializing model
Compiling model graph
Resolving undeclared variables
Allocating nodes
Graph information:
Observed stochastic nodes: 1
Unobserved stochastic nodes: 6
Total graph size: 72
Initializing model
Compiling model graph
Resolving undeclared variables
Allocating nodes
Graph information:
Observed stochastic nodes: 1
Unobserved stochastic nodes: 6
Total graph size: 72
Initializing model
Compiling model graph
Resolving undeclared variables
Allocating nodes
Graph information:
Observed stochastic nodes: 1
Unobserved stochastic nodes: 4
Total graph size: 46
Initializing model
Compiling model graph
Resolving undeclared variables
Allocating nodes
Graph information:
Observed stochastic nodes: 1
Unobserved stochastic nodes: 4
Total graph size: 46
Initializing model
Compiling model graph
Resolving undeclared variables
Allocating nodes
Graph information:
Observed stochastic nodes: 1
Unobserved stochastic nodes: 4
Total graph size: 46
Initializing model
Saving _problems/test-wiDB-21.R
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 17 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-wiDB.R:20:3'): (code run outside of `test_that()`) ─────────────
Error in `wiDB_data(minDate = "1990-01-01", maxDate = "1990-02-01", countries = "US", types = "Precipitation")`: object 'd' not found
Backtrace:
▆
1. └─isoWater::wiDB_data(...) at test-wiDB.R:20:3
2. ├─base::message(paste("Request returned error code", d$status_code))
3. └─base::paste("Request returned error code", d$status_code)
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 17 ]
Error:
! Test failures.
Execution halted
Flavor: r-release-windows-x86_64
Version: 1.2.2
Check: tests
Result: ERROR
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(curl)
Using libcurl 8.14.1 with LibreSSL/3.3.6
> library(isoWater)
>
> test_check("isoWater")
Compiling model graph
Resolving undeclared variables
Allocating nodes
Graph information:
Observed stochastic nodes: 1
Unobserved stochastic nodes: 6
Total graph size: 72
Initializing model
Compiling model graph
Resolving undeclared variables
Allocating nodes
Graph information:
Observed stochastic nodes: 1
Unobserved stochastic nodes: 6
Total graph size: 72
Compiling model graph
Resolving undeclared variables
Allocating nodes
Graph information:
Observed stochastic nodes: 1
Unobserved stochastic nodes: 6
Total graph size: 72
Initializing model
Initializing model
Compiling model graph
Resolving undeclared variables
Allocating nodes
Graph information:
Observed stochastic nodes: 1
Unobserved stochastic nodes: 6
Total graph size: 72
Initializing model
Compiling model graph
Resolving undeclared variables
Allocating nodes
Graph information:
Observed stochastic nodes: 1
Unobserved stochastic nodes: 6
Total graph size: 72
Initializing model
Compiling model graph
Resolving undeclared variables
Allocating nodes
Graph information:
Observed stochastic nodes: 1
Unobserved stochastic nodes: 4
Total graph size: 46
Initializing model
Compiling model graph
Resolving undeclared variables
Allocating nodes
Graph information:
Observed stochastic nodes: 1
Unobserved stochastic nodes: 4
Total graph size: 46
Compiling model graph
Resolving undeclared variables
Allocating nodes
Graph information:
Observed stochastic nodes: 1
Unobserved stochastic nodes: 4
Total graph size: 46
Initializing model
Initializing model
Compiling model graph
Resolving undeclared variables
Allocating nodes
Graph information:
Observed stochastic nodes: 1
Unobserved stochastic nodes: 4
Total graph size: 46
Initializing model
Compiling model graph
Resolving undeclared variables
Allocating nodes
Graph information:
Observed stochastic nodes: 1
Unobserved stochastic nodes: 4
Total graph size: 46
Initializing model
Saving _problems/test-wiDB-21.R
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 17 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-wiDB.R:20:3'): (code run outside of `test_that()`) ─────────────
Error in `wiDB_data(minDate = "1990-01-01", maxDate = "1990-02-01", countries = "US", types = "Precipitation")`: object 'd' not found
Backtrace:
▆
1. └─isoWater::wiDB_data(...) at test-wiDB.R:20:3
2. ├─base::message(paste("Request returned error code", d$status_code))
3. └─base::paste("Request returned error code", d$status_code)
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 17 ]
Error:
! Test failures.
Execution halted
Flavor: r-oldrel-macos-arm64
Version: 1.2.2
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘isoWater.Rmd’ using rmarkdown
2026-09-24 08:32:43.372 R[59103:235578] XType: Using static font registry.
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1: ar.yw.default(x, aic = aic, order.max = order.max, na.action = na.action, series = series, ...)
2: ar.yw(x, aic = aic, order.max = order.max, na.action = na.action, series = series, ...)
3: ar(x[, i], aic = TRUE)
4: spectrum0.ar(x)
5: doTryCatch(return(expr), name, parentenv, handler)
6: tryCatchOne(expr, names, parentenv, handlers[[1L]])
7: tryCatchList(expr, classes, parentenv, handlers)
8: 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))})
9: try(spectrum0.ar(x)$spec)
10: safespec0(x[[i]][, j])
11: summary.mcmc.list(x)
12: summary(x)
13: mcmc2bugs(samples, model.file = model.file, program = "jags", DIC = DIC, DICOutput = NULL, n.iter = n.iter, n.burnin = n.burnin, n.thin = n.thin, checkMissing = checkMissing)
14: jags(data = data, parameters.to.save = parameters.to.save, model.file = model.file, n.chains = 1, n.iter = n.iter, n.burnin = n.burnin, n.thin = n.thin)
15: eval(c.expr, envir = args, enclos = envir)
16: eval(c.expr, envir = args, enclos = envir)
17: doTryCatch(return(expr), name, parentenv, handler)
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
19:
Traceback:
tryCatchList(expr, classes, parentenv, handlers) 1:
ar.yw.default(x, aic = aic, order.max = order.max, na.action = na.action, 20: series = series, ...)tryCatch(eval(c.expr, envir = args, enclos = envir), error = function(e) e)
2: 21: ar.yw(x, aic = aic, order.max = order.max, na.action = na.action, FUN(X[[i]], ...) series = series, ...)
22:
lapply(X = S, FUN = FUN, ...) 3:
ar(x[, i], aic = TRUE)23:
doTryCatch(return(expr), name, parentenv, handler) 4:
spectrum0.ar(x)24:
tryCatchOne(expr, names, parentenv, handlers[[1L]]) 5:
doTryCatch(return(expr), name, parentenv, handler)25:
tryCatchList(expr, classes, parentenv, handlers) 6:
tryCatchOne(expr, names, parentenv, handlers[[1L]])26:
tryCatch(expr, error = function(e) { 7: call <- conditionCall(e)tryCatchList(expr, classes, parentenv, handlers) if (!is.null(call)) {
if (identical(call[[1L]], quote(doTryCatch))) 8: call <- sys.call(-4L)tryCatch(expr, error = function(e) { dcall <- deparse(call, nlines = 1L) call <- conditionCall(e) prefix <- paste("Error in", dcall, ": ") if (!is.null(call)) { LONG <- 75L if (identical(call[[1L]], quote(doTryCatch))) sm <- strsplit(conditionMessage(e), "\n")[[1L]] call <- sys.call(-4L) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") dcall <- deparse(call, nlines = 1L) if (is.na(w)) prefix <- paste("Error in", dcall, ": ") w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], LONG <- 75L type = "b") sm <- strsplit(conditionMessage(e), "\n")[[1L]] if (w > LONG) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") prefix <- paste0(prefix, "\n ") if (is.na(w)) } w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], else prefix <- "Error : " type = "b") msg <- paste0(prefix, conditionMessage(e), "\n") if (w > LONG) .Internal(seterrmessage(msg[1L])) prefix <- paste0(prefix, "\n ") if (!silent && isTRUE(getOption("show.error.messages"))) { } cat(msg, file = outFile) else prefix <- "Error : " .Internal(printDeferredWarnings()) msg <- paste0(prefix, conditionMessage(e), "\n") } .Internal(seterrmessage(msg[1L])) invisible(structure(msg, class = "try-error", condition = e)) if (!silent && isTRUE(getOption("show.error.messages"))) {}) cat(msg, file = outFile)
.Internal(printDeferredWarnings())27: }try(lapply(X = S, FUN = FUN, ...), silent = TRUE) invisible(structure(msg, class = "try-error", condition = e))
})28:
sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) 9:
try(spectrum0.ar(x)$spec)29:
FUN(X[[i]], ...)10:
safespec0(x[[i]][, j])30:
lapply(seq_len(cores), inner.do)
11: 31: summary.mcmc.list(x)mclapply(argsList, FUN, mc.preschedule = preschedule, mc.set.seed = set.seed,
mc.silent = silent, mc.cores = cores)12:
summary(x)32:
e$fun(obj, substitute(ex), parent.frame(), e$data)13:
mcmc2bugs(samples, model.file = model.file, program = "jags", 33: DIC = DIC, DICOutput = NULL, n.iter = n.iter, n.burnin = n.burnin, foreach(i = 1:n.cluster) %dopar% { n.thin = n.thin, checkMissing = checkMissing) jags(data = data, parameters.to.save = parameters.to.save,
model.file = model.file, n.chains = 1, n.iter = n.iter, 14: n.burnin = n.burnin, n.thin = n.thin)jags(data = data, parameters.to.save = parameters.to.save, model.file = model.file, } n.chains = 1, n.iter = n.iter, n.burnin = n.burnin, n.thin = n.thin)
34: 15: jags.parallel(data = d, parameters.to.save = p, model.file = tmf, n.iter = n.iter, n.chains = ncores, n.burnin = n.burnin, eval(c.expr, envir = args, enclos = envir) n.thin = n.thin)
16: 35: eval(c.expr, envir = args, enclos = envir)mixSource(obs, sources, slope, ngens = 20000, ncores = 2)
17: 36: doTryCatch(return(expr), name, parentenv, handler)eval(expr, envir)
18: 37: eval(expr, envir)tryCatchOne(expr, names, parentenv, handlers[[1L]])
38: 19: withVisible(eval(expr, envir))tryCatchList(expr, classes, parentenv, handlers)
39: 20: withCallingHandlers(code, error = function (e) tryCatch(eval(c.expr, envir = args, enclos = envir), error = function(e) e)rlang::entrace(e), message = function (cnd)
{21: watcher$capture_plot_and_output()FUN(X[[i]], ...) if (on_message$capture) {
watcher$push(cnd)22: }lapply(X = S, FUN = FUN, ...) if (on_message$silence) {
invokeRestart("muffleMessage")23: }doTryCatch(return(expr), name, parentenv, handler)}, warning = function (cnd)
{24: tryCatchOne(expr, names, parentenv, handlers[[1L]])
25: tryCatchList(expr, classes, parentenv, handlers) if (getOption("warn") >= 2 || getOption("warn") < 0) { return()
}26: watcher$capture_plot_and_output()tryCatch(expr, error = function(e) { if (on_warning$capture) { call <- conditionCall(e) cnd <- sanitize_call(cnd) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) watcher$push(cnd) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) } prefix <- paste("Error in", dcall, ": ") if (on_warning$silence) { LONG <- 75L invokeRestart("muffleWarning") sm <- strsplit(conditionMessage(e), "\n")[[1L]] } w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")}, error = function (cnd) if (is.na(w)) { w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], watcher$capture_plot_and_output() type = "b") cnd <- sanitize_call(cnd) if (w > LONG) watcher$push(cnd) prefix <- paste0(prefix, "\n ") switch(on_error, continue = invokeRestart("eval_continue"), } stop = invokeRestart("eval_stop"), error = NULL) else prefix <- "Error : "}) msg <- paste0(prefix, conditionMessage(e), "\n")
.Internal(seterrmessage(msg[1L]))40: if (!silent && isTRUE(getOption("show.error.messages"))) {eval(call) cat(msg, file = outFile)
.Internal(printDeferredWarnings())41: }eval(call) invisible(structure(msg, class = "try-error", condition = e))
})42:
with_handlers({27: for (expr in tle$exprs) {try(lapply(X = S, FUN = FUN, ...), silent = TRUE) ev <- withVisible(eval(expr, envir))
watcher$capture_plot_and_output()28: watcher$print_value(ev$value, ev$visible, envir)sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) }
TRUE29: }, handlers)FUN(X[[i]], ...)
43: 30: doWithOneRestart(return(expr), restart)lapply(seq_len(cores), inner.do)
44: 31: withOneRestart(expr, restarts[[1L]])mclapply(argsList, FUN, mc.preschedule = preschedule, mc.set.seed = set.seed,
mc.silent = silent, mc.cores = cores)45:
withRestartList(expr, restarts[-nr])32:
e$fun(obj, substitute(ex), parent.frame(), e$data)46:
doWithOneRestart(return(expr), restart)33:
47: foreach(i = 1:n.cluster) %dopar% {withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) jags(data = data, parameters.to.save = parameters.to.save,
model.file = model.file, n.chains = 1, n.iter = n.iter, 48: n.burnin = n.burnin, n.thin = n.thin)withRestartList(expr, restarts)}
49: 34: withRestarts(with_handlers({jags.parallel(data = d, parameters.to.save = p, model.file = tmf, for (expr in tle$exprs) { n.iter = n.iter, n.chains = ncores, n.burnin = n.burnin, ev <- withVisible(eval(expr, envir)) n.thin = n.thin) watcher$capture_plot_and_output()
watcher$print_value(ev$value, ev$visible, envir)35: }mixSource(obs, sources, slope, ngens = 20000, ncores = 2) TRUE
}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)36:
eval(expr, envir)50:
evaluate::evaluate(...)37:
eval(expr, envir)51:
evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, 38: keep_message = if (is.numeric(options$message)) TRUE else options$message, withVisible(eval(expr, envir)) stop_on_error = if (is.numeric(options$error)) options$error else {
if (options$error && options$include) 39: 0LwithCallingHandlers(code, error = function (e) else 2Lrlang::entrace(e), message = function (cnd) }, output_handler = knit_handlers(options$render, options)){
watcher$capture_plot_and_output()52: if (on_message$capture) {in_dir(input_dir(), expr)
watcher$push(cnd)53: }in_input_dir(evaluate(code, envir = env, new_device = FALSE, if (on_message$silence) { keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, invokeRestart("muffleMessage") keep_message = if (is.numeric(options$message)) TRUE else options$message, } stop_on_error = if (is.numeric(options$error)) options$error else {}, warning = function (cnd) if (options$error && options$include) { 0L if (getOption("warn") >= 2 || getOption("warn") < 0) { else 2L return() }, output_handler = knit_handlers(options$render, options))) }
watcher$capture_plot_and_output()54: if (on_warning$capture) {eng_r(options) cnd <- sanitize_call(cnd)
watcher$push(cnd)55: }block_exec(params) if (on_warning$silence) {
invokeRestart("muffleWarning")56: }call_block(x)
}, error = function (cnd) 57: {process_group(group) watcher$capture_plot_and_output()
cnd <- sanitize_call(cnd)58: watcher$push(cnd)withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), switch(on_error, continue = invokeRestart("eval_continue"), error = function(e) { stop = invokeRestart("eval_stop"), error = NULL) if (progress && is.function(pb$interrupt)) }) pb$interrupt()
if (is_R_CMD_build() || is_R_CMD_check()) 40: error <<- format(e)eval(call) })
41: 59: eval(call)with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
error = function(e) {42: if (progress && is.function(pb$interrupt)) with_handlers({ pb$interrupt() for (expr in tle$exprs) { if (is_R_CMD_build() || is_R_CMD_check()) ev <- withVisible(eval(expr, envir)) error <<- format(e) watcher$capture_plot_and_output() }), list(rlang_trace_top_env = knit_global())) watcher$print_value(ev$value, ev$visible, envir)
}60: TRUExfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), }, handlers) error = function(e) {
if (progress && is.function(pb$interrupt)) 43: pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) doWithOneRestart(return(expr), restart) error <<- format(e)
}), list(rlang_trace_top_env = knit_global())), function(loc) {44: setwd(wd)withOneRestart(expr, restarts[[1L]]) write_utf8(res, output %n% stdout())
paste0("\nQuitting from ", loc, if (!is.null(error)) 45: paste0("\n", rule(), error, "\n", rule()))withRestartList(expr, restarts[-nr])}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
46: 61: doWithOneRestart(return(expr), restart)process_file(text, output)
47: 62: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
63: 48: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), withRestartList(expr, restarts) output_dir = getwd(), ...)
49: 64: withRestarts(with_handlers({vweave_rmarkdown(...) for (expr in tle$exprs) {
ev <- withVisible(eval(expr, envir))65: watcher$capture_plot_and_output()engine$weave(file, quiet = quiet, encoding = enc) watcher$print_value(ev$value, ev$visible, envir)
}66: TRUEdoTryCatch(return(expr), name, parentenv, handler)}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
67: 50: tryCatchOne(expr, names, parentenv, handlers[[1L]])evaluate::evaluate(...)
68: 51: tryCatchList(expr, classes, parentenv, handlers)evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,
keep_message = if (is.numeric(options$message)) TRUE else options$message, 69: stop_on_error = if (is.numeric(options$error)) options$error else {tryCatch({ if (options$error && options$include) engine$weave(file, quiet = quiet, encoding = enc) 0L setwd(startdir) else 2L output <- find_vignette_product(name, by = "weave", engine = engine) }, output_handler = knit_handlers(options$render, options)) if (!have.makefile && vignette_is_tex(output)) {
texi2pdf(file = output, clean = FALSE, quiet = quiet)52: output <- find_vignette_product(name, by = "texi2pdf", in_dir(input_dir(), expr) engine = engine)
}53: outputs <- c(outputs, output)in_input_dir(evaluate(code, envir = env, new_device = FALSE, }, error = function(e) { keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, thisOK <<- FALSE keep_message = if (is.numeric(options$message)) TRUE else options$message, fails <<- c(fails, file) stop_on_error = if (is.numeric(options$error)) options$error else { message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", if (options$error && options$include) file, conditionMessage(e))) 0L}) else 2L
}, output_handler = knit_handlers(options$render, options)))70:
tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/isoWater.Rcheck/vign_test/isoWater", 54: skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpXYD0c7/filec53c4fb84db2.rds")eng_r(options)
An irrecoverable exception occurred. R is aborting now ...
55: block_exec(params)
56: call_block(x)
57: process_group(group)
58: 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) })
59: 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()))
60: 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)
61: process_file(text, output)
62: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
63: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
64: vweave_rmarkdown(...)
65: engine$weave(file, quiet = quiet, encoding = enc)
66: doTryCatch(return(expr), name, parentenv, handler)
67: tryCatchOne(expr, names, parentenv, handlers[[1L]])
68: tryCatchList(expr, classes, parentenv, handlers)
69: tryCatch({ engine$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)))})
70: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/isoWater.Rcheck/vign_test/isoWater", skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpXYD0c7/filec53c4fb84db2.rds")
An irrecoverable exception occurred. R is aborting now ...
Quitting from isoWater.Rmd:176-179 [mixSource1]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `1:n.parameters`:
! argument of length 0
---
Backtrace:
▆
1. └─isoWater::mixSource(obs, sources, slope, ngens = 20000, ncores = 2)
2. └─isoWater:::jags.parallel(...)
3. └─isoWater:::as.bugs.array2(...)
4. └─base::paste("P", 1:n.parameters, sep = "")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'isoWater.Rmd' failed with diagnostics:
argument of length 0
--- failed re-building ‘isoWater.Rmd’
SUMMARY: processing the following file failed:
‘isoWater.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-oldrel-macos-arm64