Either way, I figured you might wanna know because this might happen on CRAN too, and to some of your users. It might also be useful clue to maintainers of your package dependencies for their troubleshooting.
* using log directory ‘/c4/home/henrik/repositories/future/revdep/checks/sovereign/new/sovereign.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-manual’
* checking for file ‘sovereign/DESCRIPTION’ ... OK
* this is package ‘sovereign’ version ‘1.2.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘sovereign’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... OK
Running ‘testthat.R’
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... NONE
‘getting_started.Rmd’ using ‘UTF-8’... OK
* checking re-building of vignette outputs ... WARNING
Error(s) in re-building vignettes:
--- re-building ‘getting_started.Rmd’ using rmarkdown
`summarise()` has grouped output by 'y'. You can override using the `.groups`
argument.
Warning: Removed 1 row(s) containing missing values (geom_path).
Warning: Removed 1 row(s) containing missing values (geom_path).
Warning: Removed 1 row(s) containing missing values (geom_path).
Warning: Removed 1 row(s) containing missing values (geom_path).
Warning: Removed 1 row(s) containing missing values (geom_path).
Warning: Removed 1 row(s) containing missing values (geom_path).
Warning: Removed 3 rows containing missing values (position_stack).
Warning: Removed 3 row(s) containing missing values (geom_path).
Warning: Removed 3 rows containing missing values (position_stack).
Warning: Removed 3 row(s) containing missing values (geom_path).
Warning: Removed 3 rows containing missing values (position_stack).
Warning: Removed 3 row(s) containing missing values (geom_path).
*** caught segfault ***
address 0x4, cause 'memory not mapped'
*** recursive gc invocation
*** recursive gc invocation
*** recursive gc invocation
*** recursive gc invocation
*** recursive gc invocation
*** recursive gc invocation
*** recursive gc invocation
... [ ~ 2000 more of these ] ...
*** recursive gc invocation
*** recursive gc invocation
Traceback:
1: as.data.frame(x[[i]], optional = TRUE)
2: (function (..., row.names = NULL, check.rows = FALSE, check.names = TRUE, fix.empty.names = TRUE, stringsAsFactors = FALSE) { data.r
ow.names <- if (check.rows && is.null(row.names)) function(current, new, i) { if (is.character(current)) new
<- as.character(new) if (is.character(new)) current <- as.character(current) if (anyDuplicated(new))
return(current) if (is.null(current)) return(new) if (all(current == new) || all(current ==
"")) return(new) stop(gettextf("mismatch of row names in arguments of 'data.frame', item %d", i), do
main = NA) } else function(current, new, i) { if (is.null(current)) { if (anyDuplicated(new)) { warn
ing(gettextf("some row.names duplicated: %s --> row.names NOT used", paste(which(duplicated(new)), collapse = ",")),
domain = NA) current } else new } else current } object <- as.list(substitut
e(list(...)))[-1L] mirn <- missing(row.names) mrn <- is.null(row.names) x <- list(...) n <- length(x) if (n < 1L) { if (!
mrn) { if (is.object(row.names) || !is.integer(row.names)) row.names <- as.character(row.names) if (anyNA
(row.names)) stop("row names contain missing values") if (anyDuplicated(row.names)) stop(gettextf("d
uplicate row.names: %s", paste(unique(row.names[duplicated(row.names)]), collapse = ", ")), domain = NA) } else
row.names <- integer() return(structure(list(), names = character(), row.names = row.names, class = "data.frame")) }
vnames <- names(x) if (length(vnames) != n) vnames <- character(n) no.vn <- !nzchar(vnames) vlist <- vnames <- as.list(vnames)
nrows <- ncols <- integer(n) for (i in seq_len(n)) { xi <- if (is.character(x[[i]]) || is.list(x[[i]])) as.data.frame
(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) else as.data.frame(x[[i]], optional = TRUE) nrows[i] <- .row_names
_info(xi) ncols[i] <- length(xi) namesi <- names(xi) if (ncols[i] > 1L) { if (length(namesi) == 0L)
namesi <- seq_len(ncols[i]) vnames[[i]] <- if (no.vn[i]) namesi else paste(vnames[[i]], namesi, sep
= ".") } else if (length(namesi)) { vnames[[i]] <- namesi } else if (fix.empty.names && no.vn[[i]]) {
tmpname <- deparse(object[[i]], nlines = 1L)[1L] if (startsWith(tmpname, "I(") && endsWith(tmpname, ")")) {
ntmpn <- nchar(tmpname, "c") tmpname <- substr(tmpname, 3L, ntmpn - 1L) } vnames[[i]] <- t
mpname } if (mirn && nrows[i] > 0L) { rowsi <- attr(xi, "row.names") if (any(nzchar(rowsi)))
row.names <- data.row.names(row.names, rowsi, i) } nrows[i] <- abs(nrows[i]) vlist[[i]] <- xi }
nr <- max(nrows) for (i in seq_len(n)[nrows < nr]) { xi <- vlist[[i]] if (nrows[i] > 0L && (nr%%nrows[i] == 0L)) {
xi <- unclass(xi) fixed <- TRUE for (j in seq_along(xi)) { xi1 <- xi[[j]] if (is.vector(xi1
) || is.factor(xi1)) xi[[j]] <- rep(xi1, length.out = nr) else if (is.character(xi1) && inherits(xi1, "AsIs"))
xi[[j]] <- structure(rep(xi1, length.out = nr), class = class(xi1)) else if (inherits(xi1
, "Date") || inherits(xi1, "POSIXct")) xi[[j]] <- rep(xi1, length.out = nr) else {
fixed <- FALSE break } } if (fixed) { vlist[[i]] <- xi
next } } stop(gettextf("arguments imply differing number of rows: %s", paste(unique(nrows), collapse =
", ")), domain = NA) } value <- unlist(vlist, recursive = FALSE, use.names = FALSE) vnames <- as.character(unlist(vnames[ncols > 0L])
) if (fix.empty.names && any(noname <- !nzchar(vnames))) vnames[noname] <- paste0("Var.", seq_along(vnames))[noname] if (check.na
mes) { if (fix.empty.names) vnames <- make.names(vnames, unique = TRUE) else { nz <- nzchar(vnames)
vnames[nz] <- make.names(vnames[nz], unique = TRUE) } } names(value) <- vnames if (!mrn) { if (length(row.names) ==
1L && nr != 1L) { if (is.character(row.names)) row.names <- match(row.names, vnames, 0L) if (length(row.
names) != 1L || row.names < 1L || row.names > length(vnames)) stop("'row.names' should specify one of the varia
bles") i <- row.names row.names <- value[[i]] value <- value[-i] } else if (!is.null(row.names)
&& length(row.names) != nr) stop("row names supplied are of the wrong length") } else if (!is.null(row.names) &&
length(row.names) != nr) { warning("row names were found from a short variable and have been discarded") row.names <- NULL }
class(value) <- "data.frame" if (is.null(row.names)) attr(value, "row.names") <- .set_row_names(nr) else { if (is.object
(row.names) || !is.integer(row.names)) row.names <- as.character(row.names) if (anyNA(row.names)) stop("row name
s contain missing values") if (anyDuplicated(row.names)) stop(gettextf("duplicate row.names: %s", paste(unique(row.names[dup
licated(row.names)]), collapse = ", ")), domain = NA) row.names(value) <- row.names } value})(y = c(NA, -1.0417146
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63672681309, -0.0132115175762433, 0.418573998056765, 0.289154478393644, -0.986285400744099, 0.249808373119544, 0.600392428709123, 1.67259872328
238, 2.33085183276967, 2.11535733988075, 3.01965638726982, 5.00118457322625, 3.47680940225078, 4.34982474367077, 2.47794340190924, 2.0310044461
8739, 0.0192994727968157, -0.893240380915633, -3.17777877575101, -1.60891236504203, 0.0947521606796244, 0.963598699923005, 1.97241154043038, 2.
82466505731791, 3.05307445361194, 2.66042278262455, 1.65059372226445, 0.810878941246378, -0.782842428548953, -1.36222967130566, -1.405523629905
54, -1.13257387441334, -0.447157464852298, 0.0748035994064509, -0.466339782341318, -0.142274036256453, -0.256130892549347, 0.0977563834294668,
-0.76513815357496, -0.26909581851517, 0.935666401635122, 0.280470182972412, -0.245316544743118, -0.184939618355814, -0.696634173151836, -0.0040
9429599125666, 0.813594313230532, 1.86342822885099, 2.95084083624916, 3.3801405763815, 3.14385059355091, 2.5960001649615, 2.45150869609362, 0.9
69854891094057, -0.600891268985021, -1.69107560349037, -1.92239888707922, -1.03934152209134, 0.511969827797069, 0.916945426236975, 2.6207740938
303, 3.82223336583999, 7.35861913397419, 7.39144623943109, 5.79602882795633, 6.08377254979566, 6.42952536877234, 3.59212786400513, 2.4557233992
8662, 1.40391740896429, 0.230736911716065, -0.734312925547564, -4.64459233569219, -3.63684227050659, -3.44799602431798, -4.32153583109362, -3.9
6098452484096, 0.35136716002738, 5.33455067996009, 9.04249467018953, 7.88449001157326, 7.28388970592313, 10.3015994398349, 11.1784861875327, 8.
22812947409235, 4.04491301956841, 2.00983818144176, 2.96761245671401, 1.61860655269184, -0.288845928635615, -0.292539442983523, -0.296014763088
064, -0.602211613825021, -2.50328990050961, -2.56508956164109, -2.12101851532808, -0.802230772964393, -4.64327144644253, -3.91039392500735, -1.
15460071160882, 3.83049375412845, -2.37030289473757, -2.08821408533533, -3.10052465762332, -1.23095997340142, 4.43211364529962, 1.3149745949149
6, -2.04402201241484, 8.02977638719636, 10.8505829036364, 10.995694791389, 10.6211926733194, 5.4848879911481, 4.79306180165145, 4.5712982421827
3, 0.367553786443436, -2.94622725160109, -1.76009562233923, -0.433487058956224, 1.63454597560027, 1.44284049465666, 2.25163193432175, 3.2904864
1827065, 5.04368859939246, 3.52794597188236, 3.19794056300817, 2.10926041266811, 1.77276333481953, 1.64668772187148, 1.22975776237421, 0.314655
201488942, -0.739970400331704, -1.35982623061866, -1.74609747598452, -2.13902825070657, -2.11094428963589, -1.04820600952053, -0.91191496810680
3, 0.410786350000119, 1.52208191991891, 1.62982846522956, 3.34656927408237, 4.96864655657976, 4.34420361328081, 3.94047934398697, 5.20983224401
609, 5.96963167848529, 5.48933005458204, 4.94286585986004, 4.04891999254193, 3.13130070325309, 3.01967278137342, 1.78333398307005, 0.8949231197
68645, 0.988899033533573, -0.307086414097035, -0.576311952971396, -1.6248666592958, -2.26693568313219, -2.47771197404217, -2.20141541535038, -1
.95273473771213, -0.716230344464838, 0.0402389430615031, 0.685334920061126, 1.20338633171545, 1.16853056390743, 0.788988442622664, 0.6830796687
95772, 0.393356175737644, 0.425439733348541, 0.378859067635277, 0.755039644663279, 1.46791062903829, 1.33751215224214, 1.84328741115418, 1.2479
2077765006, 0.721037770829102, 0.464427383750023, 0.32022361280417, -0.647150917173654, -0.665273657481282, 0.267632676547496, 1.89481430005507
, 3.45410370306301, 5.14444941328464, 6.26235354370972, 6.13339525921228, 5.92180270793412, 5.24851557953395, 4.12756565127089, 2.6339444112753
9, 1.33307858050258, 1.05023341496437, 1.09052481317623, 1.24975625439351, 0.575623851749329, -0.283558088749579, -1.00204400907347, -0.9721558
17289451, -1.2621131493284, -1.62927227652552, -1.88452074333761, -2.15011870309464, -1.66978286911072, -1.00893452929436, -0.749504096647169,
0.113713745230616, 0.579832217527144, 1.64204939253438, 3.60940917500705, 4.55562897550674, 4.22349571911989, 6.65945300623272, 6.4982943993485
3, 6.10374041278938, 5.46385307322339, 3.88668606999765, 3.18774096731282, 3.14581259178947, 0.122903999899204, -1.14374584039001, -1.492756639
04242, -0.931937965275412, -0.339072313025664, -0.368897600944827, 0.231043881089862, -0.0349786631684591, 0.534197407119342, 0.184331002239386
, 0.488862219993326, 0.302451614733994, -0.362778995702077, 0.656972505606692, 0.357267204930341, 0.460991553675116, 0.362184859308279, 0.26918
6053702313, -0.0657620155263319, 0.329458067627566, 0.623345800633755, 0.0228906692237999, 0.353157416298056, 0.309802870117217, -0.19673283666
4469, -0.501336276844305, 0.337694543146422, -0.379044758987052, -1.20505884935986, -1.15330437985234, -0.0033467144413335, -0.992192438771648,
-0.655441985702172, -0.74466420364392, -0.986019771107245, -0.387124137537353, 0.402692671075361, 0.966820123019883), check.names = FALSE, fix
names = TRUE, stringsAsFactors = FALSE)
3: do.call(data.frame, c(x, alis)) [2179/28683]
4: as.data.frame.list(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors)
5: as.data.frame(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors)
6: data.frame(value, row.names = rn, check.names = FALSE)
7: Ops.data.frame(forecast[, c(regressors)], data.frame(data)[, c(regressors)])
8: .f(.x[[i]], ...)
9: purrr::map(., .f = function(forecast) { error = data.frame(forecast) error[, c(regressors)] = forecast[, c(regressors)] - data.frame(
data)[, c(regressors)] return(error)})
10: forecasts %>% purrr::map(.f = function(forecast) { error = data.frame(forecast) error[, c(regressors)] = forecast[, c(regressors)] -
data.frame(data)[, c(regressors)] return(error)})
11: .f(.x[[i]], ...)
12: purrr::map(., .f = function(regime.val) { coef = models[[paste0("regime_", regime.val)]]$coef forecasts = list() for (i in 1:horiz
on) { if (i == 1) { X = Y %>% dplyr::select(dplyr::contains(".l"), dplyr::contains("const"), dplyr::contains(
"trend")) X.date = data$date } else { X = dplyr::bind_rows(dplyr::select(data[1:i, ], date,
regressors), dplyr::select(forecast_prev[i + 1:nrow(forecast_prev), ], date = forecast.date, regressors)) %>%
n.lag(lags = p) X.date = X$date X = X %>% dplyr::filter(!is.na(date)) %>% dplyr::select(dplyr::contains(".l"))
if ("const" %in% type | "both" %in% type) { X$const = 1 } if ("trend" %in% type | "both" %in% type) {
X$trend = c(1:nrow(X)) + (i - 1) } } forecast = as.matrix(X) %*% as.matrix(t(coef[, -1])) colnames(
forecast) = regressors if (i == 1) { forecast.date = stats::na.omit(X.date) } else { forecast.date =
forecast_date(forecast.date = stats::na.omit(X.date), horizon = i - 1, freq = freq) } forecast = data.frame(date
= data$date, forecast.date = forecast.date, forecast) %>% dplyr::left_join(dplyr::select(Y, date, model.regime = regim
e), by = "date") forecasts[[paste0("H_", i)]] = forecast forecast_prev = forecast } residuals = forecasts %>% purrr::map(.f
= function(forecast) { error = data.frame(forecast) error[, c(regressors)] = forecast[, c(regressors)] - data.frame(
data)[, c(regressors)] return(error) }) residuals = residuals %>% purrr::map(.f = function(r) { return(dplyr::filter(r, reg
ime.val == model.regime)) }) forecasts = forecasts %>% purrr::map(.f = function(f) { return(dplyr::filter(f, regime.val == model.r
egime)) }) return(list(forecasts = forecasts, residuals = residuals))})
13: as.list(regimes) %>% purrr::map(.f = function(regime.val) { coef = models[[paste0("regime_", regime.val)]]$coef forecasts = list()
for (i in 1:horizon) { if (i == 1) { X = Y %>% dplyr::select(dplyr::contains(".l"), dplyr::contains("const"),
dplyr::contains("trend")) X.date = data$date } else { X = dplyr::bind_rows(dplyr::select(data[1:i, ], dat
e, regressors), dplyr::select(forecast_prev[i + 1:nrow(forecast_prev), ], date = forecast.date,
regressors)) %>% n.lag(lags = p) X.date = X$date X = X %>% dplyr::filter(!is.na(date)) %>% dplyr::select(dplyr::contains
(".l")) if ("const" %in% type | "both" %in% type) { X$const = 1 } if ("trend" %in% type | "both
" %in% type) { X$trend = c(1:nrow(X)) + (i - 1) } } forecast = as.matrix(X) %*% as.matrix(t(coef[, -1])
) colnames(forecast) = regressors if (i == 1) { forecast.date = stats::na.omit(X.date) } else {
forecast.date = forecast_date(forecast.date = stats::na.omit(X.date), horizon = i - 1, freq = freq) } forecast
= data.frame(date = data$date, forecast.date = forecast.date, forecast) %>% dplyr::left_join(dplyr::select(Y, date, mo
del.regime = regime), by = "date") forecasts[[paste0("H_", i)]] = forecast forecast_prev = forecast } residuals = forecasts
%>% purrr::map(.f = function(forecast) { error = data.frame(forecast) error[, c(regressors)] = forecast[, c(regressors)] -
data.frame(data)[, c(regressors)] return(error) }) residuals = residuals %>% purrr::map(.f = function(r) { return(dp
lyr::filter(r, regime.val == model.regime)) }) forecasts = forecasts %>% purrr::map(.f = function(f) { return(dplyr::filter(f, reg
ime.val == model.regime)) }) return(list(forecasts = forecasts, residuals = residuals))})
14: RVAR_estimate(data = data, p = p, regime = regime, horizon = horizon, freq = freq, type = type)
15: sovereign::RVAR(data = Data.rec, regime = "cycle_position", p = 1, horizon = 10, freq = "quarter")
16: eval(expr, envir, enclos)
17: eval(expr, envir, enclos)
18: eval_with_user_handlers(expr, envir, enclos, user_handlers)
19: withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers))
20: withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler,
message = mHandler)
21: handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error =
eHandler, message = mHandler))
22: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler
, error = eHandler, message = mHandler)))
23: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, debug = debug, last = i == length(out), use_try = stop_on_error !=
2L, keep_warning = keep_warning, keep_message = keep_message, output_handler = output_handler, include_timing = include_timing)
24: evaluate::evaluate(...)
25: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), sto
p_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L
}, output_handler = knit_handlers(options$render, options))
26: in_dir(input_dir(), expr)
27: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$
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$render, options)))
28: eng_r(options)
29: block_exec(params)
30: call_block(x)
31: process_group.block(group)
32: process_group(group)
33: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { setwd(wd) cat(res,
sep = "\n", file = output %n% "") message("Quitting from lines ", paste(current_lines(i), collapse = "-"), " (", knit_conco
rd$get("infile"), ") ") })
34: process_file(text, output)
35: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
36: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
37: vweave_rmarkdown(...)
38: engine$weave(file, quiet = quiet, encoding = enc)
39: doTryCatch(return(expr), name, parentenv, handler)
40: tryCatchOne(expr, names, parentenv, handlers[[1L]])
41: tryCatchList(expr, classes, parentenv, handlers)
42: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", e
ngine = 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) { t
hisOK <<- FALSE fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, c
onditionMessage(e)))})
43: tools:::buildVignettes(dir = "/c4/home/henrik/repositories/future/revdep/checks/sovereign/new/sovereign.Rcheck/vign_test/sovereign", se
r_elibs = "/scratch/henrik/493473/Rtmplr8xJT/file1a2a916199ca4.rds")
An irrecoverable exception occurred. R is aborting now ...
* DONE
Status: 1 WARNING