Last updated on 2020-02-19 10:49:12 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.4-1 | 5.18 | 101.61 | 106.79 | WARN | |
| r-devel-linux-x86_64-debian-gcc | 0.4-1 | 4.98 | 73.65 | 78.63 | WARN | |
| r-devel-linux-x86_64-fedora-clang | 0.4-1 | 122.87 | WARN | |||
| r-devel-linux-x86_64-fedora-gcc | 0.4-1 | 120.61 | WARN | |||
| r-devel-windows-ix86+x86_64 | 0.4-1 | 10.00 | 171.00 | 181.00 | NOTE | |
| r-devel-windows-ix86+x86_64-gcc8 | 0.4-1 | 17.00 | 168.00 | 185.00 | NOTE | |
| r-patched-linux-x86_64 | 0.4-1 | 5.12 | 148.19 | 153.31 | NOTE | |
| r-patched-solaris-x86 | 0.4-1 | 242.50 | NOTE | |||
| r-release-linux-x86_64 | 0.4-1 | 4.54 | 148.74 | 153.28 | NOTE | |
| r-release-windows-ix86+x86_64 | 0.4-1 | 10.00 | 168.00 | 178.00 | NOTE | |
| r-release-osx-x86_64 | 0.4-1 | NOTE | ||||
| r-oldrel-windows-ix86+x86_64 | 0.4-1 | 6.00 | 174.00 | 180.00 | NOTE | |
| r-oldrel-osx-x86_64 | 0.4-1 | NOTE |
Version: 0.4-1
Check: R code for possible problems
Result: NOTE
addRegime: no visible global function definition for 'abline'
collapseRegimes: no visible global function definition for 'abline'
convertBack: no visible global function definition for 'as'
convertTreeData: no visible global function definition for 'as'
getBranchTimes: no visible global function definition for 'as'
propRegMatch: no visible global function definition for 'as'
startingModel: no visible global function definition for 'var'
surfaceAICMultiPlot: no visible global function definition for 'points'
surfaceAICMultiPlot: no visible global function definition for 'abline'
surfaceAICPlot: no visible global function definition for 'rainbow'
surfaceAICPlot: no visible global function definition for 'abline'
surfaceAICPlot: no visible global function definition for 'points'
surfaceBackward: no visible global function definition for 'as'
surfaceForward: no visible global function definition for 'as'
surfaceSimulate : <anonymous>: no visible global function definition
for 'sd'
surfaceSimulate: no visible global function definition for 'rnorm'
surfaceSimulate: no visible global function definition for 'runif'
surfaceSimulate: no visible global function definition for 'as'
surfaceSimulate: no visible global function definition for 'rmultinom'
surfaceTraitPlot: no visible global function definition for 'as'
surfaceTraitPlot: no visible global function definition for 'rainbow'
surfaceTraitPlot: no visible global function definition for 'grey'
surfaceTraitPlot: no visible global function definition for 'polygon'
surfaceTraitPlot: no visible global function definition for 'points'
surfaceTreePlot: no visible global function definition for 'as'
surfaceTreePlot: no visible global function definition for 'rainbow'
surfaceTreePlot: no visible global function definition for 'grey'
Undefined global functions or variables:
abline as grey points polygon rainbow rmultinom rnorm runif sd var
Consider adding
importFrom("grDevices", "grey", "rainbow")
importFrom("graphics", "abline", "points", "polygon")
importFrom("methods", "as")
importFrom("stats", "rmultinom", "rnorm", "runif", "sd", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
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: 0.4-1
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building 'surface_tutorial.Rnw' using Sweave
Loading required package: ape
Loading required package: ouch
Loading required package: subplex
Loading required package: MASS
Loading required package: geiger
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
surface
--- call from context ---
surfaceSummary(fwd)
--- call from argument ---
if (class(lnls) != "matrix") lnls <- matrix(lnls, nrow = 1, dimnames = list(names(lnls)[1],
NULL))
--- R stacktrace ---
where 1: surfaceSummary(fwd)
where 2: eval(expr, .GlobalEnv)
where 3: eval(expr, .GlobalEnv)
where 4: withVisible(eval(expr, .GlobalEnv))
where 5: doTryCatch(return(expr), name, parentenv, handler)
where 6: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 7: tryCatchList(expr, classes, parentenv, handlers)
where 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)[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))
})
where 9: try(withVisible(eval(expr, .GlobalEnv)), silent = TRUE)
where 10: evalFunc(ce, options)
where 11: tryCatchList(expr, classes, parentenv, handlers)
where 12: tryCatch(evalFunc(ce, options), finally = {
cat("\n")
sink()
})
where 13: driver$runcode(drobj, chunk, chunkopts)
where 14: utils::Sweave(...)
where 15: engine$weave(file, quiet = quiet, encoding = enc)
where 16: doTryCatch(return(expr), name, parentenv, handler)
where 17: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 18: tryCatchList(expr, classes, parentenv, handlers)
where 19: tryCatch({
engine$weave(file, quiet = quiet, encoding = enc)
setwd(startdir)
output <- find_vignette_product(name, by = "weave", engine = engine)
if (!have.makefile && vignette_is_tex(output)) {
texi2pdf(file = output, clean = FALSE, quiet = quiet)
output <- find_vignette_product(name, by = "texi2pdf",
engine = engine)
}
outputs <- c(outputs, output)
}, error = function(e) {
thisOK <<- FALSE
fails <<- c(fails, file)
message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",
file, conditionMessage(e)))
})
where 20: tools:::buildVignettes(dir = "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/surface.Rcheck/vign_test/surface",
ser_elibs = "/tmp/RtmpheLSfa/file3c5f469f8511.rds")
--- value of length: 2 type: logical ---
[1] FALSE TRUE
--- function from context ---
function (fwd = NULL, bwd = NULL)
{
if (is.null(fwd))
obj <- bwd
if (is.null(bwd))
obj <- fwd
if (!is.null(fwd) & !is.null(bwd)) {
obj <- c(fwd[-length(fwd)], bwd)
}
k <- length(obj)
lnls <- sapply(obj, function(x) {
sapply(x$fit, function(y) summary(y)$loglik)
})
if (class(lnls) != "matrix")
lnls <- matrix(lnls, nrow = 1, dimnames = list(names(lnls)[1],
NULL))
aics <- sapply(obj, function(x) x$aic)
names(aics) <- 1:k
n_regimes_seq <- sapply(obj, function(x) x$n_regimes)
obj <- obj[[k]]
shifts <- obj$savedshifts
n_regimes <- obj$n_regimes
obj <- obj$fit
alpha <- sapply(obj, function(x) summary(x)$alpha)
phylhalflife <- log(2)/alpha
sigma_squared <- sapply(obj, function(x) summary(x)$sigma.squared)
theta <- sapply(obj, function(x) summary(x)$optima[[1]])
list(n_steps = k, lnls = lnls, n_regimes_seq = n_regimes_seq,
aics = aics, shifts = shifts, n_regimes = n_regimes,
alpha = alpha, phylhalflife = phylhalflife, sigma_squared = sigma_squared,
theta = theta)
}
<bytecode: 0x30f9748>
<environment: namespace:surface>
--- function search by body ---
Function surfaceSummary in namespace surface has this body.
----------- END OF FAILURE REPORT --------------
Error: processing vignette 'surface_tutorial.Rnw' failed with diagnostics:
chunk 4
Error in if (class(lnls) != "matrix") lnls <- matrix(lnls, nrow = 1, dimnames = list(names(lnls)[1], :
the condition has length > 1
--- failed re-building 'surface_tutorial.Rnw'
SUMMARY: processing the following file failed:
'surface_tutorial.Rnw'
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.4-1
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building ‘surface_tutorial.Rnw’ using Sweave
Loading required package: ape
Loading required package: ouch
Loading required package: subplex
Loading required package: MASS
Loading required package: geiger
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
surface
--- call from context ---
surfaceSummary(fwd)
--- call from argument ---
if (class(lnls) != "matrix") lnls <- matrix(lnls, nrow = 1, dimnames = list(names(lnls)[1],
NULL))
--- R stacktrace ---
where 1: surfaceSummary(fwd)
where 2: eval(expr, .GlobalEnv)
where 3: eval(expr, .GlobalEnv)
where 4: withVisible(eval(expr, .GlobalEnv))
where 5: doTryCatch(return(expr), name, parentenv, handler)
where 6: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 7: tryCatchList(expr, classes, parentenv, handlers)
where 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)[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))
})
where 9: try(withVisible(eval(expr, .GlobalEnv)), silent = TRUE)
where 10: evalFunc(ce, options)
where 11: tryCatchList(expr, classes, parentenv, handlers)
where 12: tryCatch(evalFunc(ce, options), finally = {
cat("\n")
sink()
})
where 13: driver$runcode(drobj, chunk, chunkopts)
where 14: utils::Sweave(...)
where 15: engine$weave(file, quiet = quiet, encoding = enc)
where 16: doTryCatch(return(expr), name, parentenv, handler)
where 17: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 18: tryCatchList(expr, classes, parentenv, handlers)
where 19: tryCatch({
engine$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 20: tools:::buildVignettes(dir = "/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/surface.Rcheck/vign_test/surface",
ser_elibs = "/home/hornik/tmp/scratch/Rtmpmxdc6M/file594b6b8eb1ca.rds")
--- value of length: 2 type: logical ---
[1] FALSE TRUE
--- function from context ---
function (fwd = NULL, bwd = NULL)
{
if (is.null(fwd))
obj <- bwd
if (is.null(bwd))
obj <- fwd
if (!is.null(fwd) & !is.null(bwd)) {
obj <- c(fwd[-length(fwd)], bwd)
}
k <- length(obj)
lnls <- sapply(obj, function(x) {
sapply(x$fit, function(y) summary(y)$loglik)
})
if (class(lnls) != "matrix")
lnls <- matrix(lnls, nrow = 1, dimnames = list(names(lnls)[1],
NULL))
aics <- sapply(obj, function(x) x$aic)
names(aics) <- 1:k
n_regimes_seq <- sapply(obj, function(x) x$n_regimes)
obj <- obj[[k]]
shifts <- obj$savedshifts
n_regimes <- obj$n_regimes
obj <- obj$fit
alpha <- sapply(obj, function(x) summary(x)$alpha)
phylhalflife <- log(2)/alpha
sigma_squared <- sapply(obj, function(x) summary(x)$sigma.squared)
theta <- sapply(obj, function(x) summary(x)$optima[[1]])
list(n_steps = k, lnls = lnls, n_regimes_seq = n_regimes_seq,
aics = aics, shifts = shifts, n_regimes = n_regimes,
alpha = alpha, phylhalflife = phylhalflife, sigma_squared = sigma_squared,
theta = theta)
}
<bytecode: 0x559bd55dcae0>
<environment: namespace:surface>
--- function search by body ---
Function surfaceSummary in namespace surface has this body.
----------- END OF FAILURE REPORT --------------
Error: processing vignette 'surface_tutorial.Rnw' failed with diagnostics:
chunk 4
Error in if (class(lnls) != "matrix") lnls <- matrix(lnls, nrow = 1, dimnames = list(names(lnls)[1], :
the condition has length > 1
--- failed re-building ‘surface_tutorial.Rnw’
SUMMARY: processing the following file failed:
‘surface_tutorial.Rnw’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.4-1
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
--- re-building ‘surface_tutorial.Rnw’ using Sweave
Loading required package: ape
Loading required package: ouch
Loading required package: subplex
Loading required package: MASS
Loading required package: geiger
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
surface
--- call from context ---
surfaceSummary(fwd)
--- call from argument ---
if (class(lnls) != "matrix") lnls <- matrix(lnls, nrow = 1, dimnames = list(names(lnls)[1],
NULL))
--- R stacktrace ---
where 1: surfaceSummary(fwd)
where 2: eval(expr, .GlobalEnv)
where 3: eval(expr, .GlobalEnv)
where 4: withVisible(eval(expr, .GlobalEnv))
where 5: doTryCatch(return(expr), name, parentenv, handler)
where 6: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 7: tryCatchList(expr, classes, parentenv, handlers)
where 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)[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))
})
where 9: try(withVisible(eval(expr, .GlobalEnv)), silent = TRUE)
where 10: evalFunc(ce, options)
where 11: tryCatchList(expr, classes, parentenv, handlers)
where 12: tryCatch(evalFunc(ce, options), finally = {
cat("\n")
sink()
})
where 13: driver$runcode(drobj, chunk, chunkopts)
where 14: utils::Sweave(...)
where 15: engine$weave(file, quiet = quiet, encoding = enc)
where 16: doTryCatch(return(expr), name, parentenv, handler)
where 17: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 18: tryCatchList(expr, classes, parentenv, handlers)
where 19: tryCatch({
engine$weave(file, quiet = quiet, encoding = enc)
setwd(startdir)
output <- find_vignette_product(name, by = "weave", engine = engine)
if (!have.makefile && vignette_is_tex(output)) {
texi2pdf(file = output, clean = FALSE, quiet = quiet)
output <- find_vignette_product(name, by = "texi2pdf",
engine = engine)
}
outputs <- c(outputs, output)
}, error = function(e) {
thisOK <<- FALSE
fails <<- c(fails, file)
message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",
file, conditionMessage(e)))
})
where 20: tools:::buildVignettes(dir = "/data/gannet/ripley/R/packages/tests-clang/surface.Rcheck/vign_test/surface",
ser_elibs = "/tmp/RtmpWQlVWD/file73d073c7a4cb.rds")
--- value of length: 2 type: logical ---
[1] FALSE TRUE
--- function from context ---
function (fwd = NULL, bwd = NULL)
{
if (is.null(fwd))
obj <- bwd
if (is.null(bwd))
obj <- fwd
if (!is.null(fwd) & !is.null(bwd)) {
obj <- c(fwd[-length(fwd)], bwd)
}
k <- length(obj)
lnls <- sapply(obj, function(x) {
sapply(x$fit, function(y) summary(y)$loglik)
})
if (class(lnls) != "matrix")
lnls <- matrix(lnls, nrow = 1, dimnames = list(names(lnls)[1],
NULL))
aics <- sapply(obj, function(x) x$aic)
names(aics) <- 1:k
n_regimes_seq <- sapply(obj, function(x) x$n_regimes)
obj <- obj[[k]]
shifts <- obj$savedshifts
n_regimes <- obj$n_regimes
obj <- obj$fit
alpha <- sapply(obj, function(x) summary(x)$alpha)
phylhalflife <- log(2)/alpha
sigma_squared <- sapply(obj, function(x) summary(x)$sigma.squared)
theta <- sapply(obj, function(x) summary(x)$optima[[1]])
list(n_steps = k, lnls = lnls, n_regimes_seq = n_regimes_seq,
aics = aics, shifts = shifts, n_regimes = n_regimes,
alpha = alpha, phylhalflife = phylhalflife, sigma_squared = sigma_squared,
theta = theta)
}
<bytecode: 0x6922b28>
<environment: namespace:surface>
--- function search by body ---
Function surfaceSummary in namespace surface has this body.
----------- END OF FAILURE REPORT --------------
Error: processing vignette 'surface_tutorial.Rnw' failed with diagnostics:
chunk 4
Error in if (class(lnls) != "matrix") lnls <- matrix(lnls, nrow = 1, dimnames = list(names(lnls)[1], :
the condition has length > 1
--- failed re-building ‘surface_tutorial.Rnw’
SUMMARY: processing the following file failed:
‘surface_tutorial.Rnw’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.4-1
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
--- re-building ‘surface_tutorial.Rnw’ using Sweave
Loading required package: ape
Loading required package: ouch
Loading required package: subplex
Loading required package: MASS
Loading required package: geiger
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
surface
--- call from context ---
surfaceSummary(fwd)
--- call from argument ---
if (class(lnls) != "matrix") lnls <- matrix(lnls, nrow = 1, dimnames = list(names(lnls)[1],
NULL))
--- R stacktrace ---
where 1: surfaceSummary(fwd)
where 2: eval(expr, .GlobalEnv)
where 3: eval(expr, .GlobalEnv)
where 4: withVisible(eval(expr, .GlobalEnv))
where 5: doTryCatch(return(expr), name, parentenv, handler)
where 6: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 7: tryCatchList(expr, classes, parentenv, handlers)
where 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)[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))
})
where 9: try(withVisible(eval(expr, .GlobalEnv)), silent = TRUE)
where 10: evalFunc(ce, options)
where 11: tryCatchList(expr, classes, parentenv, handlers)
where 12: tryCatch(evalFunc(ce, options), finally = {
cat("\n")
sink()
})
where 13: driver$runcode(drobj, chunk, chunkopts)
where 14: utils::Sweave(...)
where 15: engine$weave(file, quiet = quiet, encoding = enc)
where 16: doTryCatch(return(expr), name, parentenv, handler)
where 17: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 18: tryCatchList(expr, classes, parentenv, handlers)
where 19: tryCatch({
engine$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 20: tools:::buildVignettes(dir = "/data/gannet/ripley/R/packages/tests-devel/surface.Rcheck/vign_test/surface",
ser_elibs = "/tmp/RtmpP9T0mf/file22026eeb128f.rds")
--- value of length: 2 type: logical ---
[1] FALSE TRUE
--- function from context ---
function (fwd = NULL, bwd = NULL)
{
if (is.null(fwd))
obj <- bwd
if (is.null(bwd))
obj <- fwd
if (!is.null(fwd) & !is.null(bwd)) {
obj <- c(fwd[-length(fwd)], bwd)
}
k <- length(obj)
lnls <- sapply(obj, function(x) {
sapply(x$fit, function(y) summary(y)$loglik)
})
if (class(lnls) != "matrix")
lnls <- matrix(lnls, nrow = 1, dimnames = list(names(lnls)[1],
NULL))
aics <- sapply(obj, function(x) x$aic)
names(aics) <- 1:k
n_regimes_seq <- sapply(obj, function(x) x$n_regimes)
obj <- obj[[k]]
shifts <- obj$savedshifts
n_regimes <- obj$n_regimes
obj <- obj$fit
alpha <- sapply(obj, function(x) summary(x)$alpha)
phylhalflife <- log(2)/alpha
sigma_squared <- sapply(obj, function(x) summary(x)$sigma.squared)
theta <- sapply(obj, function(x) summary(x)$optima[[1]])
list(n_steps = k, lnls = lnls, n_regimes_seq = n_regimes_seq,
aics = aics, shifts = shifts, n_regimes = n_regimes,
alpha = alpha, phylhalflife = phylhalflife, sigma_squared = sigma_squared,
theta = theta)
}
<bytecode: 0x510fb78>
<environment: namespace:surface>
--- function search by body ---
Function surfaceSummary in namespace surface has this body.
----------- END OF FAILURE REPORT --------------
Error: processing vignette 'surface_tutorial.Rnw' failed with diagnostics:
chunk 4
Error in if (class(lnls) != "matrix") lnls <- matrix(lnls, nrow = 1, dimnames = list(names(lnls)[1], :
the condition has length > 1
--- failed re-building ‘surface_tutorial.Rnw’
SUMMARY: processing the following file failed:
‘surface_tutorial.Rnw’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc