Last updated on 2020-02-19 10:49:10 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.3.4 | 10.60 | 35.64 | 46.24 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 0.3.4 | 9.43 | 27.19 | 36.62 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.3.4 | 57.85 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 0.3.4 | 56.67 | ERROR | |||
| r-devel-windows-ix86+x86_64 | 0.3.4 | 27.00 | 76.00 | 103.00 | OK | |
| r-devel-windows-ix86+x86_64-gcc8 | 0.3.4 | 35.00 | 107.00 | 142.00 | OK | |
| r-patched-linux-x86_64 | 0.3.4 | 9.83 | 35.50 | 45.33 | OK | |
| r-patched-solaris-x86 | 0.3.4 | 85.60 | OK | |||
| r-release-linux-x86_64 | 0.3.4 | 10.65 | 35.44 | 46.09 | OK | |
| r-release-windows-ix86+x86_64 | 0.3.4 | 25.00 | 69.00 | 94.00 | OK | |
| r-release-osx-x86_64 | 0.3.4 | OK | ||||
| r-oldrel-windows-ix86+x86_64 | 0.3.4 | 22.00 | 80.00 | 102.00 | OK | |
| r-oldrel-osx-x86_64 | 0.3.4 | OK |
Version: 0.3.4
Check: examples
Result: ERROR
Running examples in 'SpeciesMix-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: SpeciesMix
> ### Title: Fit finite mixture models to species distributions
> ### Aliases: SpeciesMix
> ### Keywords: misc
>
> ### ** Examples
>
> G <-4
> S <- 50
> theta <- matrix(c(-9,35,-32,0,0.7,0,-16,23,-8.2,-3,-0.6,0.8),4,3,byrow=TRUE)
> dat <- data.frame(y=rep(1,200),x=runif(200,0,2.5),z=rnorm(200,10,2))
> dat <- data.frame(dat,x.sq=dat$x^2)
> dat1 <- artificial.data(y~1+x+x.sq,dat,theta,S)
> fm4 <- SpeciesMix(obs~1+x+x.sq,dat1$pa,dat,G=4,em.prefit=TRUE,em.refit=1,est.var=TRUE)
Fitting Group 4
Iteration | LogL
1 | -6009.394
2 | -4540.395
3 | -4433.871
initial value 4433.871314
iter 10 value 3959.166846
iter 20 value 3832.497287
final value 3795.236914
converged
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
SpeciesMix
--- call from context ---
SpeciesMix.bernoulli(sp.form, sp.data, covar.data, G, pars, em.prefit,
em.steps, em.refit, est.var, residuals, trace, r1 = FALSE)
--- call from argument ---
if (class(fmM.out$covar) != "try-error") {
tmp <- sqrt(diag(fmM.out$covar))
tmp <- tmp[(G):length(tmp)]
fmM.out$se <- matrix(tmp, G, ncol(fmM.out$coef))
colnames(fmM.out$se) <- colnames(fmM.out$coef)
rownames(fmM.out$se) <- rownames(fmM.out$coef)
}
--- R stacktrace ---
where 1: SpeciesMix.bernoulli(sp.form, sp.data, covar.data, G, pars, em.prefit,
em.steps, em.refit, est.var, residuals, trace, r1 = FALSE)
where 2: SpeciesMix(obs ~ 1 + x + x.sq, dat1$pa, dat, G = 4, em.prefit = TRUE,
em.refit = 1, est.var = TRUE)
--- value of length: 2 type: logical ---
[1] TRUE TRUE
--- function from context ---
function (sp.form, sp.data, covar.data, G = 2, pars = NA, em.prefit = TRUE,
em.steps = 4, em.refit = 1, est.var = FALSE, residuals = FALSE,
trace = TRUE, r1 = FALSE)
{
t.covar.data <- covar.data
t.sp.data <- sp.data
sp.form <- update.formula(sp.form, obs ~ 1 + .)
if (em.prefit | G == 1) {
prefit <- SpeciesMix.em(sp.form, sp.data, covar.data,
G, ite.max = em.steps, em.refit = em.refit, r1)
pars <- c(additive.logistic(prefit$pi, T)[1:(G - 1)],
unlist(prefit$coef))
}
S <- dim(sp.data)[2]
if (is.null(colnames(sp.data))) {
sp.name <- 1:S
}
else {
sp.name <- colnames(sp.data)
}
n <- dim(sp.data)[1]
sp <- rep(sp.name, each = n)
if (G == 1)
return(prefit)
var.names <- colnames(covar.data)
covar.data <- data.frame(kronecker(rep(1, S), as.matrix(covar.data)))
names(covar.data) <- var.names
sp.data <- as.data.frame(sp.data)
data <- data.frame(obs = as.numeric(unlist(sp.data)), covar.data)
names(data)[1] <- as.character(sp.form)[2]
fmM.out <- fitmix.cpp(sp.form, data, sp, G, pars = pars,
calc.hes = est.var, r1)
while (fmM.out$logl == 0) {
prefit <- SpeciesMix.em(sp.form, t.sp.data, t.covar.data,
G, ite.max = em.steps, em.refit = 1, r1)
pars <- c(additive.logistic(prefit$pi, T)[1:(G - 1)],
unlist(prefit$coef))
fmM.out <- fitmix.cpp(sp.form, data, sp, G, pars = pars,
calc.hes = est.var, r1)
}
rownames(fmM.out$tau) <- sp.name
fmM.out$se <- NA
if (est.var) {
fmM.out$covar <- try(solve(fmM.out$hessian))
if (class(fmM.out$covar) != "try-error") {
tmp <- sqrt(diag(fmM.out$covar))
tmp <- tmp[(G):length(tmp)]
fmM.out$se <- matrix(tmp, G, ncol(fmM.out$coef))
colnames(fmM.out$se) <- colnames(fmM.out$coef)
rownames(fmM.out$se) <- rownames(fmM.out$coef)
}
}
if (residuals)
fmM.out$residuals <- mix.residuals(fmM.out, sp.form,
data, sp)
fmM.out$formula <- sp.form
class(fmM.out) <- c("archetype", "bernoulli")
fmM.out
}
<bytecode: 0x2d664f0>
<environment: namespace:SpeciesMix>
--- function search by body ---
Function SpeciesMix.bernoulli in namespace SpeciesMix has this body.
----------- END OF FAILURE REPORT --------------
Error in if (class(fmM.out$covar) != "try-error") { :
the condition has length > 1
Calls: SpeciesMix -> SpeciesMix.bernoulli
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.3.4
Check: examples
Result: ERROR
Running examples in ‘SpeciesMix-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: SpeciesMix
> ### Title: Fit finite mixture models to species distributions
> ### Aliases: SpeciesMix
> ### Keywords: misc
>
> ### ** Examples
>
> G <-4
> S <- 50
> theta <- matrix(c(-9,35,-32,0,0.7,0,-16,23,-8.2,-3,-0.6,0.8),4,3,byrow=TRUE)
> dat <- data.frame(y=rep(1,200),x=runif(200,0,2.5),z=rnorm(200,10,2))
> dat <- data.frame(dat,x.sq=dat$x^2)
> dat1 <- artificial.data(y~1+x+x.sq,dat,theta,S)
> fm4 <- SpeciesMix(obs~1+x+x.sq,dat1$pa,dat,G=4,em.prefit=TRUE,em.refit=1,est.var=TRUE)
Fitting Group 4
Iteration | LogL
1 | -6009.394
2 | -4540.395
3 | -4433.871
initial value 4433.871314
iter 10 value 3958.782816
iter 20 value 3827.504738
final value 3795.236915
converged
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
SpeciesMix
--- call from context ---
SpeciesMix.bernoulli(sp.form, sp.data, covar.data, G, pars, em.prefit,
em.steps, em.refit, est.var, residuals, trace, r1 = FALSE)
--- call from argument ---
if (class(fmM.out$covar) != "try-error") {
tmp <- sqrt(diag(fmM.out$covar))
tmp <- tmp[(G):length(tmp)]
fmM.out$se <- matrix(tmp, G, ncol(fmM.out$coef))
colnames(fmM.out$se) <- colnames(fmM.out$coef)
rownames(fmM.out$se) <- rownames(fmM.out$coef)
}
--- R stacktrace ---
where 1: SpeciesMix.bernoulli(sp.form, sp.data, covar.data, G, pars, em.prefit,
em.steps, em.refit, est.var, residuals, trace, r1 = FALSE)
where 2: SpeciesMix(obs ~ 1 + x + x.sq, dat1$pa, dat, G = 4, em.prefit = TRUE,
em.refit = 1, est.var = TRUE)
--- value of length: 2 type: logical ---
[1] TRUE TRUE
--- function from context ---
function (sp.form, sp.data, covar.data, G = 2, pars = NA, em.prefit = TRUE,
em.steps = 4, em.refit = 1, est.var = FALSE, residuals = FALSE,
trace = TRUE, r1 = FALSE)
{
t.covar.data <- covar.data
t.sp.data <- sp.data
sp.form <- update.formula(sp.form, obs ~ 1 + .)
if (em.prefit | G == 1) {
prefit <- SpeciesMix.em(sp.form, sp.data, covar.data,
G, ite.max = em.steps, em.refit = em.refit, r1)
pars <- c(additive.logistic(prefit$pi, T)[1:(G - 1)],
unlist(prefit$coef))
}
S <- dim(sp.data)[2]
if (is.null(colnames(sp.data))) {
sp.name <- 1:S
}
else {
sp.name <- colnames(sp.data)
}
n <- dim(sp.data)[1]
sp <- rep(sp.name, each = n)
if (G == 1)
return(prefit)
var.names <- colnames(covar.data)
covar.data <- data.frame(kronecker(rep(1, S), as.matrix(covar.data)))
names(covar.data) <- var.names
sp.data <- as.data.frame(sp.data)
data <- data.frame(obs = as.numeric(unlist(sp.data)), covar.data)
names(data)[1] <- as.character(sp.form)[2]
fmM.out <- fitmix.cpp(sp.form, data, sp, G, pars = pars,
calc.hes = est.var, r1)
while (fmM.out$logl == 0) {
prefit <- SpeciesMix.em(sp.form, t.sp.data, t.covar.data,
G, ite.max = em.steps, em.refit = 1, r1)
pars <- c(additive.logistic(prefit$pi, T)[1:(G - 1)],
unlist(prefit$coef))
fmM.out <- fitmix.cpp(sp.form, data, sp, G, pars = pars,
calc.hes = est.var, r1)
}
rownames(fmM.out$tau) <- sp.name
fmM.out$se <- NA
if (est.var) {
fmM.out$covar <- try(solve(fmM.out$hessian))
if (class(fmM.out$covar) != "try-error") {
tmp <- sqrt(diag(fmM.out$covar))
tmp <- tmp[(G):length(tmp)]
fmM.out$se <- matrix(tmp, G, ncol(fmM.out$coef))
colnames(fmM.out$se) <- colnames(fmM.out$coef)
rownames(fmM.out$se) <- rownames(fmM.out$coef)
}
}
if (residuals)
fmM.out$residuals <- mix.residuals(fmM.out, sp.form,
data, sp)
fmM.out$formula <- sp.form
class(fmM.out) <- c("archetype", "bernoulli")
fmM.out
}
<bytecode: 0x558de29b9288>
<environment: namespace:SpeciesMix>
--- function search by body ---
Function SpeciesMix.bernoulli in namespace SpeciesMix has this body.
----------- END OF FAILURE REPORT --------------
Error in if (class(fmM.out$covar) != "try-error") { :
the condition has length > 1
Calls: SpeciesMix -> SpeciesMix.bernoulli
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.3.4
Check: compiled code
Result: NOTE
File ‘SpeciesMix/libs/SpeciesMix.so’:
Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’
It is good practice to register native routines and to disable symbol
search.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 0.3.4
Check: examples
Result: ERROR
Running examples in ‘SpeciesMix-Ex.R’ failed
The error most likely occurred in:
> ### Name: SpeciesMix
> ### Title: Fit finite mixture models to species distributions
> ### Aliases: SpeciesMix
> ### Keywords: misc
>
> ### ** Examples
>
> G <-4
> S <- 50
> theta <- matrix(c(-9,35,-32,0,0.7,0,-16,23,-8.2,-3,-0.6,0.8),4,3,byrow=TRUE)
> dat <- data.frame(y=rep(1,200),x=runif(200,0,2.5),z=rnorm(200,10,2))
> dat <- data.frame(dat,x.sq=dat$x^2)
> dat1 <- artificial.data(y~1+x+x.sq,dat,theta,S)
> fm4 <- SpeciesMix(obs~1+x+x.sq,dat1$pa,dat,G=4,em.prefit=TRUE,em.refit=1,est.var=TRUE)
Fitting Group 4
Iteration | LogL
1 | -6009.394
2 | -4540.395
3 | -4433.871
initial value 4433.871314
iter 10 value 3959.166846
iter 20 value 3832.497287
final value 3795.236914
converged
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
SpeciesMix
--- call from context ---
SpeciesMix.bernoulli(sp.form, sp.data, covar.data, G, pars, em.prefit,
em.steps, em.refit, est.var, residuals, trace, r1 = FALSE)
--- call from argument ---
if (class(fmM.out$covar) != "try-error") {
tmp <- sqrt(diag(fmM.out$covar))
tmp <- tmp[(G):length(tmp)]
fmM.out$se <- matrix(tmp, G, ncol(fmM.out$coef))
colnames(fmM.out$se) <- colnames(fmM.out$coef)
rownames(fmM.out$se) <- rownames(fmM.out$coef)
}
--- R stacktrace ---
where 1: SpeciesMix.bernoulli(sp.form, sp.data, covar.data, G, pars, em.prefit,
em.steps, em.refit, est.var, residuals, trace, r1 = FALSE)
where 2: SpeciesMix(obs ~ 1 + x + x.sq, dat1$pa, dat, G = 4, em.prefit = TRUE,
em.refit = 1, est.var = TRUE)
--- value of length: 2 type: logical ---
[1] TRUE TRUE
--- function from context ---
function (sp.form, sp.data, covar.data, G = 2, pars = NA, em.prefit = TRUE,
em.steps = 4, em.refit = 1, est.var = FALSE, residuals = FALSE,
trace = TRUE, r1 = FALSE)
{
t.covar.data <- covar.data
t.sp.data <- sp.data
sp.form <- update.formula(sp.form, obs ~ 1 + .)
if (em.prefit | G == 1) {
prefit <- SpeciesMix.em(sp.form, sp.data, covar.data,
G, ite.max = em.steps, em.refit = em.refit, r1)
pars <- c(additive.logistic(prefit$pi, T)[1:(G - 1)],
unlist(prefit$coef))
}
S <- dim(sp.data)[2]
if (is.null(colnames(sp.data))) {
sp.name <- 1:S
}
else {
sp.name <- colnames(sp.data)
}
n <- dim(sp.data)[1]
sp <- rep(sp.name, each = n)
if (G == 1)
return(prefit)
var.names <- colnames(covar.data)
covar.data <- data.frame(kronecker(rep(1, S), as.matrix(covar.data)))
names(covar.data) <- var.names
sp.data <- as.data.frame(sp.data)
data <- data.frame(obs = as.numeric(unlist(sp.data)), covar.data)
names(data)[1] <- as.character(sp.form)[2]
fmM.out <- fitmix.cpp(sp.form, data, sp, G, pars = pars,
calc.hes = est.var, r1)
while (fmM.out$logl == 0) {
prefit <- SpeciesMix.em(sp.form, t.sp.data, t.covar.data,
G, ite.max = em.steps, em.refit = 1, r1)
pars <- c(additive.logistic(prefit$pi, T)[1:(G - 1)],
unlist(prefit$coef))
fmM.out <- fitmix.cpp(sp.form, data, sp, G, pars = pars,
calc.hes = est.var, r1)
}
rownames(fmM.out$tau) <- sp.name
fmM.out$se <- NA
if (est.var) {
fmM.out$covar <- try(solve(fmM.out$hessian))
if (class(fmM.out$covar) != "try-error") {
tmp <- sqrt(diag(fmM.out$covar))
tmp <- tmp[(G):length(tmp)]
fmM.out$se <- matrix(tmp, G, ncol(fmM.out$coef))
colnames(fmM.out$se) <- colnames(fmM.out$coef)
rownames(fmM.out$se) <- rownames(fmM.out$coef)
}
}
if (residuals)
fmM.out$residuals <- mix.residuals(fmM.out, sp.form,
data, sp)
fmM.out$formula <- sp.form
class(fmM.out) <- c("archetype", "bernoulli")
fmM.out
}
<bytecode: 0x3c012b8>
<environment: namespace:SpeciesMix>
--- function search by body ---
Function SpeciesMix.bernoulli in namespace SpeciesMix has this body.
----------- END OF FAILURE REPORT --------------
Error in if (class(fmM.out$covar) != "try-error") { :
the condition has length > 1
Calls: SpeciesMix -> SpeciesMix.bernoulli
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.3.4
Check: examples
Result: ERROR
Running examples in ‘SpeciesMix-Ex.R’ failed
The error most likely occurred in:
> ### Name: SpeciesMix
> ### Title: Fit finite mixture models to species distributions
> ### Aliases: SpeciesMix
> ### Keywords: misc
>
> ### ** Examples
>
> G <-4
> S <- 50
> theta <- matrix(c(-9,35,-32,0,0.7,0,-16,23,-8.2,-3,-0.6,0.8),4,3,byrow=TRUE)
> dat <- data.frame(y=rep(1,200),x=runif(200,0,2.5),z=rnorm(200,10,2))
> dat <- data.frame(dat,x.sq=dat$x^2)
> dat1 <- artificial.data(y~1+x+x.sq,dat,theta,S)
> fm4 <- SpeciesMix(obs~1+x+x.sq,dat1$pa,dat,G=4,em.prefit=TRUE,em.refit=1,est.var=TRUE)
Fitting Group 4
Iteration | LogL
1 | -6009.394
2 | -4540.395
3 | -4433.871
initial value 4433.871314
iter 10 value 3959.166846
iter 20 value 3832.497287
final value 3795.236914
converged
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
SpeciesMix
--- call from context ---
SpeciesMix.bernoulli(sp.form, sp.data, covar.data, G, pars, em.prefit,
em.steps, em.refit, est.var, residuals, trace, r1 = FALSE)
--- call from argument ---
if (class(fmM.out$covar) != "try-error") {
tmp <- sqrt(diag(fmM.out$covar))
tmp <- tmp[(G):length(tmp)]
fmM.out$se <- matrix(tmp, G, ncol(fmM.out$coef))
colnames(fmM.out$se) <- colnames(fmM.out$coef)
rownames(fmM.out$se) <- rownames(fmM.out$coef)
}
--- R stacktrace ---
where 1: SpeciesMix.bernoulli(sp.form, sp.data, covar.data, G, pars, em.prefit,
em.steps, em.refit, est.var, residuals, trace, r1 = FALSE)
where 2: SpeciesMix(obs ~ 1 + x + x.sq, dat1$pa, dat, G = 4, em.prefit = TRUE,
em.refit = 1, est.var = TRUE)
--- value of length: 2 type: logical ---
[1] TRUE TRUE
--- function from context ---
function (sp.form, sp.data, covar.data, G = 2, pars = NA, em.prefit = TRUE,
em.steps = 4, em.refit = 1, est.var = FALSE, residuals = FALSE,
trace = TRUE, r1 = FALSE)
{
t.covar.data <- covar.data
t.sp.data <- sp.data
sp.form <- update.formula(sp.form, obs ~ 1 + .)
if (em.prefit | G == 1) {
prefit <- SpeciesMix.em(sp.form, sp.data, covar.data,
G, ite.max = em.steps, em.refit = em.refit, r1)
pars <- c(additive.logistic(prefit$pi, T)[1:(G - 1)],
unlist(prefit$coef))
}
S <- dim(sp.data)[2]
if (is.null(colnames(sp.data))) {
sp.name <- 1:S
}
else {
sp.name <- colnames(sp.data)
}
n <- dim(sp.data)[1]
sp <- rep(sp.name, each = n)
if (G == 1)
return(prefit)
var.names <- colnames(covar.data)
covar.data <- data.frame(kronecker(rep(1, S), as.matrix(covar.data)))
names(covar.data) <- var.names
sp.data <- as.data.frame(sp.data)
data <- data.frame(obs = as.numeric(unlist(sp.data)), covar.data)
names(data)[1] <- as.character(sp.form)[2]
fmM.out <- fitmix.cpp(sp.form, data, sp, G, pars = pars,
calc.hes = est.var, r1)
while (fmM.out$logl == 0) {
prefit <- SpeciesMix.em(sp.form, t.sp.data, t.covar.data,
G, ite.max = em.steps, em.refit = 1, r1)
pars <- c(additive.logistic(prefit$pi, T)[1:(G - 1)],
unlist(prefit$coef))
fmM.out <- fitmix.cpp(sp.form, data, sp, G, pars = pars,
calc.hes = est.var, r1)
}
rownames(fmM.out$tau) <- sp.name
fmM.out$se <- NA
if (est.var) {
fmM.out$covar <- try(solve(fmM.out$hessian))
if (class(fmM.out$covar) != "try-error") {
tmp <- sqrt(diag(fmM.out$covar))
tmp <- tmp[(G):length(tmp)]
fmM.out$se <- matrix(tmp, G, ncol(fmM.out$coef))
colnames(fmM.out$se) <- colnames(fmM.out$coef)
rownames(fmM.out$se) <- rownames(fmM.out$coef)
}
}
if (residuals)
fmM.out$residuals <- mix.residuals(fmM.out, sp.form,
data, sp)
fmM.out$formula <- sp.form
class(fmM.out) <- c("archetype", "bernoulli")
fmM.out
}
<bytecode: 0x3a45580>
<environment: namespace:SpeciesMix>
--- function search by body ---
Function SpeciesMix.bernoulli in namespace SpeciesMix has this body.
----------- END OF FAILURE REPORT --------------
Error in if (class(fmM.out$covar) != "try-error") { :
the condition has length > 1
Calls: SpeciesMix -> SpeciesMix.bernoulli
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc