Last updated on 2020-02-19 10:49:05 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.2.4 | 7.73 | 74.69 | 82.42 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 1.2.4 | 6.92 | 56.76 | 63.68 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.2.4 | 99.55 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 1.2.4 | 96.53 | ERROR | |||
| r-devel-windows-ix86+x86_64 | 1.2.4 | 14.00 | 135.00 | 149.00 | OK | |
| r-devel-windows-ix86+x86_64-gcc8 | 1.2.4 | 25.00 | 191.00 | 216.00 | OK | |
| r-patched-linux-x86_64 | 1.2.4 | 6.34 | 118.70 | 125.04 | OK | |
| r-patched-solaris-x86 | 1.2.4 | 261.10 | OK | |||
| r-release-linux-x86_64 | 1.2.4 | 6.73 | 117.28 | 124.01 | OK | |
| r-release-windows-ix86+x86_64 | 1.2.4 | 14.00 | 134.00 | 148.00 | OK | |
| r-release-osx-x86_64 | 1.2.4 | OK | ||||
| r-oldrel-windows-ix86+x86_64 | 1.2.4 | 3.00 | 4.00 | 7.00 | ERROR | |
| r-oldrel-osx-x86_64 | 1.2.4 | OK |
Version: 1.2.4
Check: examples
Result: ERROR
Running examples in 'PSTR-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: LinTest
> ### Title: Conduct the linearity tests.
> ### Aliases: LinTest WCB_LinTest
> ### Keywords: specification
>
> ### ** Examples
>
> pstr = NewPSTR(Hansen99, dep='inva', indep=4:20, indep_k=c('vala','debta','cfa','sales'),
+ tvars=c('vala'), iT=14) # create a new PSTR object
>
> pstr = LinTest(pstr)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
PSTR
--- call from context ---
LMTEST(iT = iT, iN = iN, vU = vU, mX = mX, mW = mW, mM = mM,
s2 = s2, mX2 = mX2, invXX = invXX)
--- call from argument ---
if (class(invS1) == "try-error") {
ttmp = svd(S1)
invS1 = ttmp$u %*% diag(1/ttmp$d, length(ttmp$d)) %*% t(ttmp$u)
}
--- R stacktrace ---
where 1: LMTEST(iT = iT, iN = iN, vU = vU, mX = mX, mW = mW, mM = mM,
s2 = s2, mX2 = mX2, invXX = invXX)
where 2: LinTest(pstr)
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (iT, iN, vU, mX, mW, mM, s2, mX2, invXX)
{
df1 = ncol(mW)
df2 = iT * iN - df1 - iN - ncol(mX)
mW2 = mM %*% mW
mXW2 = crossprod(mX2, mW2)
S1 = (crossprod(mW2) - t(mXW2) %*% invXX %*% mXW2) * s2
invS1 = try(chol2inv(chol(S1)), silent = T)
if (class(invS1) == "try-error") {
ttmp = svd(S1)
invS1 = ttmp$u %*% diag(1/ttmp$d, length(ttmp$d)) %*%
t(ttmp$u)
}
vW2U = crossprod(mW2, vU)
LM1_X = c(t(vW2U) %*% invS1 %*% vW2U)
PV1_X = 1 - pchisq(LM1_X, df = df1)
LM1_F = LM1_X * df2/(iT * iN * df1)
PV1_F = 1 - pf(LM1_F, df1 = df1, df2 = df2)
mZ = cbind(mX2, mW2)
Delta = 0
for (nter in 0:(iN - 1) * iT) {
itmp = (nter + 1):(nter + iT)
tmp = t(mZ[itmp, ]) %*% vU[itmp] %*% t(vU[itmp]) %*%
mZ[itmp, ]
Delta = Delta + tmp
}
tmp = cbind(-crossprod(mXW2, invXX), diag(1, df1))
S2 = tmp %*% Delta %*% t(tmp)
invS2 = try(chol2inv(chol(S2)), silent = T)
if (class(invS2) == "try-error") {
ttmp = svd(S2)
invS2 = ttmp$u %*% diag(1/ttmp$d, length(ttmp$d)) %*%
t(ttmp$u)
}
LM2_X = c(t(vW2U) %*% invS2 %*% vW2U)
PV2_X = 1 - pchisq(LM2_X, df = df1)
LM2_F = LM2_X * df2/(iT * iN * df1)
PV2_F = 1 - pf(LM2_F, df1 = df1, df2 = df2)
return(list(LM1_X = LM1_X, PV1_X = PV1_X, LM1_F = LM1_F,
PV1_F = PV1_F, LM2_X = LM2_X, PV2_X = PV2_X, LM2_F = LM2_F,
PV2_F = PV2_F))
}
<bytecode: 0x56f02a8>
<environment: namespace:PSTR>
--- function search by body ---
Function LMTEST in namespace PSTR has this body.
----------- END OF FAILURE REPORT --------------
Error in if (class(invS1) == "try-error") { :
the condition has length > 1
Calls: LinTest -> LMTEST
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.2.4
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building 'pstr-vignette.Rmd' using rmarkdown
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
PSTR
--- call from context ---
LMTEST(iT = iT, iN = iN, vU = vU, mX = mX, mW = mW, mM = mM,
s2 = s2, mX2 = mX2, invXX = invXX)
--- call from argument ---
if (class(invS1) == "try-error") {
ttmp = svd(S1)
invS1 = ttmp$u %*% diag(1/ttmp$d, length(ttmp$d)) %*% t(ttmp$u)
}
--- R stacktrace ---
where 1: LMTEST(iT = iT, iN = iN, vU = vU, mX = mX, mW = mW, mM = mM,
s2 = s2, mX2 = mX2, invXX = invXX)
where 2: LinTest(use = pstr)
where 3: eval(expr, envir, enclos)
where 4: eval(expr, envir, enclos)
where 5: withVisible(eval(expr, envir, enclos))
where 6: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler,
error = eHandler, message = mHandler)
where 7: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir,
enclos)), warning = wHandler, error = eHandler, message = mHandler))
where 8: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr,
envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
where 9: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos,
debug = debug, last = i == length(out), use_try = stop_on_error !=
2L, keep_warning = keep_warning, keep_message = keep_message,
output_handler = output_handler, include_timing = include_timing)
where 10: evaluate::evaluate(...)
where 11: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning),
keep_message = !isFALSE(options$message), stop_on_error = if (options$error &&
options$include) 0L else 2L, output_handler = knit_handlers(options$render,
options))
where 12: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE,
keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message),
stop_on_error = if (options$error && options$include) 0L else 2L,
output_handler = knit_handlers(options$render, options)))
where 13: block_exec(params)
where 14: call_block(x)
where 15: process_group.block(group)
where 16: process_group(group)
where 17: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
error = function(e) {
setwd(wd)
cat(res, sep = "\n", file = output %n% "")
message("Quitting from lines ", paste(current_lines(i),
collapse = "-"), " (", knit_concord$get("infile"),
") ")
})
where 18: process_file(text, output)
where 19: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
where 20: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),
output_dir = getwd(), ...)
where 21: vweave_rmarkdown(...)
where 22: engine$weave(file, quiet = quiet, encoding = enc)
where 23: doTryCatch(return(expr), name, parentenv, handler)
where 24: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 25: tryCatchList(expr, classes, parentenv, handlers)
where 26: tryCatch({
engine$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 27: tools:::buildVignettes(dir = "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/PSTR.Rcheck/vign_test/PSTR",
ser_elibs = "/tmp/RtmpCIB3sP/fileb4b3870d265.rds")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (iT, iN, vU, mX, mW, mM, s2, mX2, invXX)
{
df1 = ncol(mW)
df2 = iT * iN - df1 - iN - ncol(mX)
mW2 = mM %*% mW
mXW2 = crossprod(mX2, mW2)
S1 = (crossprod(mW2) - t(mXW2) %*% invXX %*% mXW2) * s2
invS1 = try(chol2inv(chol(S1)), silent = T)
if (class(invS1) == "try-error") {
ttmp = svd(S1)
invS1 = ttmp$u %*% diag(1/ttmp$d, length(ttmp$d)) %*%
t(ttmp$u)
}
vW2U = crossprod(mW2, vU)
LM1_X = c(t(vW2U) %*% invS1 %*% vW2U)
PV1_X = 1 - pchisq(LM1_X, df = df1)
LM1_F = LM1_X * df2/(iT * iN * df1)
PV1_F = 1 - pf(LM1_F, df1 = df1, df2 = df2)
mZ = cbind(mX2, mW2)
Delta = 0
for (nter in 0:(iN - 1) * iT) {
itmp = (nter + 1):(nter + iT)
tmp = t(mZ[itmp, ]) %*% vU[itmp] %*% t(vU[itmp]) %*%
mZ[itmp, ]
Delta = Delta + tmp
}
tmp = cbind(-crossprod(mXW2, invXX), diag(1, df1))
S2 = tmp %*% Delta %*% t(tmp)
invS2 = try(chol2inv(chol(S2)), silent = T)
if (class(invS2) == "try-error") {
ttmp = svd(S2)
invS2 = ttmp$u %*% diag(1/ttmp$d, length(ttmp$d)) %*%
t(ttmp$u)
}
LM2_X = c(t(vW2U) %*% invS2 %*% vW2U)
PV2_X = 1 - pchisq(LM2_X, df = df1)
LM2_F = LM2_X * df2/(iT * iN * df1)
PV2_F = 1 - pf(LM2_F, df1 = df1, df2 = df2)
return(list(LM1_X = LM1_X, PV1_X = PV1_X, LM1_F = LM1_F,
PV1_F = PV1_F, LM2_X = LM2_X, PV2_X = PV2_X, LM2_F = LM2_F,
PV2_F = PV2_F))
}
<bytecode: 0x71a1378>
<environment: namespace:PSTR>
--- function search by body ---
Function LMTEST in namespace PSTR has this body.
----------- END OF FAILURE REPORT --------------
Quitting from lines 89-91 (pstr-vignette.Rmd)
Error: processing vignette 'pstr-vignette.Rmd' failed with diagnostics:
the condition has length > 1
--- failed re-building 'pstr-vignette.Rmd'
SUMMARY: processing the following file failed:
'pstr-vignette.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.2.4
Check: examples
Result: ERROR
Running examples in ‘PSTR-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: LinTest
> ### Title: Conduct the linearity tests.
> ### Aliases: LinTest WCB_LinTest
> ### Keywords: specification
>
> ### ** Examples
>
> pstr = NewPSTR(Hansen99, dep='inva', indep=4:20, indep_k=c('vala','debta','cfa','sales'),
+ tvars=c('vala'), iT=14) # create a new PSTR object
>
> pstr = LinTest(pstr)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
PSTR
--- call from context ---
LMTEST(iT = iT, iN = iN, vU = vU, mX = mX, mW = mW, mM = mM,
s2 = s2, mX2 = mX2, invXX = invXX)
--- call from argument ---
if (class(invS1) == "try-error") {
ttmp = svd(S1)
invS1 = ttmp$u %*% diag(1/ttmp$d, length(ttmp$d)) %*% t(ttmp$u)
}
--- R stacktrace ---
where 1: LMTEST(iT = iT, iN = iN, vU = vU, mX = mX, mW = mW, mM = mM,
s2 = s2, mX2 = mX2, invXX = invXX)
where 2: LinTest(pstr)
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (iT, iN, vU, mX, mW, mM, s2, mX2, invXX)
{
df1 = ncol(mW)
df2 = iT * iN - df1 - iN - ncol(mX)
mW2 = mM %*% mW
mXW2 = crossprod(mX2, mW2)
S1 = (crossprod(mW2) - t(mXW2) %*% invXX %*% mXW2) * s2
invS1 = try(chol2inv(chol(S1)), silent = T)
if (class(invS1) == "try-error") {
ttmp = svd(S1)
invS1 = ttmp$u %*% diag(1/ttmp$d, length(ttmp$d)) %*%
t(ttmp$u)
}
vW2U = crossprod(mW2, vU)
LM1_X = c(t(vW2U) %*% invS1 %*% vW2U)
PV1_X = 1 - pchisq(LM1_X, df = df1)
LM1_F = LM1_X * df2/(iT * iN * df1)
PV1_F = 1 - pf(LM1_F, df1 = df1, df2 = df2)
mZ = cbind(mX2, mW2)
Delta = 0
for (nter in 0:(iN - 1) * iT) {
itmp = (nter + 1):(nter + iT)
tmp = t(mZ[itmp, ]) %*% vU[itmp] %*% t(vU[itmp]) %*%
mZ[itmp, ]
Delta = Delta + tmp
}
tmp = cbind(-crossprod(mXW2, invXX), diag(1, df1))
S2 = tmp %*% Delta %*% t(tmp)
invS2 = try(chol2inv(chol(S2)), silent = T)
if (class(invS2) == "try-error") {
ttmp = svd(S2)
invS2 = ttmp$u %*% diag(1/ttmp$d, length(ttmp$d)) %*%
t(ttmp$u)
}
LM2_X = c(t(vW2U) %*% invS2 %*% vW2U)
PV2_X = 1 - pchisq(LM2_X, df = df1)
LM2_F = LM2_X * df2/(iT * iN * df1)
PV2_F = 1 - pf(LM2_F, df1 = df1, df2 = df2)
return(list(LM1_X = LM1_X, PV1_X = PV1_X, LM1_F = LM1_F,
PV1_F = PV1_F, LM2_X = LM2_X, PV2_X = PV2_X, LM2_F = LM2_F,
PV2_F = PV2_F))
}
<bytecode: 0x559456c83958>
<environment: namespace:PSTR>
--- function search by body ---
Function LMTEST in namespace PSTR has this body.
----------- END OF FAILURE REPORT --------------
Error in if (class(invS1) == "try-error") { :
the condition has length > 1
Calls: LinTest -> LMTEST
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.2.4
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building ‘pstr-vignette.Rmd’ using rmarkdown
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
PSTR
--- call from context ---
LMTEST(iT = iT, iN = iN, vU = vU, mX = mX, mW = mW, mM = mM,
s2 = s2, mX2 = mX2, invXX = invXX)
--- call from argument ---
if (class(invS1) == "try-error") {
ttmp = svd(S1)
invS1 = ttmp$u %*% diag(1/ttmp$d, length(ttmp$d)) %*% t(ttmp$u)
}
--- R stacktrace ---
where 1: LMTEST(iT = iT, iN = iN, vU = vU, mX = mX, mW = mW, mM = mM,
s2 = s2, mX2 = mX2, invXX = invXX)
where 2: LinTest(use = pstr)
where 3: eval(expr, envir, enclos)
where 4: eval(expr, envir, enclos)
where 5: withVisible(eval(expr, envir, enclos))
where 6: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler,
error = eHandler, message = mHandler)
where 7: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir,
enclos)), warning = wHandler, error = eHandler, message = mHandler))
where 8: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr,
envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
where 9: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos,
debug = debug, last = i == length(out), use_try = stop_on_error !=
2L, keep_warning = keep_warning, keep_message = keep_message,
output_handler = output_handler, include_timing = include_timing)
where 10: evaluate::evaluate(...)
where 11: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning),
keep_message = !isFALSE(options$message), stop_on_error = if (options$error &&
options$include) 0L else 2L, output_handler = knit_handlers(options$render,
options))
where 12: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE,
keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message),
stop_on_error = if (options$error && options$include) 0L else 2L,
output_handler = knit_handlers(options$render, options)))
where 13: block_exec(params)
where 14: call_block(x)
where 15: process_group.block(group)
where 16: process_group(group)
where 17: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
error = function(e) {
setwd(wd)
cat(res, sep = "\n", file = output %n% "")
message("Quitting from lines ", paste(current_lines(i),
collapse = "-"), " (", knit_concord$get("infile"),
") ")
})
where 18: process_file(text, output)
where 19: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
where 20: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),
output_dir = getwd(), ...)
where 21: vweave_rmarkdown(...)
where 22: engine$weave(file, quiet = quiet, encoding = enc)
where 23: doTryCatch(return(expr), name, parentenv, handler)
where 24: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 25: tryCatchList(expr, classes, parentenv, handlers)
where 26: tryCatch({
engine$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 27: tools:::buildVignettes(dir = "/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PSTR.Rcheck/vign_test/PSTR",
ser_elibs = "/home/hornik/tmp/scratch/Rtmpqf8fYU/file699dccde8c3.rds")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (iT, iN, vU, mX, mW, mM, s2, mX2, invXX)
{
df1 = ncol(mW)
df2 = iT * iN - df1 - iN - ncol(mX)
mW2 = mM %*% mW
mXW2 = crossprod(mX2, mW2)
S1 = (crossprod(mW2) - t(mXW2) %*% invXX %*% mXW2) * s2
invS1 = try(chol2inv(chol(S1)), silent = T)
if (class(invS1) == "try-error") {
ttmp = svd(S1)
invS1 = ttmp$u %*% diag(1/ttmp$d, length(ttmp$d)) %*%
t(ttmp$u)
}
vW2U = crossprod(mW2, vU)
LM1_X = c(t(vW2U) %*% invS1 %*% vW2U)
PV1_X = 1 - pchisq(LM1_X, df = df1)
LM1_F = LM1_X * df2/(iT * iN * df1)
PV1_F = 1 - pf(LM1_F, df1 = df1, df2 = df2)
mZ = cbind(mX2, mW2)
Delta = 0
for (nter in 0:(iN - 1) * iT) {
itmp = (nter + 1):(nter + iT)
tmp = t(mZ[itmp, ]) %*% vU[itmp] %*% t(vU[itmp]) %*%
mZ[itmp, ]
Delta = Delta + tmp
}
tmp = cbind(-crossprod(mXW2, invXX), diag(1, df1))
S2 = tmp %*% Delta %*% t(tmp)
invS2 = try(chol2inv(chol(S2)), silent = T)
if (class(invS2) == "try-error") {
ttmp = svd(S2)
invS2 = ttmp$u %*% diag(1/ttmp$d, length(ttmp$d)) %*%
t(ttmp$u)
}
LM2_X = c(t(vW2U) %*% invS2 %*% vW2U)
PV2_X = 1 - pchisq(LM2_X, df = df1)
LM2_F = LM2_X * df2/(iT * iN * df1)
PV2_F = 1 - pf(LM2_F, df1 = df1, df2 = df2)
return(list(LM1_X = LM1_X, PV1_X = PV1_X, LM1_F = LM1_F,
PV1_F = PV1_F, LM2_X = LM2_X, PV2_X = PV2_X, LM2_F = LM2_F,
PV2_F = PV2_F))
}
<bytecode: 0x55a36edb0ca0>
<environment: namespace:PSTR>
--- function search by body ---
Function LMTEST in namespace PSTR has this body.
----------- END OF FAILURE REPORT --------------
Quitting from lines 89-91 (pstr-vignette.Rmd)
Error: processing vignette 'pstr-vignette.Rmd' failed with diagnostics:
the condition has length > 1
--- failed re-building ‘pstr-vignette.Rmd’
SUMMARY: processing the following file failed:
‘pstr-vignette.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.2.4
Check: examples
Result: ERROR
Running examples in ‘PSTR-Ex.R’ failed
The error most likely occurred in:
> ### Name: LinTest
> ### Title: Conduct the linearity tests.
> ### Aliases: LinTest WCB_LinTest
> ### Keywords: specification
>
> ### ** Examples
>
> pstr = NewPSTR(Hansen99, dep='inva', indep=4:20, indep_k=c('vala','debta','cfa','sales'),
+ tvars=c('vala'), iT=14) # create a new PSTR object
>
> pstr = LinTest(pstr)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
PSTR
--- call from context ---
LMTEST(iT = iT, iN = iN, vU = vU, mX = mX, mW = mW, mM = mM,
s2 = s2, mX2 = mX2, invXX = invXX)
--- call from argument ---
if (class(invS1) == "try-error") {
ttmp = svd(S1)
invS1 = ttmp$u %*% diag(1/ttmp$d, length(ttmp$d)) %*% t(ttmp$u)
}
--- R stacktrace ---
where 1: LMTEST(iT = iT, iN = iN, vU = vU, mX = mX, mW = mW, mM = mM,
s2 = s2, mX2 = mX2, invXX = invXX)
where 2: LinTest(pstr)
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (iT, iN, vU, mX, mW, mM, s2, mX2, invXX)
{
df1 = ncol(mW)
df2 = iT * iN - df1 - iN - ncol(mX)
mW2 = mM %*% mW
mXW2 = crossprod(mX2, mW2)
S1 = (crossprod(mW2) - t(mXW2) %*% invXX %*% mXW2) * s2
invS1 = try(chol2inv(chol(S1)), silent = T)
if (class(invS1) == "try-error") {
ttmp = svd(S1)
invS1 = ttmp$u %*% diag(1/ttmp$d, length(ttmp$d)) %*%
t(ttmp$u)
}
vW2U = crossprod(mW2, vU)
LM1_X = c(t(vW2U) %*% invS1 %*% vW2U)
PV1_X = 1 - pchisq(LM1_X, df = df1)
LM1_F = LM1_X * df2/(iT * iN * df1)
PV1_F = 1 - pf(LM1_F, df1 = df1, df2 = df2)
mZ = cbind(mX2, mW2)
Delta = 0
for (nter in 0:(iN - 1) * iT) {
itmp = (nter + 1):(nter + iT)
tmp = t(mZ[itmp, ]) %*% vU[itmp] %*% t(vU[itmp]) %*%
mZ[itmp, ]
Delta = Delta + tmp
}
tmp = cbind(-crossprod(mXW2, invXX), diag(1, df1))
S2 = tmp %*% Delta %*% t(tmp)
invS2 = try(chol2inv(chol(S2)), silent = T)
if (class(invS2) == "try-error") {
ttmp = svd(S2)
invS2 = ttmp$u %*% diag(1/ttmp$d, length(ttmp$d)) %*%
t(ttmp$u)
}
LM2_X = c(t(vW2U) %*% invS2 %*% vW2U)
PV2_X = 1 - pchisq(LM2_X, df = df1)
LM2_F = LM2_X * df2/(iT * iN * df1)
PV2_F = 1 - pf(LM2_F, df1 = df1, df2 = df2)
return(list(LM1_X = LM1_X, PV1_X = PV1_X, LM1_F = LM1_F,
PV1_F = PV1_F, LM2_X = LM2_X, PV2_X = PV2_X, LM2_F = LM2_F,
PV2_F = PV2_F))
}
<bytecode: 0x65a2c68>
<environment: namespace:PSTR>
--- function search by body ---
Function LMTEST in namespace PSTR has this body.
----------- END OF FAILURE REPORT --------------
Error in if (class(invS1) == "try-error") { :
the condition has length > 1
Calls: LinTest -> LMTEST
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.2.4
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
--- re-building ‘pstr-vignette.Rmd’ using rmarkdown
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
PSTR
--- call from context ---
LMTEST(iT = iT, iN = iN, vU = vU, mX = mX, mW = mW, mM = mM,
s2 = s2, mX2 = mX2, invXX = invXX)
--- call from argument ---
if (class(invS1) == "try-error") {
ttmp = svd(S1)
invS1 = ttmp$u %*% diag(1/ttmp$d, length(ttmp$d)) %*% t(ttmp$u)
}
--- R stacktrace ---
where 1: LMTEST(iT = iT, iN = iN, vU = vU, mX = mX, mW = mW, mM = mM,
s2 = s2, mX2 = mX2, invXX = invXX)
where 2: LinTest(use = pstr)
where 3: eval(expr, envir, enclos)
where 4: eval(expr, envir, enclos)
where 5: withVisible(eval(expr, envir, enclos))
where 6: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler,
error = eHandler, message = mHandler)
where 7: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir,
enclos)), warning = wHandler, error = eHandler, message = mHandler))
where 8: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr,
envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
where 9: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos,
debug = debug, last = i == length(out), use_try = stop_on_error !=
2L, keep_warning = keep_warning, keep_message = keep_message,
output_handler = output_handler, include_timing = include_timing)
where 10: evaluate::evaluate(...)
where 11: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning),
keep_message = !isFALSE(options$message), stop_on_error = if (options$error &&
options$include) 0L else 2L, output_handler = knit_handlers(options$render,
options))
where 12: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE,
keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message),
stop_on_error = if (options$error && options$include) 0L else 2L,
output_handler = knit_handlers(options$render, options)))
where 13: block_exec(params)
where 14: call_block(x)
where 15: process_group.block(group)
where 16: process_group(group)
where 17: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
error = function(e) {
setwd(wd)
cat(res, sep = "\n", file = output %n% "")
message("Quitting from lines ", paste(current_lines(i),
collapse = "-"), " (", knit_concord$get("infile"),
") ")
})
where 18: process_file(text, output)
where 19: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
where 20: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),
output_dir = getwd(), ...)
where 21: vweave_rmarkdown(...)
where 22: engine$weave(file, quiet = quiet, encoding = enc)
where 23: doTryCatch(return(expr), name, parentenv, handler)
where 24: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 25: tryCatchList(expr, classes, parentenv, handlers)
where 26: tryCatch({
engine$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 27: tools:::buildVignettes(dir = "/data/gannet/ripley/R/packages/tests-clang/PSTR.Rcheck/vign_test/PSTR",
ser_elibs = "/tmp/RtmpFLmIY9/file7bf54f8554bb.rds")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (iT, iN, vU, mX, mW, mM, s2, mX2, invXX)
{
df1 = ncol(mW)
df2 = iT * iN - df1 - iN - ncol(mX)
mW2 = mM %*% mW
mXW2 = crossprod(mX2, mW2)
S1 = (crossprod(mW2) - t(mXW2) %*% invXX %*% mXW2) * s2
invS1 = try(chol2inv(chol(S1)), silent = T)
if (class(invS1) == "try-error") {
ttmp = svd(S1)
invS1 = ttmp$u %*% diag(1/ttmp$d, length(ttmp$d)) %*%
t(ttmp$u)
}
vW2U = crossprod(mW2, vU)
LM1_X = c(t(vW2U) %*% invS1 %*% vW2U)
PV1_X = 1 - pchisq(LM1_X, df = df1)
LM1_F = LM1_X * df2/(iT * iN * df1)
PV1_F = 1 - pf(LM1_F, df1 = df1, df2 = df2)
mZ = cbind(mX2, mW2)
Delta = 0
for (nter in 0:(iN - 1) * iT) {
itmp = (nter + 1):(nter + iT)
tmp = t(mZ[itmp, ]) %*% vU[itmp] %*% t(vU[itmp]) %*%
mZ[itmp, ]
Delta = Delta + tmp
}
tmp = cbind(-crossprod(mXW2, invXX), diag(1, df1))
S2 = tmp %*% Delta %*% t(tmp)
invS2 = try(chol2inv(chol(S2)), silent = T)
if (class(invS2) == "try-error") {
ttmp = svd(S2)
invS2 = ttmp$u %*% diag(1/ttmp$d, length(ttmp$d)) %*%
t(ttmp$u)
}
LM2_X = c(t(vW2U) %*% invS2 %*% vW2U)
PV2_X = 1 - pchisq(LM2_X, df = df1)
LM2_F = LM2_X * df2/(iT * iN * df1)
PV2_F = 1 - pf(LM2_F, df1 = df1, df2 = df2)
return(list(LM1_X = LM1_X, PV1_X = PV1_X, LM1_F = LM1_F,
PV1_F = PV1_F, LM2_X = LM2_X, PV2_X = PV2_X, LM2_F = LM2_F,
PV2_F = PV2_F))
}
<bytecode: 0x7a866d8>
<environment: namespace:PSTR>
--- function search by body ---
Function LMTEST in namespace PSTR has this body.
----------- END OF FAILURE REPORT --------------
Quitting from lines 89-91 (pstr-vignette.Rmd)
Error: processing vignette 'pstr-vignette.Rmd' failed with diagnostics:
the condition has length > 1
--- failed re-building ‘pstr-vignette.Rmd’
SUMMARY: processing the following file failed:
‘pstr-vignette.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.2.4
Check: examples
Result: ERROR
Running examples in ‘PSTR-Ex.R’ failed
The error most likely occurred in:
> ### Name: LinTest
> ### Title: Conduct the linearity tests.
> ### Aliases: LinTest WCB_LinTest
> ### Keywords: specification
>
> ### ** Examples
>
> pstr = NewPSTR(Hansen99, dep='inva', indep=4:20, indep_k=c('vala','debta','cfa','sales'),
+ tvars=c('vala'), iT=14) # create a new PSTR object
>
> pstr = LinTest(pstr)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
PSTR
--- call from context ---
LMTEST(iT = iT, iN = iN, vU = vU, mX = mX, mW = mW, mM = mM,
s2 = s2, mX2 = mX2, invXX = invXX)
--- call from argument ---
if (class(invS1) == "try-error") {
ttmp = svd(S1)
invS1 = ttmp$u %*% diag(1/ttmp$d, length(ttmp$d)) %*% t(ttmp$u)
}
--- R stacktrace ---
where 1: LMTEST(iT = iT, iN = iN, vU = vU, mX = mX, mW = mW, mM = mM,
s2 = s2, mX2 = mX2, invXX = invXX)
where 2: LinTest(pstr)
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (iT, iN, vU, mX, mW, mM, s2, mX2, invXX)
{
df1 = ncol(mW)
df2 = iT * iN - df1 - iN - ncol(mX)
mW2 = mM %*% mW
mXW2 = crossprod(mX2, mW2)
S1 = (crossprod(mW2) - t(mXW2) %*% invXX %*% mXW2) * s2
invS1 = try(chol2inv(chol(S1)), silent = T)
if (class(invS1) == "try-error") {
ttmp = svd(S1)
invS1 = ttmp$u %*% diag(1/ttmp$d, length(ttmp$d)) %*%
t(ttmp$u)
}
vW2U = crossprod(mW2, vU)
LM1_X = c(t(vW2U) %*% invS1 %*% vW2U)
PV1_X = 1 - pchisq(LM1_X, df = df1)
LM1_F = LM1_X * df2/(iT * iN * df1)
PV1_F = 1 - pf(LM1_F, df1 = df1, df2 = df2)
mZ = cbind(mX2, mW2)
Delta = 0
for (nter in 0:(iN - 1) * iT) {
itmp = (nter + 1):(nter + iT)
tmp = t(mZ[itmp, ]) %*% vU[itmp] %*% t(vU[itmp]) %*%
mZ[itmp, ]
Delta = Delta + tmp
}
tmp = cbind(-crossprod(mXW2, invXX), diag(1, df1))
S2 = tmp %*% Delta %*% t(tmp)
invS2 = try(chol2inv(chol(S2)), silent = T)
if (class(invS2) == "try-error") {
ttmp = svd(S2)
invS2 = ttmp$u %*% diag(1/ttmp$d, length(ttmp$d)) %*%
t(ttmp$u)
}
LM2_X = c(t(vW2U) %*% invS2 %*% vW2U)
PV2_X = 1 - pchisq(LM2_X, df = df1)
LM2_F = LM2_X * df2/(iT * iN * df1)
PV2_F = 1 - pf(LM2_F, df1 = df1, df2 = df2)
return(list(LM1_X = LM1_X, PV1_X = PV1_X, LM1_F = LM1_F,
PV1_F = PV1_F, LM2_X = LM2_X, PV2_X = PV2_X, LM2_F = LM2_F,
PV2_F = PV2_F))
}
<bytecode: 0x7063ee8>
<environment: namespace:PSTR>
--- function search by body ---
Function LMTEST in namespace PSTR has this body.
----------- END OF FAILURE REPORT --------------
Error in if (class(invS1) == "try-error") { :
the condition has length > 1
Calls: LinTest -> LMTEST
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 1.2.4
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
--- re-building ‘pstr-vignette.Rmd’ using rmarkdown
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
PSTR
--- call from context ---
LMTEST(iT = iT, iN = iN, vU = vU, mX = mX, mW = mW, mM = mM,
s2 = s2, mX2 = mX2, invXX = invXX)
--- call from argument ---
if (class(invS1) == "try-error") {
ttmp = svd(S1)
invS1 = ttmp$u %*% diag(1/ttmp$d, length(ttmp$d)) %*% t(ttmp$u)
}
--- R stacktrace ---
where 1: LMTEST(iT = iT, iN = iN, vU = vU, mX = mX, mW = mW, mM = mM,
s2 = s2, mX2 = mX2, invXX = invXX)
where 2: LinTest(use = pstr)
where 3: eval(expr, envir, enclos)
where 4: eval(expr, envir, enclos)
where 5: withVisible(eval(expr, envir, enclos))
where 6: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler,
error = eHandler, message = mHandler)
where 7: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir,
enclos)), warning = wHandler, error = eHandler, message = mHandler))
where 8: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr,
envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
where 9: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos,
debug = debug, last = i == length(out), use_try = stop_on_error !=
2L, keep_warning = keep_warning, keep_message = keep_message,
output_handler = output_handler, include_timing = include_timing)
where 10: evaluate::evaluate(...)
where 11: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning),
keep_message = !isFALSE(options$message), stop_on_error = if (options$error &&
options$include) 0L else 2L, output_handler = knit_handlers(options$render,
options))
where 12: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE,
keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message),
stop_on_error = if (options$error && options$include) 0L else 2L,
output_handler = knit_handlers(options$render, options)))
where 13: block_exec(params)
where 14: call_block(x)
where 15: process_group.block(group)
where 16: process_group(group)
where 17: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
error = function(e) {
setwd(wd)
cat(res, sep = "\n", file = output %n% "")
message("Quitting from lines ", paste(current_lines(i),
collapse = "-"), " (", knit_concord$get("infile"),
") ")
})
where 18: process_file(text, output)
where 19: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
where 20: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),
output_dir = getwd(), ...)
where 21: vweave_rmarkdown(...)
where 22: engine$weave(file, quiet = quiet, encoding = enc)
where 23: doTryCatch(return(expr), name, parentenv, handler)
where 24: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 25: tryCatchList(expr, classes, parentenv, handlers)
where 26: tryCatch({
engine$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 27: tools:::buildVignettes(dir = "/data/gannet/ripley/R/packages/tests-devel/PSTR.Rcheck/vign_test/PSTR",
ser_elibs = "/tmp/Rtmpdwj8jt/fileb89d53ad3ce8.rds")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (iT, iN, vU, mX, mW, mM, s2, mX2, invXX)
{
df1 = ncol(mW)
df2 = iT * iN - df1 - iN - ncol(mX)
mW2 = mM %*% mW
mXW2 = crossprod(mX2, mW2)
S1 = (crossprod(mW2) - t(mXW2) %*% invXX %*% mXW2) * s2
invS1 = try(chol2inv(chol(S1)), silent = T)
if (class(invS1) == "try-error") {
ttmp = svd(S1)
invS1 = ttmp$u %*% diag(1/ttmp$d, length(ttmp$d)) %*%
t(ttmp$u)
}
vW2U = crossprod(mW2, vU)
LM1_X = c(t(vW2U) %*% invS1 %*% vW2U)
PV1_X = 1 - pchisq(LM1_X, df = df1)
LM1_F = LM1_X * df2/(iT * iN * df1)
PV1_F = 1 - pf(LM1_F, df1 = df1, df2 = df2)
mZ = cbind(mX2, mW2)
Delta = 0
for (nter in 0:(iN - 1) * iT) {
itmp = (nter + 1):(nter + iT)
tmp = t(mZ[itmp, ]) %*% vU[itmp] %*% t(vU[itmp]) %*%
mZ[itmp, ]
Delta = Delta + tmp
}
tmp = cbind(-crossprod(mXW2, invXX), diag(1, df1))
S2 = tmp %*% Delta %*% t(tmp)
invS2 = try(chol2inv(chol(S2)), silent = T)
if (class(invS2) == "try-error") {
ttmp = svd(S2)
invS2 = ttmp$u %*% diag(1/ttmp$d, length(ttmp$d)) %*%
t(ttmp$u)
}
LM2_X = c(t(vW2U) %*% invS2 %*% vW2U)
PV2_X = 1 - pchisq(LM2_X, df = df1)
LM2_F = LM2_X * df2/(iT * iN * df1)
PV2_F = 1 - pf(LM2_F, df1 = df1, df2 = df2)
return(list(LM1_X = LM1_X, PV1_X = PV1_X, LM1_F = LM1_F,
PV1_F = PV1_F, LM2_X = LM2_X, PV2_X = PV2_X, LM2_F = LM2_F,
PV2_F = PV2_F))
}
<bytecode: 0x6235548>
<environment: namespace:PSTR>
--- function search by body ---
Function LMTEST in namespace PSTR has this body.
----------- END OF FAILURE REPORT --------------
Quitting from lines 89-91 (pstr-vignette.Rmd)
Error: processing vignette 'pstr-vignette.Rmd' failed with diagnostics:
the condition has length > 1
--- failed re-building ‘pstr-vignette.Rmd’
SUMMARY: processing the following file failed:
‘pstr-vignette.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 1.2.4
Check: whether package can be installed
Result: ERROR
Installation failed.
Flavor: r-oldrel-windows-ix86+x86_64