Last updated on 2019-05-01 01:51:44 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.4 | 11.98 | 192.71 | 204.69 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 1.0.4 | 9.41 | 174.64 | 184.05 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.0.4 | 286.45 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 1.0.4 | 268.61 | OK | |||
| r-patched-linux-x86_64 | 1.0.4 | 11.75 | 225.87 | 237.62 | OK | |
| r-patched-solaris-x86 | 1.0.4 | 408.90 | WARN | |||
| r-release-linux-x86_64 | 1.0.4 | 11.81 | 225.54 | 237.35 | OK | |
| r-release-windows-ix86+x86_64 | 1.0.4 | 33.00 | 320.00 | 353.00 | OK | |
| r-release-osx-x86_64 | 1.0.4 | ERROR | ||||
| r-oldrel-windows-ix86+x86_64 | 1.0.4 | 23.00 | 313.00 | 336.00 | OK | |
| r-oldrel-osx-x86_64 | 1.0.4 | OK |
Version: 1.0.4
Check: tests
Result: ERROR
Running 'testthat.R' [85s/94s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(drtmle)
drtmle: TMLE with doubly robust inference
Version: 1.0.4
>
> test_check("drtmle")
-- 1. Error: adaptive_iptw works as expected with missing data (@test-adaptive_i
<text>:1:11: unexpected symbol
1: A~W1 + W2 A
^
1: adaptive_iptw(W = W, A = A, Y = Y, a_0 = c(0, 1), glm_g = "W1 + W2", glm_Qr = "gn") at testthat/test-adaptive_iptw-missingAY.R:19
2: future.apply::future_lapply(X = validRows, FUN = estimateG, A = A, W = W, DeltaA = DeltaA,
DeltaY = DeltaY, tolg = tolg, verbose = verbose, returnModels = returnModels,
SL_g = SL_g, glm_g = glm_g, a_0 = a_0, stratify = stratify)
3: future({
...future.globals.maxSize.org <- getOption("future.globals.maxSize")
if (!identical(...future.globals.maxSize.org, ...future.globals.maxSize)) {
oopts <- options(future.globals.maxSize = ...future.globals.maxSize)
on.exit(options(oopts), add = TRUE)
}
lapply(seq_along(...future.elements_ii), FUN = function(jj) {
...future.X_jj <- ...future.elements_ii[[jj]]
...future.FUN(...future.X_jj, ...)
})
}, envir = envir, stdout = future.stdout, conditions = future.conditions, globals = globals_ii,
packages = packages_ii, lazy = future.lazy)
4: evaluator(expr, envir = envir, substitute = FALSE, lazy = lazy, seed = seed, globals = globals,
packages = packages, ...)
5: sequential(expr, envir = envir, substitute = FALSE, lazy = lazy, seed = seed, globals = globals,
local = local, earlySignal = earlySignal, label = label, ...)
6: run(future)
7: run.UniprocessFuture(future)
8: signalEarly(future, collect = FALSE)
9: resolved(future)
10: resolved.UniprocessFuture(future)
11: NextMethod()
12: resolved.Future(future)
13: signalEarly(x, ...)
14: resignalConditions(future)
-- 2. Error: drtmle executes as expected with stratify = TRUE (@test-drtmle-miss
<text>:1:11: unexpected symbol
1: A~W1 + W2 A
^
1: drtmle(W = W, A = A, Y = Y, DeltaY = DeltaY, DeltaA = DeltaA, family = gaussian(),
stratify = FALSE, glm_Q = "W1 + W2", glm_g = list(DeltaA = "W1 + W2", DeltaY = "W1 + W2",
A = "W1 + W2"), glm_Qr = "gn", glm_gr = "Qn", guard = c("Q", "g"), reduction = "univariate") at testthat/test-drtmle-missingAY.R:23
2: future.apply::future_lapply(X = validRows, FUN = estimateG, A = A, W = W, DeltaA = DeltaA,
DeltaY = DeltaY, tolg = tolg, verbose = verbose, stratify = stratify, returnModels = returnModels,
SL_g = SL_g, glm_g = glm_g, a_0 = a_0)
3: future({
...future.globals.maxSize.org <- getOption("future.globals.maxSize")
if (!identical(...future.globals.maxSize.org, ...future.globals.maxSize)) {
oopts <- options(future.globals.maxSize = ...future.globals.maxSize)
on.exit(options(oopts), add = TRUE)
}
lapply(seq_along(...future.elements_ii), FUN = function(jj) {
...future.X_jj <- ...future.elements_ii[[jj]]
...future.FUN(...future.X_jj, ...)
})
}, envir = envir, stdout = future.stdout, conditions = future.conditions, globals = globals_ii,
packages = packages_ii, lazy = future.lazy)
4: evaluator(expr, envir = envir, substitute = FALSE, lazy = lazy, seed = seed, globals = globals,
packages = packages, ...)
5: sequential(expr, envir = envir, substitute = FALSE, lazy = lazy, seed = seed, globals = globals,
local = local, earlySignal = earlySignal, label = label, ...)
6: run(future)
7: run.UniprocessFuture(future)
8: signalEarly(future, collect = FALSE)
9: resolved(future)
10: resolved.UniprocessFuture(future)
11: NextMethod()
12: resolved.Future(future)
13: signalEarly(x, ...)
14: resignalConditions(future)
-- 3. Error: drtmle executes as expected with stratify = FALSE (@test-drtmle-mis
<text>:1:11: unexpected symbol
1: A~W1 + W2 A
^
1: drtmle(W = W, A = A, Y = Y, family = gaussian(), stratify = FALSE, glm_Q = "W1 + W2",
glm_g = "W1 + W2", glm_Qr = "gn", glm_gr = "Qn", guard = c("Q", "g"), reduction = "univariate") at testthat/test-drtmle-missingAY.R:188
2: future.apply::future_lapply(X = validRows, FUN = estimateG, A = A, W = W, DeltaA = DeltaA,
DeltaY = DeltaY, tolg = tolg, verbose = verbose, stratify = stratify, returnModels = returnModels,
SL_g = SL_g, glm_g = glm_g, a_0 = a_0)
3: future({
...future.globals.maxSize.org <- getOption("future.globals.maxSize")
if (!identical(...future.globals.maxSize.org, ...future.globals.maxSize)) {
oopts <- options(future.globals.maxSize = ...future.globals.maxSize)
on.exit(options(oopts), add = TRUE)
}
lapply(seq_along(...future.elements_ii), FUN = function(jj) {
...future.X_jj <- ...future.elements_ii[[jj]]
...future.FUN(...future.X_jj, ...)
})
}, envir = envir, stdout = future.stdout, conditions = future.conditions, globals = globals_ii,
packages = packages_ii, lazy = future.lazy)
4: evaluator(expr, envir = envir, substitute = FALSE, lazy = lazy, seed = seed, globals = globals,
packages = packages, ...)
5: sequential(expr, envir = envir, substitute = FALSE, lazy = lazy, seed = seed, globals = globals,
local = local, earlySignal = earlySignal, label = label, ...)
6: run(future)
7: run.UniprocessFuture(future)
8: signalEarly(future, collect = FALSE)
9: resolved(future)
10: resolved.UniprocessFuture(future)
11: NextMethod()
12: resolved.Future(future)
13: signalEarly(x, ...)
14: resignalConditions(future)
-- 4. Error: GitHub error #16 resolves (@test-drtmle.R#503) -------------------
<text>:1:5: unexpected symbol
1: A~X A
^
1: drtmle(W = X, A = A, Y = Y, a_0 = 1, glm_Q = "X", glm_g = "X", SL_Qr = "SL.npreg",
guard = "Q", returnModel = TRUE) at testthat/test-drtmle.R:503
2: future.apply::future_lapply(X = validRows, FUN = estimateG, A = A, W = W, DeltaA = DeltaA,
DeltaY = DeltaY, tolg = tolg, verbose = verbose, stratify = stratify, returnModels = returnModels,
SL_g = SL_g, glm_g = glm_g, a_0 = a_0)
3: future({
...future.globals.maxSize.org <- getOption("future.globals.maxSize")
if (!identical(...future.globals.maxSize.org, ...future.globals.maxSize)) {
oopts <- options(future.globals.maxSize = ...future.globals.maxSize)
on.exit(options(oopts), add = TRUE)
}
lapply(seq_along(...future.elements_ii), FUN = function(jj) {
...future.X_jj <- ...future.elements_ii[[jj]]
...future.FUN(...future.X_jj, ...)
})
}, envir = envir, stdout = future.stdout, conditions = future.conditions, globals = globals_ii,
packages = packages_ii, lazy = future.lazy)
4: evaluator(expr, envir = envir, substitute = FALSE, lazy = lazy, seed = seed, globals = globals,
packages = packages, ...)
5: sequential(expr, envir = envir, substitute = FALSE, lazy = lazy, seed = seed, globals = globals,
local = local, earlySignal = earlySignal, label = label, ...)
6: run(future)
7: run.UniprocessFuture(future)
8: signalEarly(future, collect = FALSE)
9: resolved(future)
10: resolved.UniprocessFuture(future)
11: NextMethod()
12: resolved.Future(future)
13: signalEarly(x, ...)
14: resignalConditions(future)
-- 5. Error: Fail safe kicks in (@test-fluctuate.R#36) ------------------------
<text>:1:11: unexpected symbol
1: A~W1 + W2 A
^
1: lapply(X = validRows, FUN = estimateG, A = A, W = W, DeltaA = DeltaA, DeltaY = DeltaY,
tolg = tolg, verbose = verbose, stratify = stratify, returnModels = returnModels,
SL_g = SL_g, glm_g = glm_g, a_0 = a_0) at testthat/test-fluctuate.R:36
2: FUN(X[[i]], ...)
3: stats::glm(stats::as.formula(paste0("A~", glm_g)), data = thisDat, family = stats::binomial())
4: eval(mf, parent.frame())
5: eval(mf, parent.frame())
6: stats::model.frame(formula = stats::as.formula(paste0("A~", glm_g)), data = thisDat,
drop.unused.levels = TRUE)
7: stats::as.formula(paste0("A~", glm_g))
8: formula(object, env = baseenv())
9: formula.character(object, env = baseenv())
10: str2lang(x)
-- 6. Error: drtmle executes as expected with multiple treatment levels (@test-m
<text>:1:11: unexpected symbol
1: A~W1 + W2 A
^
1: drtmle(W = W, A = A, Y = Y, a_0 = c(0, 1, 2), family = gaussian(), stratify = TRUE,
glm_Q = "W1 + W2", glm_g = "W1 + W2", glm_Qr = "gn", glm_gr = "Qn", guard = c("Q",
"g"), reduction = "univariate", returnModels = TRUE) at testthat/test-multileveltrt.R:16
2: future.apply::future_lapply(X = validRows, FUN = estimateG, A = A, W = W, DeltaA = DeltaA,
DeltaY = DeltaY, tolg = tolg, verbose = verbose, stratify = stratify, returnModels = returnModels,
SL_g = SL_g, glm_g = glm_g, a_0 = a_0)
3: future({
...future.globals.maxSize.org <- getOption("future.globals.maxSize")
if (!identical(...future.globals.maxSize.org, ...future.globals.maxSize)) {
oopts <- options(future.globals.maxSize = ...future.globals.maxSize)
on.exit(options(oopts), add = TRUE)
}
lapply(seq_along(...future.elements_ii), FUN = function(jj) {
...future.X_jj <- ...future.elements_ii[[jj]]
...future.FUN(...future.X_jj, ...)
})
}, envir = envir, stdout = future.stdout, conditions = future.conditions, globals = globals_ii,
packages = packages_ii, lazy = future.lazy)
4: evaluator(expr, envir = envir, substitute = FALSE, lazy = lazy, seed = seed, globals = globals,
packages = packages, ...)
5: sequential(expr, envir = envir, substitute = FALSE, lazy = lazy, seed = seed, globals = globals,
local = local, earlySignal = earlySignal, label = label, ...)
6: run(future)
7: run.UniprocessFuture(future)
8: signalEarly(future, collect = FALSE)
9: resolved(future)
10: resolved.UniprocessFuture(future)
11: NextMethod()
12: resolved.Future(future)
13: signalEarly(x, ...)
14: resignalConditions(future)
-- 7. Error: adaptive_iptw executes as expected with multiple treatment levels (
<text>:1:11: unexpected symbol
1: A~W1 + W2 A
^
1: adaptive_iptw(W = W, A = A, Y = Y, a_0 = c(0, 1, 2), glm_g = "W1 + W2", returnModels = TRUE,
glm_Qr = "gn") at testthat/test-multileveltrt.R:95
2: future.apply::future_lapply(X = validRows, FUN = estimateG, A = A, W = W, DeltaA = DeltaA,
DeltaY = DeltaY, tolg = tolg, verbose = verbose, returnModels = returnModels,
SL_g = SL_g, glm_g = glm_g, a_0 = a_0, stratify = stratify)
3: future({
...future.globals.maxSize.org <- getOption("future.globals.maxSize")
if (!identical(...future.globals.maxSize.org, ...future.globals.maxSize)) {
oopts <- options(future.globals.maxSize = ...future.globals.maxSize)
on.exit(options(oopts), add = TRUE)
}
lapply(seq_along(...future.elements_ii), FUN = function(jj) {
...future.X_jj <- ...future.elements_ii[[jj]]
...future.FUN(...future.X_jj, ...)
})
}, envir = envir, stdout = future.stdout, conditions = future.conditions, globals = globals_ii,
packages = packages_ii, lazy = future.lazy)
4: evaluator(expr, envir = envir, substitute = FALSE, lazy = lazy, seed = seed, globals = globals,
packages = packages, ...)
5: sequential(expr, envir = envir, substitute = FALSE, lazy = lazy, seed = seed, globals = globals,
local = local, earlySignal = earlySignal, label = label, ...)
6: run(future)
7: run.UniprocessFuture(future)
8: signalEarly(future, collect = FALSE)
9: resolved(future)
10: resolved.UniprocessFuture(future)
11: NextMethod()
12: resolved.Future(future)
13: signalEarly(x, ...)
14: resignalConditions(future)
== testthat results ===========================================================
OK: 451 SKIPPED: 0 WARNINGS: 31 FAILED: 7
1. Error: adaptive_iptw works as expected with missing data (@test-adaptive_iptw-missingAY.R#19)
2. Error: drtmle executes as expected with stratify = TRUE (@test-drtmle-missingAY.R#23)
3. Error: drtmle executes as expected with stratify = FALSE (@test-drtmle-missingAY.R#188)
4. Error: GitHub error #16 resolves (@test-drtmle.R#503)
5. Error: Fail safe kicks in (@test-fluctuate.R#36)
6. Error: drtmle executes as expected with multiple treatment levels (@test-multileveltrt.R#16)
7. Error: adaptive_iptw executes as expected with multiple treatment levels (@test-multileveltrt.R#95)
Error: testthat unit tests failed
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.0.4
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building ‘using_drtmle.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
drtmle: TMLE with doubly robust inference
Version: 1.0.4
Loading required package: nnls
Super Learner
Version: 2.0-24
Package created on 2018-08-10
Loading required package: nloptr
Loading required package: nloptr
Loading required package: nloptr
Loading required package: nloptr
Loading required package: quadprog
Loading required package: earth
Loading required package: Formula
Loading required package: plotmo
Loading required package: plotrix
Loading required package: TeachingDemos
Loading required package: quadprog
Loading required package: earth
Loading required package: Formula
Loading required package: plotmo
Loading required package: plotrix
Loading required package: TeachingDemos
Loading required package: quadprog
Loading required package: earth
Loading required package: Formula
Loading required package: plotmo
Loading required package: plotrix
Loading required package: TeachingDemos
Loading required package: quadprog
Loading required package: earth
Loading required package: Formula
Loading required package: plotmo
Loading required package: plotrix
Loading required package: TeachingDemos
Loading required package: future
Quitting from lines 1049-1062 (using_drtmle.Rmd)
Error: processing vignette 'using_drtmle.Rmd' failed with diagnostics:
there is no package called 'snow'
--- failed re-building ‘using_drtmle.Rmd’
SUMMARY: processing the following file failed:
‘using_drtmle.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-patched-solaris-x86
Version: 1.0.4
Check: examples
Result: ERROR
Running examples in ‘drtmle-Ex.R’ failed
The error occurred in:
R version 3.6.0 beta (2019-04-15 r76395) -- "Planting of a Tree"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> pkgname <- "drtmle"
> source(file.path(R.home("share"), "R", "examples-header.R"))
> options(warn = 1)
> library('drtmle')
Error: package or namespace load failed for ‘drtmle’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
there is no package called ‘data.table’
Execution halted
Flavor: r-release-osx-x86_64
Version: 1.0.4
Check: tests
Result: ERROR
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(drtmle)
Error: package or namespace load failed for 'drtmle' in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
there is no package called 'data.table'
Execution halted
Flavor: r-release-osx-x86_64
Version: 1.0.4
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building ‘using_drtmle.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 385-393 (using_drtmle.Rmd)
Error: processing vignette 'using_drtmle.Rmd' failed with diagnostics:
package or namespace load failed for 'drtmle' in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
there is no package called 'data.table'
--- failed re-building ‘using_drtmle.Rmd’
SUMMARY: processing the following file failed:
‘using_drtmle.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-release-osx-x86_64