CRAN Package Check Results for Package txshift

Last updated on 2021-10-20 00:49:58 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.3.5 12.19 1255.63 1267.82 ERROR
r-devel-linux-x86_64-debian-gcc 0.3.6 10.77 151.56 162.33 NOTE
r-devel-linux-x86_64-fedora-clang 0.3.6 272.03 NOTE
r-devel-linux-x86_64-fedora-gcc 0.3.6 272.58 NOTE
r-devel-windows-x86_64 0.3.6 13.00 236.00 249.00 NOTE
r-devel-windows-x86_64-gcc10-UCRT 0.3.5 ERROR
r-patched-linux-x86_64 0.3.5 10.59 1181.25 1191.84 ERROR
r-patched-solaris-x86 0.3.6 274.30 NOTE
r-release-linux-x86_64 0.3.5 11.42 1176.77 1188.19 ERROR
r-release-macos-arm64 0.3.5 NOTE
r-release-macos-x86_64 0.3.5 NOTE
r-release-windows-ix86+x86_64 0.3.5 29.00 1474.00 1503.00 ERROR
r-oldrel-macos-x86_64 0.3.5 NOTE
r-oldrel-windows-ix86+x86_64 0.3.5 30.00 157.00 187.00 ERROR

Check Details

Version: 0.3.5
Check: package dependencies
Result: NOTE
    Package which this enhances but not available for checking: 'sl3'
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-windows-x86_64-gcc10-UCRT, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-ix86+x86_64, r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64

Version: 0.3.5
Check: LazyData
Result: NOTE
     'LazyData' is specified without a 'data' directory
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-windows-x86_64-gcc10-UCRT, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-ix86+x86_64

Version: 0.3.5
Check: tests
Result: ERROR
     Running 'testthat.R' [9s/11s]
    Running the tests in 'tests/testthat.R' failed.
    Complete output:
     > library(testthat)
     > library(txshift)
     txshift v0.3.5: Efficient Estimation of the Causal Effects of Stochastic
     Interventions
     >
     > test_check("txshift")
     == Failed tests ================================================================
     -- Error (test-censoring_mech.R:20:1): (code run outside of `test_that()`) -----
     Error in `origami::cross_validate(cv_fun = cv_haldensify, folds = folds,
     long_data = long_data, wts = wts_long, lambda_seq = lambda_seq,
     smoothness_orders = smoothness_orders, ..., use_future = FALSE,
     .combine = FALSE)`: formal argument "use_future" matched by multiple actual arguments
     Backtrace:
     x
     1. \-txshift:::est_g_exp(...) test-censoring_mech.R:20:0
     2. +-base::do.call(haldensify::haldensify, fit_args)
     3. \-(function (A, W, wts = rep(1, length(A)), grid_type = "equal_range", ...
     4. \-future.apply::future_mapply(...)
     5. \-future.apply:::future_xapply(...)
     6. +-future::value(fs)
     7. \-future:::value.list(fs)
     8. +-future::resolve(...)
     9. \-future:::resolve.list(...)
     10. \-future:::signalConditionsASAP(obj, resignal = FALSE, pos = ii)
     11. \-future:::signalConditions(...)
     -- Error (test-tmle_comparison.R:124:1): (code run outside of `test_that()`) ---
     Error in `hal9001::fit_hal(X = as.matrix(data_internal[, ..v_names]), Y = as.numeric(eif_eval$eif_unweighted[C_samp ==
     1]), max_degree = NULL, fit_type = "glmnet", family = "gaussian",
     return_lasso = FALSE, standardize = FALSE, type.measure = "mse",
     nlambda = 1000, lambda.min.ratio = 1/nrow(data_internal),
     yolo = FALSE)`: unused arguments (fit_type = "glmnet", standardize = FALSE, type.measure = "mse", nlambda = 1000, lambda.min.ratio = 1/nrow(data_internal))
     Backtrace:
     x
     1. \-txshift::txshift(...) test-tmle_comparison.R:124:0
     2. \-txshift:::tmle_txshift(...)
     3. \-txshift:::ipcw_eif_update(...)
    
     [ FAIL 2 | WARN 3 | SKIP 0 | PASS 7 ]
     Error: Test failures
     Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 0.3.6
Check: package dependencies
Result: NOTE
    Package which this enhances but not available for checking: ‘sl3’
Flavors: r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-patched-solaris-x86

Version: 0.3.5
Check: dependencies in R code
Result: NOTE
    Namespace in Imports field not imported from: 'tibble'
     All declared Imports should be used.
Flavors: r-devel-windows-x86_64-gcc10-UCRT, r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-x86_64

Version: 0.3.5
Check: tests
Result: ERROR
     Running 'testthat.R'
    Running the tests in 'tests/testthat.R' failed.
    Complete output:
     > library(testthat)
     > library(txshift)
     txshift v0.3.5: Efficient Estimation of the Causal Effects of Stochastic
     Interventions
     >
     > test_check("txshift")
     ══ Failed tests ════════════════════════════════════════════════════════════════
     ── Error (test-censoring_mech.R:20:1): (code run outside of `test_that()`) ─────
     Error in `origami::cross_validate(cv_fun = cv_haldensify, folds = folds,
     long_data = long_data, wts = wts_long, lambda_seq = lambda_seq,
     smoothness_orders = smoothness_orders, ..., use_future = FALSE,
     .combine = FALSE)`: formal argument "use_future" matched by multiple actual arguments
     Backtrace:
     █
     1. └─txshift:::est_g_exp(...) test-censoring_mech.R:20:0
     2. ├─base::do.call(haldensify::haldensify, fit_args)
     3. └─(function (A, W, wts = rep(1, length(A)), grid_type = "equal_range", ...
     4. └─future.apply::future_mapply(...)
     5. └─future.apply:::future_xapply(...)
     6. ├─future::value(fs)
     7. └─future:::value.list(fs)
     8. ├─future::resolve(...)
     9. └─future:::resolve.list(...)
     10. └─future:::signalConditionsASAP(obj, resignal = FALSE, pos = ii)
     11. └─future:::signalConditions(...)
     ── Error (test-tmle_comparison.R:124:1): (code run outside of `test_that()`) ───
     Error in `hal9001::fit_hal(X = as.matrix(data_internal[, ..v_names]), Y = as.numeric(eif_eval$eif_unweighted[C_samp ==
     1]), max_degree = NULL, fit_type = "glmnet", family = "gaussian",
     return_lasso = FALSE, standardize = FALSE, type.measure = "mse",
     nlambda = 1000, lambda.min.ratio = 1/nrow(data_internal),
     yolo = FALSE)`: unused arguments (fit_type = "glmnet", standardize = FALSE, type.measure = "mse", nlambda = 1000, lambda.min.ratio = 1/nrow(data_internal))
     Backtrace:
     █
     1. └─txshift::txshift(...) test-tmle_comparison.R:124:0
     2. └─txshift:::tmle_txshift(...)
     3. └─txshift:::ipcw_eif_update(...)
    
     [ FAIL 2 | WARN 3 | SKIP 0 | PASS 7 ]
     Error: Test failures
     Execution halted
Flavor: r-devel-windows-x86_64-gcc10-UCRT

Version: 0.3.5
Check: tests
Result: ERROR
     Running ‘testthat.R’ [8s/9s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > library(testthat)
     > library(txshift)
     txshift v0.3.5: Efficient Estimation of the Causal Effects of Stochastic
     Interventions
     >
     > test_check("txshift")
     ══ Failed tests ════════════════════════════════════════════════════════════════
     ── Error (test-censoring_mech.R:20:1): (code run outside of `test_that()`) ─────
     Error in `origami::cross_validate(cv_fun = cv_haldensify, folds = folds,
     long_data = long_data, wts = wts_long, lambda_seq = lambda_seq,
     smoothness_orders = smoothness_orders, ..., use_future = FALSE,
     .combine = FALSE)`: formal argument "use_future" matched by multiple actual arguments
     Backtrace:
     █
     1. └─txshift:::est_g_exp(...) test-censoring_mech.R:20:0
     2. ├─base::do.call(haldensify::haldensify, fit_args)
     3. └─(function (A, W, wts = rep(1, length(A)), grid_type = "equal_range", ...
     4. └─future.apply::future_mapply(...)
     5. └─future.apply:::future_xapply(...)
     6. ├─future::value(fs)
     7. └─future:::value.list(fs)
     8. ├─future::resolve(...)
     9. └─future:::resolve.list(...)
     10. └─future:::signalConditionsASAP(obj, resignal = FALSE, pos = ii)
     11. └─future:::signalConditions(...)
     ── Error (test-tmle_comparison.R:124:1): (code run outside of `test_that()`) ───
     Error in `hal9001::fit_hal(X = as.matrix(data_internal[, ..v_names]), Y = as.numeric(eif_eval$eif_unweighted[C_samp ==
     1]), max_degree = NULL, fit_type = "glmnet", family = "gaussian",
     return_lasso = FALSE, standardize = FALSE, type.measure = "mse",
     nlambda = 1000, lambda.min.ratio = 1/nrow(data_internal),
     yolo = FALSE)`: unused arguments (fit_type = "glmnet", standardize = FALSE, type.measure = "mse", nlambda = 1000, lambda.min.ratio = 1/nrow(data_internal))
     Backtrace:
     █
     1. └─txshift::txshift(...) test-tmle_comparison.R:124:0
     2. └─txshift:::tmle_txshift(...)
     3. └─txshift:::ipcw_eif_update(...)
    
     [ FAIL 2 | WARN 3 | SKIP 0 | PASS 7 ]
     Error: Test failures
     Execution halted
Flavors: r-patched-linux-x86_64, r-release-linux-x86_64

Version: 0.3.5
Check: tests
Result: ERROR
     Running 'testthat.R' [10s]
    Running the tests in 'tests/testthat.R' failed.
    Complete output:
     > library(testthat)
     > library(txshift)
     txshift v0.3.5: Efficient Estimation of the Causal Effects of Stochastic
     Interventions
     >
     > test_check("txshift")
     == Failed tests ================================================================
     -- Error (test-censoring_mech.R:20:1): (code run outside of `test_that()`) -----
     Error in `origami::cross_validate(cv_fun = cv_haldensify, folds = folds,
     long_data = long_data, wts = wts_long, lambda_seq = lambda_seq,
     smoothness_orders = smoothness_orders, ..., use_future = FALSE,
     .combine = FALSE)`: formal argument "use_future" matched by multiple actual arguments
     Backtrace:
     x
     1. \-txshift:::est_g_exp(...) test-censoring_mech.R:20:0
     2. +-base::do.call(haldensify::haldensify, fit_args)
     3. \-(function (A, W, wts = rep(1, length(A)), grid_type = "equal_range", ...
     4. \-future.apply::future_mapply(...)
     5. \-future.apply:::future_xapply(...)
     6. +-future::value(fs)
     7. \-future:::value.list(fs)
     8. +-future::resolve(...)
     9. \-future:::resolve.list(...)
     10. \-future:::signalConditionsASAP(obj, resignal = FALSE, pos = ii)
     11. \-future:::signalConditions(...)
     -- Error (test-tmle_comparison.R:124:1): (code run outside of `test_that()`) ---
     Error in `hal9001::fit_hal(X = as.matrix(data_internal[, ..v_names]), Y = as.numeric(eif_eval$eif_unweighted[C_samp ==
     1]), max_degree = NULL, fit_type = "glmnet", family = "gaussian",
     return_lasso = FALSE, standardize = FALSE, type.measure = "mse",
     nlambda = 1000, lambda.min.ratio = 1/nrow(data_internal),
     yolo = FALSE)`: unused arguments (fit_type = "glmnet", standardize = FALSE, type.measure = "mse", nlambda = 1000, lambda.min.ratio = 1/nrow(data_internal))
     Backtrace:
     x
     1. \-txshift::txshift(...) test-tmle_comparison.R:124:0
     2. \-txshift:::tmle_txshift(...)
     3. \-txshift:::ipcw_eif_update(...)
    
     [ FAIL 2 | WARN 3 | SKIP 0 | PASS 7 ]
     Error: Test failures
     Execution halted
Flavor: r-release-windows-ix86+x86_64

Version: 0.3.5
Check: examples
Result: ERROR
    Running examples in 'txshift-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: confint.txshift
    > ### Title: Confidence Intervals for Counterfactual Mean Under Stochastic
    > ### Intervention
    > ### Aliases: confint.txshift
    >
    > ### ** Examples
    >
    > set.seed(429153)
    > n_obs <- 100
    > W <- replicate(2, rbinom(n_obs, 1, 0.5))
    > A <- rnorm(n_obs, mean = 2 * W, sd = 1)
    > Y <- rbinom(n_obs, 1, plogis(A + W + rnorm(n_obs, mean = 0, sd = 1)))
    > txout <- txshift(
    + W = W, A = A, Y = Y, delta = 0.5,
    + estimator = "tmle",
    + g_exp_fit_args = list(
    + fit_type = "hal", n_bins = 5,
    + grid_type = "equal_mass",
    + lambda_seq = exp(-1:-9)
    + ),
    + Q_fit_args = list(
    + fit_type = "glm",
    + glm_formula = "Y ~ ."
    + )
    + )
    Warning in origami::cross_validate(cv_fun = cv_haldensify, folds = folds, :
     All iterations resulted in errors
    Error in apply(density_pred_unscaled, 2, function(x) { :
     dim(X) must have a positive length
    Calls: txshift ... do.call -> <Anonymous> -> mapply -> <Anonymous> -> apply
    Execution halted
Flavor: r-oldrel-windows-ix86+x86_64

Version: 0.3.5
Check: tests
Result: ERROR
     Running 'testthat.R' [10s]
    Running the tests in 'tests/testthat.R' failed.
    Complete output:
     > library(testthat)
     > library(txshift)
     txshift v0.3.5: Efficient Estimation of the Causal Effects of Stochastic
     Interventions
     >
     > test_check("txshift")
     == Failed tests ================================================================
     -- Error (test-censoring_mech.R:20:1): (code run outside of `test_that()`) -----
     Error in `apply(density_pred_unscaled, 2, function(x) {
     pred <- x/bin_sizes[long_data[in_bin == 1, bin_id]]
     return(pred)
     })`: dim(X) must have a positive length
     Backtrace:
     x
     1. \-txshift:::est_g_exp(...) test-censoring_mech.R:20:0
     2. +-base::do.call(haldensify::haldensify, fit_args)
     3. \-(function (A, W, wts = rep(1, length(A)), grid_type = "equal_range", ...
     4. \-base::mapply(...)
     5. \-(function (A, W, wts = rep(1, length(A)), grid_type = "equal_range", ...
     6. \-base::apply(...)
     -- Error (test-tmle_comparison.R:124:1): (code run outside of `test_that()`) ---
     Error in `hal9001::fit_hal(X = as.matrix(data_internal[, ..v_names]), Y = as.numeric(eif_eval$eif_unweighted[C_samp ==
     1]), max_degree = NULL, fit_type = "glmnet", family = "gaussian",
     return_lasso = FALSE, standardize = FALSE, type.measure = "mse",
     nlambda = 1000, lambda.min.ratio = 1/nrow(data_internal),
     yolo = FALSE)`: unused arguments (fit_type = "glmnet", standardize = FALSE, type.measure = "mse", nlambda = 1000, lambda.min.ratio = 1/nrow(data_internal))
     Backtrace:
     x
     1. \-txshift::txshift(...) test-tmle_comparison.R:124:0
     2. \-txshift:::tmle_txshift(...)
     3. \-txshift:::ipcw_eif_update(...)
    
     [ FAIL 2 | WARN 4 | SKIP 0 | PASS 7 ]
     Error: Test failures
     Execution halted
Flavor: r-oldrel-windows-ix86+x86_64

Version: 0.3.5
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building 'intro_txshift.Rmd' using rmarkdown
    Quitting from lines 107-116 (intro_txshift.Rmd)
    Error: processing vignette 'intro_txshift.Rmd' failed with diagnostics:
    dim(X) must have a positive length
    --- failed re-building 'intro_txshift.Rmd'
    
    --- re-building 'ipcw_txshift.Rmd' using rmarkdown
    Quitting from lines 129-141 (ipcw_txshift.Rmd)
    Error: processing vignette 'ipcw_txshift.Rmd' failed with diagnostics:
    dim(X) must have a positive length
    --- failed re-building 'ipcw_txshift.Rmd'
    
    SUMMARY: processing the following files failed:
     'intro_txshift.Rmd' 'ipcw_txshift.Rmd'
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-oldrel-windows-ix86+x86_64