CRAN Package Check Results for Maintainer ‘Jamie Lentin <lentinj at shuttlethread.com>’

Last updated on 2025-05-15 09:53:04 CEST.

Package	ERROR	NOTE	OK
gadget3	1		12
mfdb		4	9
unittest			13

Package gadget3

Current CRAN status: ERROR: 1, OK: 12

Version: 0.13-0
Check: tests
Result: ERROR Running 'test-aab_env.R' [1s] Running 'test-action_age.R' [4s] Running 'test-action_grow-methods.R' [6s] Running 'test-action_grow.R' [3s] Running 'test-action_mature.R' [3s] Running 'test-action_migrate.R' [3s] Running 'test-action_naturalmortality.R' [1s] Running 'test-action_predate-catchability.R' [6s] Running 'test-action_predate-numberfleet.R' [3s] Running 'test-action_predate-predator.R' [19s] Running 'test-action_predate-timebasedsuitability.R' [4s] Running 'test-action_predate.R' [8s] Running 'test-action_renewal-otherfood.R' [10s] Running 'test-action_renewal.R' [6s] Running 'test-action_report.R' [2s] Running 'test-action_spawn-multipleoutputs.R' [6s] Running 'test-action_spawn.R' [6s] Running 'test-action_spmodel.R' [2s] Running 'test-action_tagging.R' [3s] Running 'test-action_time.R' [2s] Running 'test-action_weightloss.R' [3s] Running 'test-array_utils.R' [4s] Running 'test-env_dif.R' [2s] Running 'test-eval.R' [1s] Running 'test-formula_utils.R' [1s] Running 'test-init_val.R' [2s] Running 'test-likelihood_bounds.R' [3s] Running 'test-likelihood_data.R' [5s] Running 'test-likelihood_distribution-surveyindices.R' [3s] Running 'test-likelihood_distribution.R' [18s] Running 'test-likelihood_random.R' [1s] Running 'test-likelihood_sparsesample.R' [5s] Running 'test-likelihood_tagging_ckmr.R' [5s] Running 'test-likelihood_understocking.R' [0s] Running 'test-param_project-ar1.R' [5s] Running 'test-param_project-logar1.R' [4s] Running 'test-param_project.R' [2s] Running 'test-params.R' [3s] Running 'test-quota-assess.R' [7s] Running 'test-quota-hockeyfleet.R' [5s] Running 'test-quota.R' [2s] Running 'test-regression.R' [1s] Running 'test-run.R' [1s] Running 'test-run_r.R' [3s] Running 'test-run_tmb-reporting_enabled.R' [1s] Running 'test-run_tmb.R' [5s] Running 'test-step.R' [3s] Running 'test-stock.R' [1s] Running 'test-stock_age.R' [2s] Running 'test-stock_areas.R' [3s] Running 'test-stock_product.R' [0s] Running 'test-stock_tag.R' [2s] Running 'test-stock_time-fishingyear.R' [2s] Running 'test-stock_time.R' [1s] Running 'test-suitability-report.R' [9s] Running 'test-suitability.R' [3s] Running 'test-timedata.R' [2s] Running 'test-timevariable.R' [1s] Running the tests in 'tests/test-env_dif.R' failed. Complete output: > library(unittest) > > library(gadget3) > > params <- list() > actions <- list() > > # NB: Should test under both CppAD and TMBAD > # options(gadget3.tmb.framework = "CppAD") > > ############################################################################### > > dif_pmax_scl_dbl_in <- runif(1, 0, 100) > dif_pmax_vec_in <- runif(10, 0, 100) > dif_pmax_vec_vec_max <- runif(10, 0, 10) * 10 > actions[['dif_pmax_vec']] <- g3_formula( + { + expect_dif_pmax_scl_dbl <- dif_pmax(dif_pmax_scl_dbl_in, 40.0, 1e5) + expect_dif_pmax_vec_typ <- dif_pmax(dif_pmax_vec_in, dif_pmax_vec_typ_max, 1e5) + expect_dif_pmax_dervec_typ <- dif_pmax(dif_pmax_vec_in * 2, dif_pmax_vec_typ_max, 1e5) + expect_dif_pmax_vec_dbl <- dif_pmax(dif_pmax_vec_in, 30.0, 1e5) + expect_dif_pmax_vec_int <- dif_pmax(dif_pmax_vec_in, dif_pmax_vec_int_max, 1e5) + expect_dif_pmax_vec_vec <- dif_pmax(dif_pmax_vec_in, dif_pmax_vec_vec_max, 1e5) + }, + dif_pmax_scl_dbl_in = dif_pmax_scl_dbl_in, + dif_pmax_vec_in = dif_pmax_vec_in, + dif_pmax_vec_typ_max = 40.0, + dif_pmax_vec_int_max = 60L, + dif_pmax_vec_vec_max = dif_pmax_vec_vec_max, + expect_dif_pmax_scl_dbl = pmax(dif_pmax_scl_dbl_in, 40), + expect_dif_pmax_vec_typ = pmax(dif_pmax_vec_in, 40.0), + expect_dif_pmax_dervec_typ = pmax(dif_pmax_vec_in * 2, 40.0), + expect_dif_pmax_vec_dbl = pmax(dif_pmax_vec_in, 30.0), + expect_dif_pmax_vec_int = pmax(dif_pmax_vec_in, 60L), + expect_dif_pmax_vec_vec = pmax(dif_pmax_vec_in, dif_pmax_vec_vec_max), + end = NULL ) > > dif_pmax_arr_in <- array(runif(10, 0, 9), dim = c(3, 3)) > dif_pmax_arr_vec_max <- runif(3, 0, 10) * 10 > actions[['dif_pmax_arr']] <- g3_formula( + { + expect_dif_pmax_arr_typ <- dif_pmax(dif_pmax_arr_in, dif_pmax_arr_typ_max, 1e5) + expect_dif_pmax_dearr_typ <- dif_pmax(dif_pmax_arr_in * 2, dif_pmax_arr_typ_max, 1e5) + expect_dif_pmax_arr_dbl <- dif_pmax(dif_pmax_arr_in, 30.0, 1e5) + expect_dif_pmax_arr_int <- dif_pmax(dif_pmax_arr_in, dif_pmax_arr_int_max, 1e5) + expect_dif_pmax_arr_vec <- dif_pmax(dif_pmax_arr_in, dif_pmax_arr_vec_max, 1e5) + }, + dif_pmax_arr_in = dif_pmax_arr_in, + dif_pmax_arr_typ_max = 40.0, + dif_pmax_arr_int_max = 60L, + dif_pmax_arr_vec_max = dif_pmax_arr_vec_max, + expect_dif_pmax_arr_typ = pmax(dif_pmax_arr_in, 40.0), + expect_dif_pmax_dearr_typ = pmax(dif_pmax_arr_in * 2, 40.0), + expect_dif_pmax_arr_dbl = pmax(dif_pmax_arr_in, 30.0), + expect_dif_pmax_arr_int = pmax(dif_pmax_arr_in, 60L), + expect_dif_pmax_arr_vec = pmax(dif_pmax_arr_in, dif_pmax_arr_vec_max), + end = NULL ) > > dif_pmin_vec_in <- runif(10, 0, 100) > dif_pmin_vec_vec_max <- runif(10, 0, 10) * 10 > actions[['dif_pmin_vec']] <- g3_formula( + { + expect_dif_pmin_vec_typ <- dif_pmin(dif_pmin_vec_in, dif_pmin_vec_typ_max, 1e5) + expect_dif_pmin_vec_dbl <- dif_pmin(dif_pmin_vec_in, 30.0, 1e5) + expect_dif_pmin_vec_int <- dif_pmin(dif_pmin_vec_in, dif_pmin_vec_int_max, 1e5) + expect_dif_pmin_vec_vec <- dif_pmin(dif_pmin_vec_in, dif_pmin_vec_vec_max, 1e5) + }, + dif_pmin_vec_in = dif_pmin_vec_in, + dif_pmin_vec_typ_max = 40.0, + dif_pmin_vec_int_max = 60L, + dif_pmin_vec_vec_max = dif_pmin_vec_vec_max, + expect_dif_pmin_vec_typ = pmin(dif_pmin_vec_in, 40.0), + expect_dif_pmin_vec_dbl = pmin(dif_pmin_vec_in, 30.0), + expect_dif_pmin_vec_int = pmin(dif_pmin_vec_in, 60L), + expect_dif_pmin_vec_vec = pmin(dif_pmin_vec_in, dif_pmin_vec_vec_max), + end = NULL ) > > dif_pmin_arr_in <- array(runif(10, 0, 9), dim = c(3, 3)) > dif_pmin_arr_vec_max <- runif(3, 0, 10) * 10 > actions[['dif_pmin_arr']] <- g3_formula( + { + expect_dif_pmin_arr_typ <- dif_pmin(dif_pmin_arr_in, dif_pmin_arr_typ_max, 1e5) + expect_dif_pmin_arr_dbl <- dif_pmin(dif_pmin_arr_in, 30.0, 1e5) + expect_dif_pmin_arr_int <- dif_pmin(dif_pmin_arr_in, dif_pmin_arr_int_max, 1e5) + expect_dif_pmin_arr_vec <- dif_pmin(dif_pmin_arr_in, dif_pmin_arr_vec_max, 1e5) + }, + dif_pmin_arr_in = dif_pmin_arr_in, + dif_pmin_arr_typ_max = 40.0, + dif_pmin_arr_int_max = 60L, + dif_pmin_arr_vec_max = dif_pmin_arr_vec_max, + expect_dif_pmin_arr_typ = pmin(dif_pmin_arr_in, 40.0), + expect_dif_pmin_arr_dbl = pmin(dif_pmin_arr_in, 30.0), + expect_dif_pmin_arr_int = pmin(dif_pmin_arr_in, 60L), + expect_dif_pmin_arr_vec = pmin(dif_pmin_arr_in, dif_pmin_arr_vec_max), + end = NULL ) > > dif_pminmax_vec_in <- runif(10, 0, 100) > dif_pminmax_vec_vec_l <- runif(10, 0, 50) > dif_pminmax_vec_vec_u <- 50 + runif(10, 0, 50) > actions[['dif_pminmax_vec']] <- g3_formula( + { + expect_dif_pminmax_vec_dbl <- dif_pminmax(dif_pminmax_vec_in, 30.0, 60.0, 1e5) + expect_dif_pminmax_vec_vec <- dif_pminmax(dif_pminmax_vec_in, dif_pminmax_vec_vec_l, dif_pminmax_vec_vec_u, 1e5) + }, + dif_pminmax_vec_in = dif_pminmax_vec_in, + dif_pminmax_vec_vec_l = dif_pminmax_vec_vec_l, + dif_pminmax_vec_vec_u = dif_pminmax_vec_vec_u, + expect_dif_pminmax_vec_dbl = pmin(pmax(dif_pminmax_vec_in, 30.0), 60.0), + expect_dif_pminmax_vec_vec = pmin(pmax(dif_pminmax_vec_in, dif_pminmax_vec_vec_l), dif_pminmax_vec_vec_u), + end = NULL ) > > ############################################################################### > > expecteds <- new.env(parent = emptyenv()) > > for (i in seq_along(actions)) { + exp_names <- grep("^expect_", names(environment(actions[[i]])), value = TRUE) + + # For each expect_ variable, move to expecteds + for (exp_name in exp_names) { + expecteds[[exp_name]] <- environment(actions[[i]])[[exp_name]] + environment(actions[[i]])[[exp_name]][] <- 0 + } + + # REPORT every expect_ + reports <- lapply(exp_names, function (exp_name) { + substitute(REPORT(sym), list(sym = as.symbol(exp_name))) + }) + # Convert list to { REPORT(x) ; REPORT(y); ... } + reports <- as.call(c(as.symbol("{"), reports)) + + # Top/tail actions with a comment of their name & reports + actions[[i]] <- gadget3:::f_substitute(quote({ + comment(act_name) + act_f + reports + }), list( + act_name = names(actions)[[i]], + act_f = actions[[i]], + reports = reports)) + } > > actions[['z']] <- g3_formula({ + comment('done') + nll <- nll + g3_param('rv') + return(nll) + }, nll = 0.0) > params$rv <- 0.0 > > model_fn <- g3_to_r(actions) > model_cpp <- g3_to_tmb(actions) > result <- model_fn(params) > > # Compare everything we've been told to compare > for (n in ls(expecteds)) { + tol <- sqrt(.Machine$double.eps) + if (!is.null(attr(expecteds[[n]], "tol"))) { + tol <- attr(expecteds[[n]], "tol") + attr(expecteds[[n]], "tol") <- NULL + } + ok(ut_cmp_equal( + attr(result, n), + expecteds[[n]], + tolerance = tol ), n) + } ok - expect_dif_pmax_arr_dbl ok - expect_dif_pmax_arr_int ok - expect_dif_pmax_arr_typ ok - expect_dif_pmax_arr_vec ok - expect_dif_pmax_dearr_typ ok - expect_dif_pmax_dervec_typ ok - expect_dif_pmax_scl_dbl ok - expect_dif_pmax_vec_dbl ok - expect_dif_pmax_vec_int ok - expect_dif_pmax_vec_typ ok - expect_dif_pmax_vec_vec ok - expect_dif_pmin_arr_dbl ok - expect_dif_pmin_arr_int ok - expect_dif_pmin_arr_typ ok - expect_dif_pmin_arr_vec ok - expect_dif_pmin_vec_dbl ok - expect_dif_pmin_vec_int ok - expect_dif_pmin_vec_typ ok - expect_dif_pmin_vec_vec not ok - expect_dif_pminmax_vec_dbl # Test returned non-TRUE value: # Mean relative difference: 1.577177e-07 # --- attr(result, n) # +++ expecteds[[n]] # num [1:10] 41.95813669 [-30.00000473-]{+30+} 60 60 37.03350888 60 60 30 30 58.40689812 ok - expect_dif_pminmax_vec_vec > > gadget3:::ut_tmb_r_compare2(model_fn, model_cpp, params) # skip: not running TMB tests NULL > > proc.time() user system elapsed 0.93 0.10 1.59 1..21 # Looks like you failed 1 of 21 tests. # 20: expect_dif_pminmax_vec_dbl Flavor: r-oldrel-windows-x86_64

Package mfdb

Current CRAN status: NOTE: 4, OK: 9

Version: 7.3-1
Check: for unstated dependencies in ‘demo’
Result: NOTE 'library' or 'require' call not declared from: ‘tibble’ Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64

Package unittest

Current CRAN status: OK: 13