Package check result: OK Changes to worse in reverse depends: Package: cvwrapr Check: tests New result: ERROR Running ‘testthat.R’ [19s/20s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(cvwrapr) > > test_check("cvwrapr") Loading required package: Matrix Loaded glmnet 4.1-9 Attaching package: 'glmnet' The following object is masked from 'package:cvwrapr': coxnet.deviance Loading required package: foreach Loading required package: iterators [ FAIL 14 | WARN 0 | SKIP 0 | PASS 348 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-kfoldcv-glmnet-family.R:179:3'): glmnet cox-deviance ───────── cvm doesn't match not equal to new_fit$cvm. 46/46 mismatches (average diff: 0.0134) [1] 5.71 - 5.72 == -0.0113 [2] 5.67 - 5.68 == -0.0126 [3] 5.61 - 5.63 == -0.0134 [4] 5.56 - 5.57 == -0.0135 [5] 5.51 - 5.53 == -0.0134 [6] 5.47 - 5.49 == -0.0133 [7] 5.44 - 5.45 == -0.0133 [8] 5.42 - 5.43 == -0.0132 [9] 5.40 - 5.41 == -0.0133 ... Backtrace: ▆ 1. └─cvwrapr:::compare_glmnet_fits(target_fit, cv_fit, family = "cox") at test-kfoldcv-glmnet-family.R:179:3 2. └─testthat::expect_equal(target_fit$cvm, new_fit$cvm, label = "cvm doesn't match") at tests/testthat/setup.R:27:3 ── Failure ('test-kfoldcv-glmnet-family.R:179:3'): glmnet cox-deviance ───────── cvsd doesn't match not equal to new_fit$cvsd. 46/46 mismatches (average diff: 0.0508) [1] 0.249 - 0.403 == -0.1533 [2] 0.243 - 0.409 == -0.1654 [3] 0.244 - 0.403 == -0.1589 [4] 0.249 - 0.390 == -0.1408 [5] 0.255 - 0.376 == -0.1203 [6] 0.260 - 0.363 == -0.1028 [7] 0.265 - 0.353 == -0.0878 [8] 0.269 - 0.344 == -0.0750 [9] 0.273 - 0.336 == -0.0632 ... Backtrace: ▆ 1. └─cvwrapr:::compare_glmnet_fits(target_fit, cv_fit, family = "cox") at test-kfoldcv-glmnet-family.R:179:3 2. └─testthat::expect_equal(target_fit$cvsd, new_fit$cvsd, label = "cvsd doesn't match") at tests/testthat/setup.R:29:3 ── Failure ('test-kfoldcv-glmnet-family.R:179:3'): glmnet cox-deviance ───────── cvup doesn't match not equal to new_fit$cvup. 46/46 mismatches (average diff: 0.0504) [1] 5.96 - 6.12 == -0.1646 [2] 5.91 - 6.09 == -0.1781 [3] 5.86 - 6.03 == -0.1723 [4] 5.81 - 5.96 == -0.1543 [5] 5.77 - 5.90 == -0.1337 [6] 5.73 - 5.85 == -0.1161 [7] 5.71 - 5.81 == -0.1011 [8] 5.68 - 5.77 == -0.0882 [9] 5.67 - 5.74 == -0.0765 ... Backtrace: ▆ 1. └─cvwrapr:::compare_glmnet_fits(target_fit, cv_fit, family = "cox") at test-kfoldcv-glmnet-family.R:179:3 2. └─testthat::expect_equal(target_fit$cvup, new_fit$cvup, label = "cvup doesn't match") at tests/testthat/setup.R:31:3 ── Failure ('test-kfoldcv-glmnet-family.R:179:3'): glmnet cox-deviance ───────── cvlo doesn't match not equal to new_fit$cvlo. 46/46 mismatches (average diff: 0.0547) [1] 5.46 - 5.32 == 0.1420 [2] 5.43 - 5.27 == 0.1528 [3] 5.37 - 5.23 == 0.1456 [4] 5.31 - 5.18 == 0.1273 [5] 5.26 - 5.15 == 0.1069 [6] 5.21 - 5.12 == 0.0894 [7] 5.18 - 5.10 == 0.0745 [8] 5.15 - 5.09 == 0.0617 [9] 5.12 - 5.07 == 0.0499 ... Backtrace: ▆ 1. └─cvwrapr:::compare_glmnet_fits(target_fit, cv_fit, family = "cox") at test-kfoldcv-glmnet-family.R:179:3 2. └─testthat::expect_equal(target_fit$cvlo, new_fit$cvlo, label = "cvlo doesn't match") at tests/testthat/setup.R:33:3 ── Failure ('test-kfoldcv-glmnet-family.R:179:3'): glmnet cox-deviance ───────── fit.preval doesn't match not equal to new_fit$fit.preval. Attributes: < Component "cvraw": Mean relative difference: 0.3317 > Backtrace: ▆ 1. └─cvwrapr:::compare_glmnet_fits(target_fit, cv_fit, family = "cox") at test-kfoldcv-glmnet-family.R:179:3 2. └─testthat::expect_equal(...) at tests/testthat/setup.R:39:3 ── Failure ('test-kfoldcv-glmnet-family.R:179:3'): glmnet cox-deviance ───────── lambda.1se doesn't match not equal to new_fit$lambda.1se. 1/1 mismatches [1] 0.261 - 0.287 == -0.0255 Backtrace: ▆ 1. └─cvwrapr:::compare_glmnet_fits(target_fit, cv_fit, family = "cox") at test-kfoldcv-glmnet-family.R:179:3 2. └─testthat::expect_equal(...) at tests/testthat/setup.R:43:3 ── Failure ('test-kfoldcv-glmnet-family.R:179:3'): glmnet cox-deviance ───────── index doesn't match not equal to new_fit$index. 1/2 mismatches [2] 3 - 2 == 1 Backtrace: ▆ 1. └─cvwrapr:::compare_glmnet_fits(target_fit, cv_fit, family = "cox") at test-kfoldcv-glmnet-family.R:179:3 2. └─testthat::expect_equal(target_fit$index, new_fit$index, label = "index doesn't match") at tests/testthat/setup.R:45:3 ── Failure ('test-kfoldcv-glmnet-family.R:193:3'): glmnet cox-deviance, grouped = FALSE ── cvm doesn't match not equal to new_fit$cvm. 46/46 mismatches (average diff: 0.0341) [1] 2.54 - 2.51 == 0.0242 [2] 2.50 - 2.48 == 0.0230 [3] 2.45 - 2.43 == 0.0228 [4] 2.40 - 2.38 == 0.0234 [5] 2.36 - 2.34 == 0.0244 [6] 2.33 - 2.30 == 0.0252 [7] 2.30 - 2.27 == 0.0259 [8] 2.27 - 2.25 == 0.0265 [9] 2.26 - 2.23 == 0.0272 ... Backtrace: ▆ 1. └─cvwrapr:::compare_glmnet_fits(target_fit, cv_fit, family = "cox") at test-kfoldcv-glmnet-family.R:193:3 2. └─testthat::expect_equal(target_fit$cvm, new_fit$cvm, label = "cvm doesn't match") at tests/testthat/setup.R:27:3 ── Failure ('test-kfoldcv-glmnet-family.R:193:3'): glmnet cox-deviance, grouped = FALSE ── cvsd doesn't match not equal to new_fit$cvsd. 46/46 mismatches (average diff: 0.123) [1] 0.182 - 0.166 == 0.01574 [2] 0.177 - 0.172 == 0.00504 [3] 0.175 - 0.167 == 0.00870 [4] 0.178 - 0.156 == 0.02187 [5] 0.183 - 0.146 == 0.03718 [6] 0.187 - 0.137 == 0.05018 [7] 0.191 - 0.130 == 0.06122 [8] 0.195 - 0.124 == 0.07074 [9] 0.199 - 0.120 == 0.07944 ... Backtrace: ▆ 1. └─cvwrapr:::compare_glmnet_fits(target_fit, cv_fit, family = "cox") at test-kfoldcv-glmnet-family.R:193:3 2. └─testthat::expect_equal(target_fit$cvsd, new_fit$cvsd, label = "cvsd doesn't match") at tests/testthat/setup.R:29:3 ── Failure ('test-kfoldcv-glmnet-family.R:193:3'): glmnet cox-deviance, grouped = FALSE ── cvup doesn't match not equal to new_fit$cvup. 46/46 mismatches (average diff: 0.157) [1] 2.72 - 2.68 == 0.0399 [2] 2.68 - 2.65 == 0.0280 [3] 2.63 - 2.60 == 0.0315 [4] 2.58 - 2.54 == 0.0453 [5] 2.54 - 2.48 == 0.0615 [6] 2.51 - 2.44 == 0.0754 [7] 2.49 - 2.40 == 0.0871 [8] 2.47 - 2.37 == 0.0973 [9] 2.46 - 2.35 == 0.1066 ... Backtrace: ▆ 1. └─cvwrapr:::compare_glmnet_fits(target_fit, cv_fit, family = "cox") at test-kfoldcv-glmnet-family.R:193:3 2. └─testthat::expect_equal(target_fit$cvup, new_fit$cvup, label = "cvup doesn't match") at tests/testthat/setup.R:31:3 ── Failure ('test-kfoldcv-glmnet-family.R:193:3'): glmnet cox-deviance, grouped = FALSE ── cvlo doesn't match not equal to new_fit$cvlo. 46/46 mismatches (average diff: 0.0908) [1] 2.36 - 2.35 == 0.00841 [2] 2.32 - 2.31 == 0.01792 [3] 2.28 - 2.26 == 0.01408 [4] 2.23 - 2.22 == 0.00157 [5] 2.18 - 2.19 == -0.01282 [6] 2.14 - 2.16 == -0.02501 [7] 2.11 - 2.14 == -0.03534 [8] 2.08 - 2.12 == -0.04421 [9] 2.06 - 2.11 == -0.05225 ... Backtrace: ▆ 1. └─cvwrapr:::compare_glmnet_fits(target_fit, cv_fit, family = "cox") at test-kfoldcv-glmnet-family.R:193:3 2. └─testthat::expect_equal(target_fit$cvlo, new_fit$cvlo, label = "cvlo doesn't match") at tests/testthat/setup.R:33:3 ── Failure ('test-kfoldcv-glmnet-family.R:193:3'): glmnet cox-deviance, grouped = FALSE ── fit.preval doesn't match not equal to new_fit$fit.preval. Attributes: < Component "cvraw": Mean relative difference: 0.3433054 > Backtrace: ▆ 1. └─cvwrapr:::compare_glmnet_fits(target_fit, cv_fit, family = "cox") at test-kfoldcv-glmnet-family.R:193:3 2. └─testthat::expect_equal(...) at tests/testthat/setup.R:39:3 ── Failure ('test-kfoldcv-glmnet-family.R:193:3'): glmnet cox-deviance, grouped = FALSE ── lambda.1se doesn't match not equal to new_fit$lambda.1se. 1/1 mismatches [1] 0.238 - 0.197 == 0.0404 Backtrace: ▆ 1. └─cvwrapr:::compare_glmnet_fits(target_fit, cv_fit, family = "cox") at test-kfoldcv-glmnet-family.R:193:3 2. └─testthat::expect_equal(...) at tests/testthat/setup.R:43:3 ── Failure ('test-kfoldcv-glmnet-family.R:193:3'): glmnet cox-deviance, grouped = FALSE ── index doesn't match not equal to new_fit$index. 1/2 mismatches [2] 4 - 6 == -2 Backtrace: ▆ 1. └─cvwrapr:::compare_glmnet_fits(target_fit, cv_fit, family = "cox") at test-kfoldcv-glmnet-family.R:193:3 2. └─testthat::expect_equal(target_fit$index, new_fit$index, label = "index doesn't match") at tests/testthat/setup.R:45:3 [ FAIL 14 | WARN 0 | SKIP 0 | PASS 348 ] Error: Test failures Execution halted Package: hdnom Check: examples New result: ERROR Running examples in ‘hdnom-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: as_nomogram > ### Title: Construct nomogram ojects for high-dimensional Cox models > ### Aliases: as_nomogram > > ### ** Examples > > data(smart) > x <- as.matrix(smart[, -c(1, 2)]) > time <- smart$TEVENT > event <- smart$EVENT > y <- survival::Surv(time, event) > > fit <- fit_lasso(x, y, nfolds = 5, rule = "lambda.1se", seed = 11) > > nom <- as_nomogram( + fit, x, time, event, pred.at = 365 * 2, + funlabel = "2-Year Overall Survival Probability" + ) > > print(nom) Points per unit of linear predictor: 4.987753e+16 Linear predictor units per point : 2.004911e-17 AGE Points 15 0 20 7 25 14 30 21 35 29 40 36 45 43 50 50 55 57 60 64 65 71 70 79 75 86 80 93 85 100 Total Points 2-Year Overall Survival Probability > plot(nom) Error in axis(sides[jj], at = scaled[jj], labels = fat[jj], pos = y, cex.axis = cex.axis, : no locations are finite Calls: plot ... plot.hdnom.nomogram -> plot -> plot.nomogram.raw -> axis Execution halted Package: hdnom Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘hdnom.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/CRAN_recheck/hdnom.Rcheck/vign_test/hdnom/vignettes/hdnom_files/figure-html/unnamed-chunk-7-1.png 1152x1152 pixels, 3x8 bits/pixel, RGB Reducing image to 8 bits/pixel, grayscale Input IDAT size = 46984 bytes Input file size = 47140 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 19713 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 19713 Output IDAT size = 19713 bytes (27271 bytes decrease) Output file size = 19805 bytes (27335 bytes = 57.99% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/hdnom.Rcheck/vign_test/hdnom/vignettes/hdnom_files/figure-html/unnamed-chunk-9-1.png 1152x1152 pixels, 3x8 bits/pixel, RGB Input IDAT size = 96347 bytes Input file size = 96575 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 92673 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 92673 Output IDAT size = 92673 bytes (3674 bytes decrease) Output file size = 92769 bytes (3806 bytes = 3.94% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/hdnom.Rcheck/vign_test/hdnom/vignettes/hdnom_files/figure-html/unnamed-chunk-10-1.png 1152x1152 pixels, 3x8 bits/pixel, RGB Input IDAT size = 43126 bytes Input file size = 43282 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 39441 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 39441 Output IDAT size = 39441 bytes (3685 bytes decrease) Output file size = 39537 bytes (3745 bytes = 8.65% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/hdnom.Rcheck/vign_test/hdnom/vignettes/hdnom_files/figure-html/unnamed-chunk-12-1.png 1152x1152 pixels, 3x8 bits/pixel, RGB Input IDAT size = 61526 bytes Input file size = 61706 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 53391 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 53391 Output IDAT size = 53391 bytes (8135 bytes decrease) Output file size = 53487 bytes (8219 bytes = 13.32% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/hdnom.Rcheck/vign_test/hdnom/vignettes/hdnom_files/figure-html/unnamed-chunk-13-1.png 1152x1152 pixels, 3x8 bits/pixel, RGB Input IDAT size = 61935 bytes Input file size = 62115 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 53924 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 53924 Output IDAT size = 53924 bytes (8011 bytes decrease) Output file size = 54020 bytes (8095 bytes = 13.03% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/hdnom.Rcheck/vign_test/hdnom/vignettes/hdnom_files/figure-html/unnamed-chunk-14-1.png 1296x864 pixels, 3x8 bits/pixel, RGB Input IDAT size = 55779 bytes Input file size = 55947 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 42516 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 42516 Output IDAT size = 42516 bytes (13263 bytes decrease) Output file size = 42612 bytes (13335 bytes = 23.84% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/hdnom.Rcheck/vign_test/hdnom/vignettes/hdnom_files/figure-html/unnamed-chunk-14-2.png 1296x864 pixels, 3x8 bits/pixel, RGB Input IDAT size = 51011 bytes Input file size = 51179 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 39014 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 39014 Output IDAT size = 39014 bytes (11997 bytes decrease) Output file size = 39110 bytes (12069 bytes = 23.58% decrease) Quitting from hdnom.Rmd:377-390 [unnamed-chunk-16] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `fit_alasso()`: ! Null model produced by the full fit (all coefficients are zero). Please try to tune rule, seed, nfolds, or increase sample size. --- Backtrace: ▆ 1. └─hdnom::compare_by_validate(...) 2. └─hdnom::fit_alasso(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'hdnom.Rmd' failed with diagnostics: Null model produced by the full fit (all coefficients are zero). Please try to tune rule, seed, nfolds, or increase sample size. --- failed re-building ‘hdnom.Rmd’ SUMMARY: processing the following file failed: ‘hdnom.Rmd’ Error: Vignette re-building failed. Execution halted Package: plasso Check: tests New result: ERROR Running ‘testthat.R’ [5s/5s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/tests.html > # * https://testthat.r-lib.org/reference/test_package.html#special-files > > library(testthat) > library(plasso) > > test_check("plasso") [ FAIL 4 | WARN 0 | SKIP 0 | PASS 52 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-predict.R:117:3'): predict.plasso response for single lambda value ── dimnames(pred_p[["plasso"]]) (`actual`) not identical to dimnames(pred_g) (`expected`). `actual[[2]]`: "s1" `expected[[2]]`: "s0" ── Failure ('test-predict.R:118:3'): predict.plasso response for single lambda value ── dimnames(pred_p[["lasso"]]) (`actual`) not identical to dimnames(pred_g) (`expected`). `actual[[2]]`: "s1" `expected[[2]]`: "s0" ── Failure ('test-predict.R:121:3'): predict.plasso response for single lambda value ── dimnames(coef_p[["plasso"]]) (`actual`) not identical to dimnames(coef_g) (`expected`). `actual[[2]]`: "s1" `expected[[2]]`: "s0" ── Failure ('test-predict.R:122:3'): predict.plasso response for single lambda value ── dimnames(coef_p[["lasso"]]) (`actual`) not identical to dimnames(coef_g) (`expected`). `actual[[2]]`: "s1" `expected[[2]]`: "s0" [ FAIL 4 | WARN 0 | SKIP 0 | PASS 52 ] Error: Test failures Execution halted Package: starnet Check: tests New result: ERROR Running ‘testthat.R’ [16s/16s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(starnet) > > testthat::test_check(package="starnet",stop_on_warning=FALSE) [ FAIL 1 | WARN 1 | SKIP 0 | PASS 32 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test.R:183:7'): same loss ───────────────────────────────────────── abs(a - b) < 0.001 is not TRUE `actual`: FALSE `expected`: TRUE [ FAIL 1 | WARN 1 | SKIP 0 | PASS 32 ] Error: Test failures Execution halted Package: transreg Check: examples New result: ERROR Running examples in ‘transreg-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: plot.transreg > ### Title: Plot transreg-object > ### Aliases: plot.transreg > > ### ** Examples > > #--- simulation --- > set.seed(1) > n <- 100; p <- 500 > X <- matrix(rnorm(n=n*p),nrow=n,ncol=p) > beta <- rnorm(p) #*rbinom(n=n,size=1,prob=0.2) > prior1 <- beta + rnorm(p) > prior2 <- beta + rnorm(p) > prior3 <- rnorm(p) > prior4 <- rnorm(p) > y <- X %*% beta > > prior <- cbind(prior1,prior2,prior3,prior4) > object <- transreg(y=y,X=X,prior=prior,alpha=0,stack=c("sta","sim")) > > plot(object,stack="sta") Error in .subscript.2ary(x, i, j, drop = TRUE) : subscript out of bounds Calls: plot ... eval -> eval -> .coef.sta -> [ -> [ -> .subscript.2ary Execution halted Package: transreg Check: tests New result: ERROR Running ‘testthat.R’ [23s/23s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(transreg) > > testthat::test_check(package="transreg",stop_on_warning=FALSE) [ FAIL 1 | WARN 0 | SKIP 0 | PASS 3 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test.R:56:5'): (code run outside of `test_that()`) ────────────────── Error in `.subscript.2ary(x, i, j, drop = TRUE)`: subscript out of bounds Backtrace: ▆ 1. ├─stats::coef(object = object) at test.R:56:5 2. └─transreg:::coef.transreg(object = object) 3. ├─base::eval(parse(text = paste0(".coef.", stack, "(object=object,...)"))) 4. │ └─base::eval(parse(text = paste0(".coef.", stack, "(object=object,...)"))) 5. └─transreg:::.coef.sta(object = object, ...) 6. ├─beta["(Intercept)", "s2"] 7. └─beta["(Intercept)", "s2"] 8. └─Matrix:::.subscript.2ary(x, i, j, drop = TRUE) [ FAIL 1 | WARN 0 | SKIP 0 | PASS 3 ] Error: Test failures Execution halted