Package check result: OK Changes to worse in reverse depends: Package: GauPro Check: tests New result: ERROR Running ‘testthat.R’ [137s/138s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(GauPro) Loading required package: mixopt Loading required package: dplyr Attaching package: 'dplyr' The following object is masked from 'package:testthat': matches The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union Loading required package: ggplot2 Loading required package: splitfngr Loading required package: numDeriv Loading required package: rmarkdown Loading required package: tidyr Attaching package: 'tidyr' The following object is masked from 'package:testthat': matches > > test_check("GauPro") Increasing nugget to get invertibility from 4.280076e-06 to 8.560153e-06 [ FAIL 1 | WARN 6 | SKIP 0 | PASS 3109 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test_kernel_model_and_kernels.R:703:7'): Factor kernels ─────────── `predict(gp, 1:3, se.fit = T)` generated warnings: * Negative s2 predictions are being set to 8.49449401954341e-06 (1 values, min=-5.54614026260225e-07) bad pred in OrderedFactorKernel [ FAIL 1 | WARN 6 | SKIP 0 | PASS 3109 ] Error: Test failures Execution halted Package: mlpack Check: whether package can be installed New result: WARNING Found the following significant warnings: /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEnsmallen/include/ensmallen_bits/fw/atoms.hpp:100:14: warning: ‘eT arma::Mat::min(arma::uword&) const [with eT = double; arma::uword = long long unsigned int]’ is deprecated: use .index_min() instead [-Wdeprecated-declarations] ../inst/include/mlpack/methods/adaboost/adaboost_impl.hpp:207:29: warning: ‘eT arma::subview_col::max(arma::uword&) const [with eT = double; arma::uword = long long unsigned int]’ is deprecated: use .index_max() instead [-Wdeprecated-declarations] ../inst/include/mlpack/methods/perceptron/perceptron_impl.hpp:327:21: warning: ‘eT arma::Mat::max(arma::uword&) const [with eT = double; arma::uword = long long unsigned int]’ is deprecated: use .index_max() instead [-Wdeprecated-declarations] ../inst/include/mlpack/methods/perceptron/perceptron_impl.hpp:249:23: warning: ‘eT arma::Mat::max(arma::uword&, arma::uword&) const [with eT = double; arma::uword = long long unsigned int]’ is deprecated [-Wdeprecated-declarations] ../inst/include/mlpack/methods/decision_tree/decision_tree_impl.hpp:1168:25: warning: ‘eT arma::Mat::max(arma::uword&) const [with eT = double; arma::uword = long long unsigned int]’ is deprecated: use .index_max() instead [-Wdeprecated-declarations] ../inst/include/mlpack/methods/approx_kfn/drusilla_select_impl.hpp:98:14: warning: ‘eT arma::Mat::max(arma::uword&) const [with eT = double; arma::uword = long long unsigned int]’ is deprecated: use .index_max() instead [-Wdeprecated-declarations] ../inst/include/mlpack/methods/kmeans/max_variance_new_cluster_impl.hpp:39:16: warning: ‘eT arma::Mat::max(arma::uword&) const [with eT = double; arma::uword = long long unsigned int]’ is deprecated: use .index_max() instead [-Wdeprecated-declarations] ../inst/include/mlpack/methods/hmm/hmm_impl.hpp:531:36: warning: ‘eT arma::Mat::max(arma::uword&) const [with eT = double; arma::uword = long long unsigned int]’ is deprecated: use .index_max() instead [-Wdeprecated-declarations] ../inst/include/mlpack/methods/hmm/hmm_impl.hpp:537:50: warning: ‘eT arma::Mat::max(arma::uword&) const [with eT = double; arma::uword = long long unsigned int]’ is deprecated: use .index_max() instead [-Wdeprecated-declarations] ../inst/include/mlpack/methods/hoeffding_trees/hoeffding_categorical_split_impl.hpp:83:18: warning: ‘eT arma::Mat::max(arma::uword&) const [with eT = long unsigned int; arma::uword = long long unsigned int]’ is deprecated: use .index_max() instead [-Wdeprecated-declarations] ../inst/include/mlpack/methods/hoeffding_trees/hoeffding_numeric_split_impl.hpp:148:16: warning: ‘eT arma::Mat::max(arma::uword&) const [with eT = long unsigned int; arma::uword = long long unsigned int]’ is deprecated: use .index_max() instead [-Wdeprecated-declarations] ../inst/include/mlpack/methods/hoeffding_trees/hoeffding_numeric_split_impl.hpp:158:20: warning: ‘eT arma::Mat::max(arma::uword&) const [with eT = long unsigned int; arma::uword = long long unsigned int]’ is deprecated: use .index_max() instead [-Wdeprecated-declarations] ../inst/include/mlpack/methods/hoeffding_trees/binary_numeric_split_impl.hpp:159:18: warning: ‘eT arma::Mat::max(arma::uword&) const [with eT = long unsigned int; arma::uword = long long unsigned int]’ is deprecated: use .index_max() instead [-Wdeprecated-declarations] ../inst/include/mlpack/methods/hoeffding_trees/hoeffding_categorical_split_impl.hpp:68:43: warning: ‘eT arma::Mat::max(arma::uword&) const [with eT = long unsigned int; arma::uword = long long unsigned int]’ is deprecated: use .index_max() instead [-Wdeprecated-declarations] ../inst/include/mlpack/methods/hoeffding_trees/hoeffding_numeric_split_impl.hpp:126:43: warning: ‘eT arma::Mat::max(arma::uword&) const [with eT = long unsigned int; arma::uword = long long unsigned int]’ is deprecated: use .index_max() instead [-Wdeprecated-declarations] ../inst/include/mlpack/methods/hoeffding_trees/binary_numeric_split_impl.hpp:145:27: warning: ‘eT arma::Mat::max(arma::uword&) const [with eT = long unsigned int; arma::uword = long long unsigned int]’ is deprecated: use .index_max() instead [-Wdeprecated-declarations] ../inst/include/mlpack/methods/hoeffding_trees/binary_numeric_split_impl.hpp:147:27: warning: ‘eT arma::Mat::max(arma::uword&) const [with eT = long unsigned int; arma::uword = long long unsigned int]’ is deprecated: use .index_max() instead [-Wdeprecated-declarations] ../inst/include/mlpack/methods/naive_bayes/naive_bayes_classifier_impl.hpp:388:37: warning: ‘eT arma::Mat::max(arma::uword&) const [with eT = double; arma::uword = long long unsigned int]’ is deprecated: use .index_max() instead [-Wdeprecated-declarations] ../inst/include/mlpack/methods/radical/radical_impl.hpp:107:13: warning: ‘eT arma::Mat::min(arma::uword&) const [with eT = double; arma::uword = long long unsigned int]’ is deprecated: use .index_min() instead [-Wdeprecated-declarations] ../inst/include/mlpack/methods/random_forest/random_forest_impl.hpp:360:20: warning: ‘eT arma::Mat::max(arma::uword&) const [with eT = double; arma::uword = long long unsigned int]’ is deprecated: use .index_max() instead [-Wdeprecated-declarations] See ‘/home/hornik/tmp/CRAN_recheck/mlpack.Rcheck/00install.out’ for details. Used C++ compiler: ‘g++-14 (Debian 14.2.0-3) 14.2.0’ Package: phenofit Check: tests New result: ERROR Running ‘testthat.R’ [64s/64s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(phenofit) > > test_check("phenofit") List of 5 $ AG : tibble [6 × 8] (S3: tbl_df/tbl/data.frame) $ Beck : tibble [6 × 7] (S3: tbl_df/tbl/data.frame) $ Elmore: tibble [6 × 8] (S3: tbl_df/tbl/data.frame) $ Gu : tibble [6 × 10] (S3: tbl_df/tbl/data.frame) $ Zhang : tibble [6 × 8] (S3: tbl_df/tbl/data.frame) NULL # A tibble: 6 × 8 flag t0 mn mx rsp a3 rau a5 1 1999_1 -135. 0.201 0.636 0.00932 2.85 0.00852 2 2 2000_1 189. 0.238 0.635 0.0126 2.47 0.00801 3.21 3 2001_1 569. 0.252 0.626 0.0108 2.96 0.00950 2.96 4 2002_1 892. 0.253 0.614 0.0159 2 0.00724 3.08 5 2003_1 1268. 0.236 0.577 0.0121 2.88 0.00723 2.88 6 2004_1 1677. 0.202 0.576 0.00832 2.84 0.00990 3.48 meth R2 NSE R RMSE pvalue n_sim 1: AG 0.9986908 0.9985845 0.9993452 9.940385e-03 4.489925e-65 46 2: Beck 1.0000000 1.0000000 1.0000000 1.389780e-09 0.000000e+00 46 3: Elmore 1.0000000 1.0000000 1.0000000 4.161813e-10 0.000000e+00 46 4: Gu 1.0000000 1.0000000 1.0000000 4.891365e-11 0.000000e+00 46 5: Zhang 1.0000000 1.0000000 1.0000000 5.529073e-06 8.043461e-208 46 $AG formula: mn + (mx - mn) * exp(-((t0 - t) * rsp)^a3) formula: mn + (mx - mn) * exp(-((t - t0) * rau)^a5) pars: t0 mn mx rsp a3 rau a5 nlminb 149.8926 0.1020656 0.7095242 0.009389263 6 0.009367765 6 warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 1.65502e-16); attempting approx solution warning: solve(): system is singular (rcond: 2.19427e-17); attempting approx solution warning: solve(): system is singular (rcond: 1.65502e-16); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 1.33432e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 2.38811e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 2.03034e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 1.33432e-17); attempting approx solution warning: solve(): system is singular (rcond: 3.31005e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 3.08395e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 2.36432e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 6.97437e-18); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 1.85037e-16); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 2.80681e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 5.43896e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 2.38811e-17); attempting approx solution warning: solve(): system is singular (rcond: 3.05447e-17); attempting approx solution warning: solve(): system is singular (rcond: 2.11109e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 6.04329e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 1.85037e-16); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 2.80681e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 5.43896e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 3.31005e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 2.38811e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 3.31005e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 2.38811e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 1.94249e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 3.84957e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 3.31005e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 8.58712e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 2.38811e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 2.09346e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 3.82199e-17); attempting approx solution warning: solve(): system is singular (rcond: 2.38705e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 2.38811e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 5.88785e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 1.85037e-16); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 7.40149e-17); attempting approx solution warning: solve(): system is singular (rcond: 6.20634e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 2.38811e-17); attempting approx solution warning: solve(): system is singular (rcond: 3.05447e-17); attempting approx solution warning: solve(): system is singular (rcond: 2.11109e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 5.43896e-17); attempting approx solution warning: solve(): system is singular (rcond: 4.38854e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 1.00786e-16); attempting approx solution warning: solve(): system is singular (rcond: 1.46031e-17); attempting approx solution warning: solve(): system is singular (rcond: 5.02097e-17); attempting approx solution warning: solve(): system is singular (rcond: 1.25524e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 3.31005e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 3.31005e-17); attempting approx solution [ FAIL 1 | WARN 2 | SKIP 0 | PASS 69 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-curvefit.R:18:5'): curvefit works ──────────────────────────── all.equal(p1, p2, tolerance = 1e-06) is not TRUE `actual` is a character vector ('Component "Elmore": Component "mn": Mean relative difference: 1.990404e-06') `expected` is a logical vector (TRUE) [ FAIL 1 | WARN 2 | SKIP 0 | PASS 69 ] Error: Test failures Execution halted