* using log directory ‘/data/localhost/ripley/R/packages/tests-MKL/Dyn4cast.Rcheck’ * using R Under development (unstable) (2026-10-28 r90786) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (GCC) 16.2.1 20260819 (Red Hat 16.2.1-2) GNU Fortran (GCC) 16.2.1 20260819 (Red Hat 16.2.1-2) * running under: Fedora Linux 44 (Server Edition) * using session charset: UTF-8 * current time: 2026-10-29 11:38:55 UTC * using option ‘--no-stop-on-test-error’ * checking for file ‘Dyn4cast/DESCRIPTION’ ... OK * this is package ‘Dyn4cast’ version ‘11.11.26’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘Dyn4cast’ can be installed ... [10s/17s] OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [18s/56s] OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [27s/50s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘spelling.R’ Running ‘testthat.R’ [110s/149s] [111s/150s] ERROR Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(Dyn4cast) > library(readr) Attaching package: 'readr' The following objects are masked from 'package:testthat': edition_get, local_edition > test_check("Dyn4cast") Rows: 333 Columns: 4 -- Column specification -------------------------------------------------------- Delimiter: "," dbl (3): Day, Case, Cum_case date (1): Date i Use `spec()` to retrieve the full column specification for this data. i Specify the column types or set `show_col_types = FALSE` to quiet this message. -- Attaching core tidyverse packages ------------------------ tidyverse 2.0.0 -- v dplyr 1.2.1 v purrr 1.2.2 v forcats 1.0.1 v stringr 1.6.0 v ggplot2 4.0.3 v tibble 3.3.1 v lubridate 1.9.5 v tidyr 1.3.2 -- Conflicts ------------------------------------------ tidyverse_conflicts() -- x readr::edition_get() masks testthat::edition_get() x dplyr::filter() masks stats::filter() x dplyr::lag() masks stats::lag() x readr::local_edition() masks testthat::local_edition() i Use the conflicted package () to force all conflicts to become errors New names: * `` -> `...1` * `V1` -> `V1...2` * `V1` -> `V1...5` * `` -> `...6` New names: * `` -> `...1` * `V1` -> `V1...2` * `V1` -> `V1...6` * `` -> `...7` New names: * `` -> `...1` * `V1` -> `V1...2` * `V1` -> `V1...7` * `` -> `...8` New names: * `` -> `...1` * `V1` -> `V1...2` * `V1` -> `V1...8` * `` -> `...9` New names: * `` -> `...1` * `V1` -> `V1...2` * `V1` -> `V1...8` * `` -> `...9` New names: * `` -> `...1` * `V1` -> `V1...2` * `V1` -> `V1...9` * `` -> `...10` New names: * `` -> `...1` * `V1` -> `V1...2` * `V1` -> `V1...10` * `` -> `...11` New names: * `` -> `...1` * `V1` -> `V1...2` * `V1` -> `V1...11` * `` -> `...12` New names: * `` -> `...1` * `V1` -> `V1...2` * `V1` -> `V1...12` * `` -> `...13` New names: * `` -> `...1` * `V1` -> `V1...2` * `V1` -> `V1...13` * `` -> `...14` New names: * `` -> `...1` * `V1` -> `V1...2` * `V1` -> `V1...14` * `` -> `...15` New names: * `` -> `...1` * `V1` -> `V1...2` * `V1` -> 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`` -> `...9` Attaching package: 'psych' The following objects are masked from 'package:ggplot2': %+%, alpha The following object is masked from 'package:testthat': describe Parallel analysis suggests that the number of factors = 5 and the number of components = NA Loadings: MR1 MR2 MR3 MR5 MR4 x11 0.513 0.053 0.124 0.217 0.137 x12 0.611 0.127 -0.090 0.075 0.134 x13 0.559 0.354 0.115 0.020 -0.172 x20 0.556 0.049 0.083 0.306 0.059 x24 0.617 -0.284 -0.168 0.056 0.527 x25 0.718 -0.169 0.063 0.065 0.196 x26 0.595 0.048 0.104 0.205 0.139 x01 0.124 0.625 -0.077 -0.066 0.066 x02 0.039 0.783 -0.012 0.206 0.541 x10 0.254 0.631 -0.139 0.255 -0.081 x28 -0.086 -0.610 0.092 0.320 0.111 x04 0.239 -0.176 0.740 -0.101 -0.039 x05 0.149 0.065 0.792 0.074 -0.015 x06 -0.043 -0.260 0.720 0.157 0.186 x08 -0.130 0.016 0.594 0.255 0.452 x17 0.142 -0.192 0.044 0.667 0.137 x18 0.263 0.161 -0.041 0.527 0.073 x19 0.290 0.066 0.069 0.592 0.134 x03 0.087 -0.015 0.309 0.286 0.523 x07 0.302 -0.031 0.240 0.417 0.090 x09 0.112 -0.301 0.305 0.403 0.154 x14 0.345 0.153 0.203 0.203 -0.080 x15 0.480 0.275 0.262 0.069 -0.181 x16 0.125 -0.299 0.346 0.374 0.291 x21 0.492 -0.037 0.064 0.344 -0.065 x22 0.303 -0.238 0.039 0.286 0.481 x23 0.360 -0.440 0.021 0.207 0.499 x27 0.092 0.056 0.465 x29 0.216 -0.392 0.355 0.070 0.262 MR1 MR2 MR3 MR5 MR4 SS loadings 3.854 2.895 2.786 2.441 2.203 Proportion Var 0.133 0.100 0.096 0.084 0.076 Cumulative Var 0.133 0.233 0.329 0.413 0.489 Loadings: MR1 MR2 MR3 MR5 MR4 x11 0.513 0.053 0.124 0.217 0.137 x12 0.611 0.127 -0.090 0.075 0.134 x13 0.559 0.354 0.115 0.020 -0.172 x20 0.556 0.049 0.083 0.306 0.059 x24 0.617 -0.284 -0.168 0.056 0.527 x25 0.718 -0.169 0.063 0.065 0.196 x26 0.595 0.048 0.104 0.205 0.139 x01 0.124 0.625 -0.077 -0.066 0.066 x02 0.039 0.783 -0.012 0.206 0.541 x10 0.254 0.631 -0.139 0.255 -0.081 x28 -0.086 -0.610 0.092 0.320 0.111 x04 0.239 -0.176 0.740 -0.101 -0.039 x05 0.149 0.065 0.792 0.074 -0.015 x06 -0.043 -0.260 0.720 0.157 0.186 x08 -0.130 0.016 0.594 0.255 0.452 x17 0.142 -0.192 0.044 0.667 0.137 x18 0.263 0.161 -0.041 0.527 0.073 x19 0.290 0.066 0.069 0.592 0.134 x03 0.087 -0.015 0.309 0.286 0.523 x07 0.302 -0.031 0.240 0.417 0.090 x09 0.112 -0.301 0.305 0.403 0.154 x14 0.345 0.153 0.203 0.203 -0.080 x15 0.480 0.275 0.262 0.069 -0.181 x16 0.125 -0.299 0.346 0.374 0.291 x21 0.492 -0.037 0.064 0.344 -0.065 x22 0.303 -0.238 0.039 0.286 0.481 x23 0.360 -0.440 0.021 0.207 0.499 x27 0.092 0.056 0.465 x29 0.216 -0.392 0.355 0.070 0.262 MR1 MR2 MR3 MR5 MR4 SS loadings 3.854 2.895 2.786 2.441 2.203 Proportion Var 0.133 0.100 0.096 0.084 0.076 Cumulative Var 0.133 0.233 0.329 0.413 0.489 Waiting for profiling to be done... Attaching package: 'MASS' The following object is masked from 'package:dplyr': select Re-fitting to get Hessian Waiting for profiling to be done... Re-fitting to get Hessian Waiting for profiling to be done... Waiting for profiling to be done... Waiting for profiling to be done... Waiting for profiling to be done... Waiting for profiling to be done... # weights: 18 (10 variable) initial value 164.791843 iter 10 value 16.177348 iter 20 value 7.111438 iter 30 value 6.182999 iter 40 value 5.984028 iter 50 value 5.961278 iter 60 value 5.954900 iter 70 value 5.951851 iter 80 value 5.950343 iter 90 value 5.949904 iter 100 value 5.949867 final value 5.949867 stopped after 100 iterations Loading required package: mvtnorm Loading required package: maxLik Loading required package: miscTools Please cite the 'maxLik' package as: Henningsen, Arne and Toomet, Ott (2011). maxLik: A package for maximum likelihood estimation in R. Computational Statistics 26(3), 443-458. DOI 10.1007/s00180-010-0217-1. If you have questions, suggestions, or comments regarding the 'maxLik' package, please use its GitHub page and the issues there: https://github.com/arne-henningsen/maxLik Loading required package: abind Waiting for profiling to be done... Saving _problems/test-odds_summary-87.R Re-fitting to get Hessian Waiting for profiling to be done... Re-fitting to get Hessian Waiting for profiling to be done... Saving _problems/test-odds_summary-89.R Waiting for profiling to be done... Waiting for profiling to be done... Waiting for profiling to be done... Waiting for profiling to be done... [ FAIL 2 | WARN 2041 | SKIP 0 | PASS 112 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-odds_summary.R:87:3'): odds_summary works ──────────────────── Expected `ts` to be identical to `odds_summary(glm.D93)`. Differences: actual vs expected CI_lower actual[1, ] 14.8176865102766 actual[2, ] 0.674856752244522 - actual[3, ] 0.674856752244532 + expected[3, ] 0.674856752244533 actual[4, ] 0.424135695597257 actual[5, ] 0.50896827248296 actual[6, ] actual$CI_lower | expected$CI_lower [1] "14.8176865102766" | "14.8176865102766" [1] [2] "0.674856752244522" | "0.674856752244522" [2] [3] "0.674856752244532" - "0.674856752244533" [3] [4] "0.424135695597257" | "0.424135695597257" [4] [5] "0.50896827248296" | "0.50896827248296" [5] [6] " " | " " [6] ── Failure ('test-odds_summary.R:89:3'): odds_summary works ──────────────────── Expected `ts2` to be identical to `odds_summary(anorex.1)`. Differences: actual vs expected CI_lower actual[1, ] 16478351698.4954 actual[2, ] 0.414181716045278 actual[3, ] 0.000406371479433907 - actual[4, ] 1.46492065063456 + expected[4, ] 1.46492065063457 actual[5, ] actual$CI_lower | expected$CI_lower [1] "16478351698.4954" | "16478351698.4954" [1] [2] "0.414181716045278" | "0.414181716045278" [2] [3] "0.000406371479433907" | "0.000406371479433907" [3] [4] "1.46492065063456" - "1.46492065063457" [4] [5] " " | " " [5] [ FAIL 2 | WARN 2041 | SKIP 0 | PASS 112 ] Error: ! Test failures. Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [20s/46s] OK * checking PDF version of manual ... OK * checking HTML version of manual ... OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR See ‘/data/localhost/ripley/R/packages/tests-MKL/Dyn4cast.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 6:54.73, 218.33 + 14.35