* using log directory ‘/data/localhost/ripley/R/packages/tests-MKL/probably.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: 2026-10-30 06:45:48 UTC * using option ‘--no-stop-on-test-error’ * checking for file ‘probably/DESCRIPTION’ ... OK * this is package ‘probably’ version ‘1.2.0’ * 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 ‘probably’ can be installed ... [12s/14s] 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 whether startup messages can be suppressed ... 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 ... [20s/21s] 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 ... [19s/20s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ [128s/137s] [129s/137s] ERROR 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(probably) Attaching package: 'probably' The following objects are masked from 'package:base': as.factor, as.ordered > > test_check("probably") Attaching package: 'dplyr' The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union Saving _problems/test-cal-estimate-logistic-169.R [ FAIL 1 | WARN 0 | SKIP 59 | PASS 628 ] ══ Skipped tests (59) ══════════════════════════════════════════════════════════ • On CRAN (58): 'test-bound_prediction.R:1:1', 'test-bound_prediction.R:37:1', 'test-cal-estimate-beta.R:1:1', 'test-cal-estimate-beta.R:29:1', 'test-cal-estimate-beta.R:60:1', 'test-cal-estimate-isotonic.R:1:1', 'test-cal-estimate-isotonic.R:29:1', 'test-cal-estimate-isotonic.R:58:1', 'test-cal-estimate-isotonic.R:64:1', 'test-cal-estimate-isotonic.R:95:1', 'test-cal-estimate-isotonic.R:122:1', 'test-cal-estimate-isotonic.R:155:1', 'test-cal-estimate-isotonic.R:161:1', 'test-cal-estimate-linear.R:1:1', 'test-cal-estimate-linear.R:36:1', 'test-cal-estimate-linear.R:44:1', 'test-cal-estimate-linear.R:51:1', 'test-cal-estimate-linear.R:82:1', 'test-cal-estimate-linear.R:95:1', 'test-cal-estimate-logistic.R:1:1', 'test-cal-estimate-logistic.R:64:1', 'test-cal-estimate-logistic.R:78:1', 'test-cal-estimate-logistic.R:85:1', 'test-cal-estimate-logistic.R:110:1', 'test-cal-estimate-logistic.R:129:1', 'test-cal-estimate-multinomial.R:1:1', 'test-cal-estimate-multinomial.R:49:1', 'test-cal-estimate-multinomial.R:88:1', 'test-cal-estimate-multinomial.R:103:1', 'test-cal-estimate-none.R:1:1', 'test-cal-estimate-none.R:80:1', 'test-cal-estimate-none.R:123:1', 'test-cal-plot-breaks.R:37:1', 'test-cal-plot-breaks.R:130:1', 'test-cal-plot-breaks.R:177:1', 'test-cal-plot-logistic.R:111:1', 'test-cal-plot-logistic.R:165:1', 'test-cal-plot-regression.R:142:1', 'test-cal-plot-windowed.R:96:1', 'test-cal-validate.R:1:1', 'test-cal-validate.R:197:1', 'test-cal-validate.R:404:1', 'test-cal-validate.R:833:1', 'test-cal-validate.R:863:1', 'test-class-pred.R:198:1', 'test-conformal_infer_cv.R:1:1', 'test-conformal_infer_cv.R:80:3', 'test-conformal_infer_cv.R:155:1', 'test-conformal_infer_full.R:1:1', 'test-conformal_infer_full.R:112:3', 'test-conformal_infer_full.R:197:1', 'test-conformal_infer_quantile.R:1:1', 'test-conformal_infer_split.R:1:1', 'test-make_class_pred.R:80:1', 'test-make_class_pred.R:89:1', 'test-make_class_pred.R:98:1', 'test-make_class_pred.R:107:1', 'test-threshold_perf.R:140:1' • R.version[["arch"]] != "aarch64" is TRUE (1): 'test-cal-plot-regression.R:3:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-cal-estimate-logistic.R:166:3'): Logistic spline switches to linear if too few unique ── Expected `sl_gam$estimates` to be identical to `sl_lm$estimates`. Differences: actual[[2]]$estimate$effects[1:53] vs expected[[2]]$estimate$effects[1:53] -5.24486858073313034 - -1.30495601164137720 + -1.30495601164137742 - -1.30495601164137720 + -1.30495601164137742 - -1.30495601164137720 + -1.30495601164137742 0.75299683035228615 0.75299683035228615 0.75299683035228615 - -1.30495601164137720 + -1.30495601164137742 0.75299683035228615 - -1.30495601164137720 + -1.30495601164137742 and 43 more ... actual[[2]]$estimate$effects[57:158] vs expected[[2]]$estimate$effects[57:158] 0.75299683035228615 0.75299683035228615 0.75299683035228615 - -1.30495601164137720 + -1.30495601164137742 0.75299683035228615 - -1.30495601164137720 + -1.30495601164137742 0.75299683035228615 - -1.30495601164137720 + -1.30495601164137742 0.75299683035228615 0.75299683035228615 and 92 more ... actual[[2]]$estimate$effects[159:243] vs expected[[2]]$estimate$effects[159:243] 0.75299683035228615 0.75299683035228615 0.75299683035228615 - -1.30495601164137720 + -1.30495601164137742 - -1.30495601164137720 + -1.30495601164137742 0.75299683035228615 - -1.30495601164137720 + -1.30495601164137742 0.75299683035228615 0.75299683035228615 0.75299683035228615 and 75 more ... actual[[2]]$estimate$effects[250:274] vs expected[[2]]$estimate$effects[250:274] 0.75299683035228615 0.75299683035228615 0.75299683035228615 - -1.30495601164137720 + -1.30495601164137742 0.75299683035228615 - -1.30495601164137720 + -1.30495601164137742 0.75299683035228615 - -1.30495601164137720 + -1.30495601164137742 - -1.30495601164137720 + -1.30495601164137742 0.75299683035228615 and 15 more ... actual[[2]]$estimate$effects[277:317] vs expected[[2]]$estimate$effects[277:317] 0.75299683035228615 0.75299683035228615 0.75299683035228615 - -1.30495601164137720 + -1.30495601164137742 0.75299683035228615 - -1.30495601164137720 + -1.30495601164137742 0.75299683035228615 - -1.30495601164137720 + -1.30495601164137742 0.75299683035228615 - -1.30495601164137720 + -1.30495601164137742 and 31 more ... actual[[2]]$estimate$effects[321:353] vs expected[[2]]$estimate$effects[321:353] 0.75299683035228615 0.75299683035228615 0.75299683035228615 - -1.30495601164137720 + -1.30495601164137742 0.75299683035228615 0.75299683035228615 0.75299683035228615 0.75299683035228615 - -1.30495601164137720 + -1.30495601164137742 - -1.30495601164137720 + -1.30495601164137742 and 23 more ... actual[[2]]$estimate$effects | expected[[2]]$estimate$effects [354] 0.75299683035228615 | 0.75299683035228615 [354] [355] 0.75299683035228615 | 0.75299683035228615 [355] [356] 0.75299683035228615 | 0.75299683035228615 [356] [357] -1.30495601164137720 - -1.30495601164137742 [357] [358] -1.30495601164137720 - -1.30495601164137742 [358] [359] 0.75299683035228615 | 0.75299683035228615 [359] [360] 0.75299683035228615 | 0.75299683035228615 [360] [361] 0.75299683035228615 | 0.75299683035228615 [361] actual[[2]]$estimate$effects[364:418] vs expected[[2]]$estimate$effects[364:418] 0.75299683035228615 0.75299683035228615 0.75299683035228615 - -1.30495601164137720 + -1.30495601164137742 - -1.30495601164137720 + -1.30495601164137742 0.75299683035228615 0.75299683035228615 0.75299683035228615 0.75299683035228615 - -1.30495601164137720 + -1.30495601164137742 and 45 more ... actual[[2]]$estimate$effects[420:445] vs expected[[2]]$estimate$effects[420:445] 0.75299683035228615 0.75299683035228615 0.75299683035228615 - -1.30495601164137720 + -1.30495601164137742 0.75299683035228615 0.75299683035228615 0.75299683035228615 - -1.30495601164137720 + -1.30495601164137742 0.75299683035228615 - -1.30495601164137720 + -1.30495601164137742 and 16 more ... actual[[2]]$estimate$effects[448:505] vs expected[[2]]$estimate$effects[448:505] 0.75299683035228615 0.75299683035228615 0.75299683035228615 - -1.30495601164137720 + -1.30495601164137742 0.75299683035228615 - -1.30495601164137720 + -1.30495601164137742 - -1.30495601164137720 + -1.30495601164137742 0.75299683035228615 0.75299683035228615 0.75299683035228615 and 48 more ... actual[[2]]$estimate$R vs expected[[2]]$estimate$R [,1] [,2] actual[[2]]$estimate$R[1, ] -10.91969 -1.091969e+01 - actual[[2]]$estimate$R[2, ] 0.00000 -1.767668e-16 + expected[[2]]$estimate$R[2, ] 0.00000 3.827250e-15 actual[[2]]$estimate$qr$qr vs expected[[2]]$estimate$qr$qr [,1] [,2] actual[[2]]$estimate$qr$qr[1, ] -10.91968902 -1.091969e+01 - actual[[2]]$estimate$qr$qr[2, ] 0.04449942 -1.767668e-16 + expected[[2]]$estimate$qr$qr[2, ] 0.04449942 3.827250e-15 actual[[2]]$estimate$qr$qr[3, ] 0.04449942 4.454354e-02 actual[[2]]$estimate$qr$qr[4, ] 0.04449942 4.454354e-02 actual[[2]]$estimate$qr$qr[5, ] 0.04449942 4.454354e-02 actual[[2]]$estimate$weights vs expected[[2]]$estimate$weights - 0.236118036263608500 + 0.236118036263608555 - 0.236118036263608500 + 0.236118036263608555 - 0.236118036263608500 + 0.236118036263608555 - 0.236118036263608500 + 0.236118036263608555 - 0.236118036263608500 + 0.236118036263608555 - 0.236118036263608500 + 0.236118036263608555 - 0.236118036263608500 + 0.236118036263608555 - 0.236118036263608500 + 0.236118036263608555 - 0.236118036263608500 + 0.236118036263608555 - 0.236118036263608500 + 0.236118036263608555 and 495 more ... [ FAIL 1 | WARN 0 | SKIP 59 | PASS 628 ] Error: ! Test failures. Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [19s/23s] 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/probably.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 4:54.74, 254.12 + 14.99