* using log directory ‘/data/localhost/ripley/R/packages/tests-MKL/pigauto.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 06:13:10 UTC * using option ‘--no-stop-on-test-error’ * checking for file ‘pigauto/DESCRIPTION’ ... OK * this is package ‘pigauto’ version ‘0.11.0’ * 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 ‘pigauto’ can be installed ... [28s/76s] 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 ... [46s/73s] 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 ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ [173s/242s] [173s/243s] ERROR Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(pigauto) > > test_check("pigauto") 1 tree tip(s) have no trait data and will have all-NA rows. Auto-detected trait type "count" (log1p-encoded) for integer column(s): counts. If any is a continuous measurement stored as whole numbers (common after read.csv), override it: trait_types = c(counts = "continuous"). Auto-detected trait type "count" (log1p-encoded) for integer column(s): count. If any is a continuous measurement stored as whole numbers (common after read.csv), override it: trait_types = c(count = "continuous"). pigauto: the exact ("exact") joint baseline route was not usable for a fit (fewer than 2 joint columns (K < 2)); used the per-column baseline for that fit instead. This happens either while predict_method = "auto" (the default) is comparing its "exact" candidate, or when "exact" is itself the resolved route and fell back. This message is shown at most once per R session; pass predict_method = "per_column" to use the per-column path throughout, or predict_method = "exact" explicitly if you want a warning every time this happens. Auto-detected trait type "count" (log1p-encoded) for integer column(s): count, zi. If any is a continuous measurement stored as whole numbers (common after read.csv), override it: trait_types = c(count = "continuous"). Auto-detected trait type "count" (log1p-encoded) for integer column(s): count. If any is a continuous measurement stored as whole numbers (common after read.csv), override it: trait_types = c(count = "continuous"). Auto-detected trait type "count" (log1p-encoded) for integer column(s): count. If any is a continuous measurement stored as whole numbers (common after read.csv), override it: trait_types = c(count = "continuous"). Building phylogenetic graph (reused across folds)... Rep 1/1, Fold 1/2 (seed=1)... Building phylogenetic graph (reused across folds)... Rep 1/1, Fold 1/2 (seed=1)... === Replicate 1/1 (seed 1) === Fitting baseline... Fitting pigauto... === Replicate 1/1 (seed 1) === Fitting baseline... Fitting pigauto... draws_method = "auto": using "conformal" because some traits are not continuous (binary: binary). These draws show the spread of plausible values but are not proper multiple imputations; with_imputations() and pool_mi() refuse them. See ?multi_impute. pigauto: the exact ("exact") joint baseline route was not usable for a fit (problem too large, or a numerically unusable Sigma); used the per-column baseline for that fit instead. This happens either while predict_method = "auto" (the default) is comparing its "exact" candidate, or when "exact" is itself the resolved route and fell back. This message is shown at most once per R session; pass predict_method = "per_column" to use the per-column path throughout, or predict_method = "exact" explicitly if you want a warning every time this happens. Auto-detected trait type "count" (log1p-encoded) for integer column(s): clutch. If any is a continuous measurement stored as whole numbers (common after read.csv), override it: trait_types = c(clutch = "continuous"). pigauto: the exact ("exact") joint baseline route was not usable for a fit (fewer than 2 joint columns (K < 2)); used the per-column baseline for that fit instead. This happens either while predict_method = "auto" (the default) is comparing its "exact" candidate, or when "exact" is itself the resolved route and fell back. This message is shown at most once per R session; pass predict_method = "per_column" to use the per-column path throughout, or predict_method = "exact" explicitly if you want a warning every time this happens. Saving _problems/test-mi-posterior-464.R Saving _problems/test-mi-posterior-465.R Saving _problems/test-mi-posterior-466.R Saving _problems/test-mi-posterior-471.R Auto-detected trait type "count" (log1p-encoded) for integer column(s): clutch. If any is a continuous measurement stored as whole numbers (common after read.csv), override it: trait_types = c(clutch = "continuous"). Auto-detected trait type "count" (log1p-encoded) for integer column(s): clutch. If any is a continuous measurement stored as whole numbers (common after read.csv), override it: trait_types = c(clutch = "continuous"). Auto-detected trait type "count" (log1p-encoded) for integer column(s): clutch. If any is a continuous measurement stored as whole numbers (common after read.csv), override it: trait_types = c(clutch = "continuous"). Auto-detected trait type "count" (log1p-encoded) for integer column(s): clutch. If any is a continuous measurement stored as whole numbers (common after read.csv), override it: trait_types = c(clutch = "continuous"). Auto-detected trait type "count" (log1p-encoded) for integer column(s): clutch. If any is a continuous measurement stored as whole numbers (common after read.csv), override it: trait_types = c(clutch = "continuous"). 6 tree tip(s) have no trait data and will have all-NA rows. 6 tree tip(s) have no trait data and will have all-NA rows. ml lambda_hat = 0.005, cv lambda_hat = 0.010 (true mix = 0.2) Auto-detected trait type "count" (log1p-encoded) for integer column(s): count_trait. If any is a continuous measurement stored as whole numbers (common after read.csv), override it: trait_types = c(count_trait = "continuous"). Model saved to /tmp/Rtmpw6qMfH/working_dir/RtmpVp9sZW/fileb57f75bf9e5ae.pigauto (3,684 bytes) Model saved to /tmp/Rtmpw6qMfH/working_dir/RtmpVp9sZW/fileb57f718d13117.pigauto (3,684 bytes) Auto-detected trait type "count" (log1p-encoded) for integer column(s): cnt. If any is a continuous measurement stored as whole numbers (common after read.csv), override it: trait_types = c(cnt = "continuous"). c1: chosen=exact exact=0.1817 per_column=0.2215; c2: chosen=per_column exact=0.3039 per_column=0.2961 Auto-detected trait type "count" (log1p-encoded) for integer column(s): cnt. If any is a continuous measurement stored as whole numbers (common after read.csv), override it: trait_types = c(cnt = "continuous"). mixed-route seeds (of 12): 1, 2, 4, 6, 7, 9, 10, 11, 12 pigauto: the exact ("exact") joint baseline route was not usable for a fit (fewer than 2 joint columns (K < 2)); used the per-column baseline for that fit instead. This happens either while predict_method = "auto" (the default) is comparing its "exact" candidate, or when "exact" is itself the resolved route and fell back. This message is shown at most once per R session; pass predict_method = "per_column" to use the per-column path throughout, or predict_method = "exact" explicitly if you want a warning every time this happens. 3 tree tip(s) have no trait data and will have all-NA rows. 8 tree tip(s) have no trait data and will have all-NA rows. gnn = FALSE: mc_dropout draws are BM-posterior draws (no dropout). [ FAIL 4 | WARN 28 | SKIP 178 | PASS 2438 ] ══ Skipped tests (178) ═════════════════════════════════════════════════════════ • BIEN cache not found (1): 'test-phylo-signal-gate.R:162:3' • NEWS.md not found (1): 'test-lambda-default.R:224:3' • On CRAN (50): 'test-draws-auto.R:67:3', 'test-draws-auto.R:82:3', 'test-gnn-off.R:58:3', 'test-gnn-off.R:104:3', 'test-gnn-off.R:158:3', 'test-gnn-off.R:192:3', 'test-gnn-off.R:209:3', 'test-gnn-off.R:247:3', 'test-gnn-off.R:267:3', 'test-gnn-off.R:298:3', 'test-gnn-off.R:311:3', 'test-gnn-off.R:329:3', 'test-gnn-off.R:352:3', 'test-gnn-off.R:368:3', 'test-gnn-off.R:397:3', 'test-gnn-off.R:406:3', 'test-gnn-off.R:450:3', 'test-gnn-off.R:459:3', 'test-gnn-off.R:477:3', 'test-joint-baseline.R:12:3', 'test-joint-baseline.R:64:3', 'test-joint-baseline.R:107:3', 'test-joint-baseline.R:152:3', 'test-joint-baseline.R:189:3', 'test-joint-lambda.R:98:3', 'test-joint-lambda.R:130:3', 'test-joint-lambda.R:277:3', 'test-joint-refine-iter.R:27:3', 'test-joint-refine-iter.R:39:3', 'test-joint-refine-iter.R:66:3', 'test-joint-refine-iter.R:77:3', 'test-joint-refine-iter.R:88:3', 'test-joint-refine-iter.R:99:3', 'test-joint-solver.R:27:3', 'test-joint-solver.R:39:3', 'test-joint-solver.R:58:3', 'test-joint-solver.R:74:3', 'test-lambda-covariates.R:98:3', 'test-lambda-dispatch.R:343:3', 'test-liability.R:132:3', 'test-mi-posterior.R:311:3', 'test-mi-posterior.R:487:3', 'test-mi-posterior.R:556:3', 'test-multi-impute-posterior.R:367:3', 'test-multi-impute-posterior.R:393:3', 'test-multi-proportion.R:76:3', 'test-pagel-eigendecomp.R:106:3', 'test-pagel-lambda.R:310:3', 'test-pool-mi-backends.R:35:3', 'test-pool-mi-backends.R:43:3' • libtorch not installed (4): 'test-gnn-train-cal-symmetry.R:24:3', 'test-gnn-train-cal-symmetry.R:53:3', 'test-gnn-train-cal-symmetry.R:89:3', 'test-gnn-train-cal-symmetry.R:112:3' • rgbif IS installed; cannot test missing-rgbif branch (1): 'test-gbif-centroids.R:92:3' • script/gha helpers are not shipped in the built package (7): 'test-gha-helpers.R:19:3', 'test-gha-helpers.R:34:3', 'test-gha-helpers.R:68:3', 'test-gha-helpers.R:104:3', 'test-gha-helpers.R:147:3', 'test-gha-helpers.R:176:3', 'test-gha-helpers.R:214:3' • script/gha/_bace_compat.R not found at ../../script/gha/_bace_compat.R (4): 'test-bace-compat-eval.R:22:5', 'test-bace-compat-eval.R:85:5', 'test-bace-compat-eval.R:129:5', 'test-bace-compat-eval.R:177:5' • slow integration - set NOT_CRAN=TRUE to run (1): 'test-gbif-centroids.R:226:3' • slow integration -- NOT_CRAN=TRUE to run (2): 'test-worldclim-covariates.R:267:3', 'test-worldclim-covariates.R:362:3' • smcfcs is installed; integration test covers this route (1): 'test-multi-impute-analysis.R:244:3' • source file not installed during R CMD check: ../../R/phylo_signal.R (1): 'test-docs-phytools-warning.R:36:3' • source file not installed during R CMD check: ../../README.md (3): 'test-docs-phytools-warning.R:26:3', 'test-docs-phytools-warning.R:43:3', 'test-docs-phytools-warning.R:53:3' • source file not installed during R CMD check: ../../vignettes/getting-started.Rmd (1): 'test-docs-phytools-warning.R:17:3' • source-only development archive is excluded from the package tarball (1): 'test-community-surface.R:193:5' • source-only pkgdown configuration is excluded from the package tarball (1): 'test-community-surface.R:75:5' • source-surface assertions run in the dedicated repository gate (5): 'test-community-surface.R:10:3', 'test-community-surface.R:57:3', 'test-community-surface.R:85:3', 'test-community-surface.R:97:3', 'test-community-surface.R:146:3' • terra IS installed; cannot test missing-terra branch (1): 'test-worldclim-covariates.R:175:3' • torch backend not installed (93): 'test-active-impute.R:146:3', 'test-active-impute.R:172:3', 'test-active-impute.R:211:3', 'test-active-impute.R:228:3', 'test-active-impute.R:250:3', 'test-active-impute.R:276:3', 'test-active-impute.R:296:3', 'test-active-impute.R:376:3', 'test-active-impute.R:394:3', 'test-active-impute.R:424:3', 'test-active-impute.R:447:3', 'test-active-impute.R:482:3', 'test-active-impute.R:548:3', 'test-active-impute.R:601:3', 'test-bm-internal.R:129:3', 'test-bm-internal.R:154:3', 'test-check-pigauto.R:351:3', 'test-clamp-outliers.R:61:3', 'test-clamp-outliers.R:91:3', 'test-clamp-outliers.R:134:3', 'test-clamp-outliers.R:162:3', 'test-covariate-alignment.R:108:3', 'test-fit-predict.R:1:1', 'test-graph-transformer-block.R:2:3', 'test-graph-transformer-block.R:25:3', 'test-graph-transformer-block.R:50:3', 'test-graph-transformer-block.R:84:3', 'test-graph-transformer-block.R:113:3', 'test-graph-transformer-block.R:132:3', 'test-joint-refine-iter.R:109:3', 'test-joint-solver.R:94:3', 'test-mondrian-conformal.R:9:1', 'test-mondrian-mi-draws.R:14:1', 'test-monomorphic-discrete.R:36:3', 'test-monomorphic-discrete.R:56:3', 'test-multi-impute-posterior.R:301:3', 'test-multi-impute-trees.R:1:1', 'test-multi-impute.R:1:1', 'test-new-features.R:1:1', 'test-ovr-categorical.R:69:3', 'test-pagel-lambda.R:243:3', 'test-phase6-em.R:117:3', 'test-phase9-integration.R:2:3', 'test-phase9-integration.R:39:3', 'test-phase9-integration.R:67:3', 'test-phase9-integration.R:91:3', 'test-phase9-integration.R:108:3', 'test-phase9-integration.R:150:3', 'test-phase9-integration.R:176:3', 'test-phase9-integration.R:222:3', 'test-phylo-signal-gate.R:52:3', 'test-phylo-signal-gate.R:78:3', 'test-phylo-signal-gate.R:105:3', 'test-phylo-signal-gate.R:133:3', 'test-phylo-signal-gate.R:208:1', 'test-pmm.R:142:3', 'test-pmm.R:166:3', 'test-pmm.R:187:3', 'test-pmm.R:211:3', 'test-pmm.R:235:3', 'test-pmm.R:254:3', 'test-pmm.R:278:3', 'test-pmm.R:293:3', 'test-pmm.R:324:3', 'test-property-invariants.R:21:3', 'test-result-save-209.R:38:3', 'test-safety-floor.R:186:3', 'test-safety-floor.R:211:3', 'test-safety-floor.R:260:3', 'test-safety-floor.R:283:3', 'test-safety-floor.R:317:3', 'test-safety-floor.R:348:3', 'test-safety-floor.R:373:3', 'test-safety-floor.R:402:3', 'test-safety-floor.R:488:3', 'test-safety-floor.R:607:3', 'test-safety-floor.R:1155:1', 'test-safety-nets.R:12:3', 'test-safety-nets.R:23:3', 'test-safety-nets.R:51:3', 'test-safety-nets.R:72:1', 'test-share-gnn.R:2:3', 'test-share-gnn.R:86:3', 'test-share-gnn.R:136:3', 'test-share-gnn.R:219:3', 'test-shipping-coverage.R:103:3', 'test-shipping-coverage.R:116:3', 'test-shipping-coverage.R:133:3', 'test-shipping-coverage.R:148:3', 'test-shipping-coverage.R:164:3', 'test-shipping-coverage.R:311:1', 'test-zi-count-conformal-intervals.R:1:1', 'test-zi-count-splits.R:67:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-mi-posterior.R:464:3'): an extended fit equals one run longer with the thinning scaled ── Expected `ext$ymis` to be identical to `one$ymis`. Differences: actual | expected [1] -0.6675215086109212 - -0.6675215086120616 [1] [2] -1.4111187449816447 - -1.4111187449818965 [2] [3] -2.2123134497293973 - -2.2123134497306527 [3] [4] -0.9959817698746679 - -0.9959817698747231 [4] [5] -1.6841294514064189 - -1.6841294514071985 [5] [6] -0.0118465277507198 - -0.0118465277504615 [6] [7] 0.5166074742956885 - 0.5166074742956653 [7] [8] 0.3279455175986190 - 0.3279455175981466 [8] [9] 0.2433082302777510 - 0.2433082302777848 [9] [10] 0.5660682381321291 - 0.5660682381322022 [10] ... ... ... and 210 more ... ── Failure ('test-mi-posterior.R:465:3'): an extended fit equals one run longer with the thinning scaled ── Expected `ext$params` to be identical to `one$params`. Differences: actual$Sigma_P | expected$Sigma_P [1] 0.5544080125588766 - 0.5544080125594040 [1] [2] 0.0166272093565912 - 0.0166272093566135 [2] [3] 0.0166272093565912 - 0.0166272093566135 [3] [4] 0.0018633844243528 - 0.0018633844243565 [4] [5] 0.0595917045329065 - 0.0595917045329496 [5] [6] -0.0037810937995718 - -0.0037810937995864 [6] [7] -0.0037810937995718 - -0.0037810937995864 [7] [8] 0.0343310081606838 - 0.0343310081606709 [8] [9] 0.6292194984338281 - 0.6292194984347368 [9] [10] 0.0691416898844645 - 0.0691416898847053 [10] ... ... ... and 70 more ... actual$Sigma_E | expected$Sigma_E [1] 0.212459705897888 - 0.212459705897714 [1] [2] 0.063066812207288 - 0.063066812207148 [2] [3] 0.063066812207288 - 0.063066812207148 [3] [4] 0.269453337735505 | 0.269453337735505 [4] [5] 0.580286795852197 - 0.580286795851722 [5] [6] 0.139838595346418 - 0.139838595346161 [6] [7] 0.139838595346418 - 0.139838595346161 [7] [8] 0.336442578403468 | 0.336442578403468 [8] [9] 0.400433282192665 - 0.400433282192337 [9] [10] -0.031486068005598 - -0.031486068005729 [10] ... ... ... and 70 more ... actual$lambda | expected$lambda [1] 0.7229512981385636 - 0.7229512981389179 [1] [2] 0.0931297183716001 - 0.0931297183717303 [2] [3] 0.6110987220866622 - 0.6110987220871998 [3] [4] 0.6705964895814158 - 0.6705964895818936 [4] [5] 0.3656042439131215 - 0.3656042439127272 [5] [6] 0.5166503419617948 - 0.5166503419617871 [6] [7] 0.3341423495917235 - 0.3341423495918710 [7] [8] 0.0544673325787514 - 0.0544673325789739 [8] [9] 0.0216979381332330 - 0.0216979381331583 [9] [10] 0.6226163061199569 - 0.6226163061203119 [10] ... ... ... and 30 more ... actual$mu | expected$mu [1] -1.403108374525533 - -1.403108374526160 [1] [2] -0.428487459547569 - -0.428487459547833 [2] [3] -1.147449485958712 - -1.147449485959356 [3] [4] 0.512655529242841 - 0.512655529243410 [4] [5] -0.299571372192027 - -0.299571372191434 [5] [6] -0.448302308887434 - -0.448302308887261 [6] [7] 0.196163381813012 - 0.196163381813041 [7] [8] -0.261023988777946 - -0.261023988778324 [8] [9] -0.142763046375250 - -0.142763046375351 [9] [10] 0.712265296801902 - 0.712265296801873 [10] ... ... ... and 30 more ... ── Failure ('test-mi-posterior.R:466:3'): an extended fit equals one run longer with the thinning scaled ── Expected `ext$improper` to be identical to `one$improper`. Differences: actual$ymis | expected$ymis [1] 1.0468198107517410 - 1.0468198107546449 [1] [2] 0.5864710978081111 - 0.5864710978101707 [2] [3] -0.3035432982019316 - -0.3035432982031819 [3] [4] -0.0575068552863404 - -0.0575068552873423 [4] [5] -0.6269501838348523 - -0.6269501838335958 [5] [6] -0.9579051954304550 - -0.9579051954299376 [6] [7] -1.4622893829044243 - -1.4622893829051982 [7] [8] 0.0342409544799763 - 0.0342409544810857 [8] [9] -1.0096587099335612 - -1.0096587099334540 [9] [10] 0.7050216139415515 - 0.7050216139413982 [10] ... ... ... and 210 more ... actual$Sigma_P | expected$Sigma_P [1] 0.5548455958255840 - 0.5548455958285577 [1] [2] -0.0010324061104215 - -0.0010324061103914 [2] [3] -0.0010324061104215 - -0.0010324061103914 [3] [4] 0.1475318364197217 - 0.1475318364197140 [4] actual$Sigma_E | expected$Sigma_E [1] 0.33373916105223 - 0.33373916105183 [1] [2] 0.05713210835123 - 0.05713210835158 [2] [3] 0.05713210835123 - 0.05713210835158 [3] [4] 0.30568120575932 | 0.30568120575932 [4] ── Failure ('test-mi-posterior.R:471:3'): an extended fit equals one run longer with the thinning scaled ── Expected `dg` to be identical to `one$diagnostics`. Differences: actual vs expected rhat - actual[1, ] 1.051665 + expected[1, ] 1.051323 actual[2, ] 1.054214 actual[3, ] 1.014046 actual[4, ] 1.094538 - actual[5, ] 1.050473 + expected[5, ] 1.050816 actual[6, ] 1.057600 - actual[7, ] 1.043850 + expected[7, ] 1.043772 actual[8, ] 1.010643 actual$rhat | expected$rhat [1] 1.051665 - 1.051323 [1] [2] 1.054214 | 1.054214 [2] [3] 1.014046 | 1.014046 [3] [4] 1.094538 | 1.094538 [4] [5] 1.050473 - 1.050816 [5] [6] 1.057600 | 1.057600 [6] [7] 1.043850 - 1.043772 [7] [8] 1.010643 | 1.010643 [8] [ FAIL 4 | WARN 28 | SKIP 178 | PASS 2438 ] Error: ! Test failures. Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [25s/28s] 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/pigauto.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 9:55.77, 343.12 + 15.58