* using log directory ‘/data/localhost/ripley/R/packages/tests-MKL/BJM.Rcheck’ * using R Under development (unstable) (2026-10-31 r90816) * 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: 2026-10-31 16:45:50 UTC * using option ‘--no-stop-on-test-error’ * checking for file ‘BJM/DESCRIPTION’ ... OK * this is package ‘BJM’ version ‘0.3.0’ * 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 ‘BJM’ can be installed ... [14s/15s] 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 ... [29s/31s] 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 ... [12s/12s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ [216s/217s] [216s/217s] ERROR Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(BJM) Loading required package: survival > > test_check("BJM") Tracing function "predictRisk" in package "namespace:BJM" Saving _problems/test-longitudinalSubCopula-60.R Saving _problems/test-longitudinalSubCopula-65.R Ignoring unknown labels: * fill : "status2" Ignoring unknown labels: * fill : "Event type" [ FAIL 2 | WARN 10 | SKIP 64 | PASS 753 ] ══ Skipped tests (64) ══════════════════════════════════════════════════════════ • On CRAN (59): 'test-baseline-characterization-noCR.R:69:3', 'test-baseline-characterization.R:71:3', 'test-boxQuadrature.R:94:3', 'test-dynamicPredictionBioAll.R:144:3', 'test-dynamicPredictionBioAll.R:167:3', 'test-dynamicPredictionBioAll.R:188:3', 'test-dynamicPredictionBioAll.R:214:3', 'test-dynamicPredictionBioCopula.R:86:3', 'test-dynamicPredictionBioCopula.R:112:3', 'test-dynamicPredictionBioCopula.R:168:3', 'test-dynamicPredictionBioCopula.R:190:3', 'test-imputeLongitudinal.R:138:3', 'test-imputeLongitudinal.R:283:3', 'test-imputeLongitudinal.R:319:3', 'test-longitudinalSub.R:159:3', 'test-longitudinalSubCopula.R:92:3', 'test-longitudinalSubCopula.R:114:3', 'test-longitudinalSubCopula.R:126:3', 'test-longitudinalSubCopula.R:143:3', 'test-longitudinalSubCopula.R:182:3', 'test-longitudinalSubCopula.R:195:3', 'test-longitudinalSubCopula.R:205:3', 'test-longitudinalSubCopula.R:223:3', 'test-longitudinalSubCopula.R:239:3', 'test-performanceInterval.R:4:3', 'test-performanceInterval.R:70:3', 'test-plots.R:10:3', 'test-plots.R:22:3', 'test-plots.R:33:3', 'test-plots.R:54:3', 'test-plots.R:134:3', 'test-plots.R:147:3', 'test-plots.R:175:3', 'test-plots.R:192:3', 'test-plots.R:248:3', 'test-plots.R:275:3', 'test-plots.R:322:3', 'test-plots.R:368:3', 'test-plots.R:392:3', 'test-poolLongitudinalSub.R:256:3', 'test-predictLongitudinal.R:70:3', 'test-predictLongitudinal.R:89:3', 'test-predictLongitudinal.R:139:3', 'test-predictRisk.R:296:3', 'test-predictRisk.R:450:3', 'test-predictRisk.R:464:3', 'test-predictRisk.R:553:3', 'test-predictRiskCopula.R:92:3', 'test-predictRiskCopula.R:114:3', 'test-predictRiskCopula.R:166:3', 'test-predictRiskCopula.R:208:3', 'test-predictRiskCopula.R:245:3', 'test-rightcensor-reference.R:4:3', 'test-simulateTrajectory.R:123:3', 'test-simulateTrajectory.R:164:3', 'test-survivalSubInterval.R:122:3', 'test-survivalSubInterval.R:262:3', 'test-survivalSubInterval.R:432:3', 'test-survivalSubInterval.R:509:3' • torch backend (LibTorch) is not installed (5): 'test-imputeLongitudinal.R:184:3', 'test-imputeLongitudinal.R:202:3', 'test-imputeLongitudinal.R:237:3', 'test-imputeLongitudinal.R:254:3', 'test-poolLongitudinalSub.R:186:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-longitudinalSubCopula.R:60:3'): all-continuous input is completely unaffected by biomarker_type (hard requirement) ── Expected `fit_multi_dispatch` to be identical to `fit_multi_direct`. Differences: actual$lfit[[1]]$modelStruct$reStruct$id vs expected$lfit[[1]]$modelStruct$reStruct$id - 0.845093799645480 + 0.845093799641895 - -1.003273911672614 + -1.003273911674486 - 0.043331729020344 + 0.043331729020430 actual$lfit[[1]]$coefficients$fixed vs expected$lfit[[1]]$coefficients$fixed - 1.0885147619294580 + 1.0885147619297850 - 0.2747350678480704 + 0.2747350678480296 - -0.0051877016786222 + -0.0051877016786265 - 0.2017491813195650 + 0.2017491813193858 actual$lfit[[1]]$coefficients$random$id vs expected$lfit[[1]]$coefficients$random$id [,1] [,2] actual$lfit[[1]]$coefficients$random$id[161, ] -1.040635202 -0.0909711424 actual$lfit[[1]]$coefficients$random$id[162, ] 0.973876894 0.0200552384 actual$lfit[[1]]$coefficients$random$id[163, ] 0.433022797 0.0969949712 - actual$lfit[[1]]$coefficients$random$id[164, ] 0.532608958 0.0933565213 + expected$lfit[[1]]$coefficients$random$id[164, ] 0.532608958 0.0933565212 actual$lfit[[1]]$coefficients$random$id[165, ] 1.137483762 -0.0198786154 actual$lfit[[1]]$coefficients$random$id[166, ] -0.009024028 0.0015074274 actual$lfit[[1]]$coefficients$random$id[167, ] -0.369366964 0.0095429293 actual$lfit[[1]]$varFix | expected$lfit[[1]]$varFix [1] 0.2083620895705378673 - 0.2083620895694883179 [1] [2] -0.0000638364496213727 - -0.0000638364496215873 [2] [3] -0.0030438308486493921 - -0.0030438308486341048 [3] [4] -0.0555033050489676730 - -0.0555033050486870155 [4] [5] -0.0000638364496213727 - -0.0000638364496215873 [5] [6] 0.0003281064792798844 - 0.0003281064792795572 [6] [7] 0.0000002237154359049 - 0.0000002237154359069 [7] [8] -0.0000008470606919322 - -0.0000008470606919261 [8] [9] -0.0030438308486493921 - -0.0030438308486341048 [9] [10] 0.0000002237154359049 - 0.0000002237154359069 [10] ... ... ... and 6 more ... `actual$lfit[[1]]$sigma`: 0.41960177746343 `expected$lfit[[1]]$sigma`: 0.41960177746376 attr(actual$lfit[[1]]$apVar, 'Pars') vs attr(expected$lfit[[1]]$apVar, 'Pars') - -0.02335536673334 + -0.02335536673613 - -1.86478882477353 + -1.86478882477456 - 0.23580154445009 + 0.23580154445100 - -0.86844916637882 + -0.86844916637802 actual$lfit[[1]]$apVar vs expected$lfit[[1]]$apVar [,1] [,2] [,3] [,4] - actual$lfit[[1]]$apVar[1, ] 3.448214e-03 2.953078e-05 -0.0013875550 -7.883226e-05 + expected$lfit[[1]]$apVar[1, ] 3.732619e-03 3.792340e-05 -0.0022010659 -8.937789e-05 - actual$lfit[[1]]$apVar[2, ] 2.953078e-05 1.279161e-02 -0.0019334647 -6.918010e-04 + expected$lfit[[1]]$apVar[2, ] 3.792340e-05 1.279436e-02 -0.0020456578 -6.926048e-04 - actual$lfit[[1]]$apVar[3, ] -1.387555e-03 -1.933465e-03 0.0756816596 4.386723e-04 + expected$lfit[[1]]$apVar[3, ] -2.201066e-03 -2.045658e-03 0.0803973046 4.812061e-04 - actual$lfit[[1]]$apVar[4, ] -7.883226e-05 -6.918010e-04 0.0004386723 8.764462e-04 + expected$lfit[[1]]$apVar[4, ] -8.937789e-05 -6.926048e-04 0.0004812061 8.769260e-04 `actual$lfit[[1]]$logLik`: -825.07004096653554 `expected$lfit[[1]]$logLik`: -825.07004096653600 actual$lfit[[1]]$fitted vs expected$lfit[[1]]$fitted [,1] [,2] actual$lfit[[1]]$fitted[518, ] 0.7362243 0.336168521 actual$lfit[[1]]$fitted[519, ] 1.0525535 1.488644215 actual$lfit[[1]]$fitted[520, ] 1.1691451 1.607235350 - actual$lfit[[1]]$fitted[521, ] 0.8141307 -0.304462120 + expected$lfit[[1]]$fitted[521, ] 0.8141307 -0.304462119 actual$lfit[[1]]$fitted[522, ] 1.0454943 0.436364260 actual$lfit[[1]]$fitted[523, ] 1.1846521 0.583483548 actual$lfit[[1]]$fitted[524, ] 1.3102702 0.716288527 attr(actual$lfit[[1]]$residuals, 'std') vs attr(expected$lfit[[1]]$residuals, 'std') - 0.41960177746343 + 0.41960177746376 - 0.41960177746343 + 0.41960177746376 - 0.41960177746343 + 0.41960177746376 - 0.41960177746343 + 0.41960177746376 - 0.41960177746343 + 0.41960177746376 - 0.41960177746343 + 0.41960177746376 - 0.41960177746343 + 0.41960177746376 - 0.41960177746343 + 0.41960177746376 - 0.41960177746343 + 0.41960177746376 - 0.41960177746343 + 0.41960177746376 and 862 more ... actual$lfit[[1]]$residuals vs expected$lfit[[1]]$residuals [,1] [,2] actual$lfit[[1]]$residuals[342, ] 1.480641607 0.2306116635 actual$lfit[[1]]$residuals[343, ] 0.855295967 -0.1715707403 actual$lfit[[1]]$residuals[344, ] 1.407028755 0.3575864719 - actual$lfit[[1]]$residuals[345, ] 0.799018118 0.4780299663 + expected$lfit[[1]]$residuals[345, ] 0.799018118 0.4780299664 actual$lfit[[1]]$residuals[346, ] 0.047599361 -0.2855780782 actual$lfit[[1]]$residuals[347, ] -0.070092924 -0.4165491969 actual$lfit[[1]]$residuals[348, ] 0.664335878 0.2806988718 actual$lfit[[1]]$residuals vs expected$lfit[[1]]$residuals [,1] [,2] actual$lfit[[1]]$residuals[669, ] 0.958913484 0.0666263357 actual$lfit[[1]]$residuals[670, ] -1.262516129 -0.1977719925 actual$lfit[[1]]$residuals[671, ] -1.283890873 -0.2605031558 - actual$lfit[[1]]$residuals[672, ] -0.997764393 -0.0206511558 + expected$lfit[[1]]$residuals[672, ] -0.997764393 -0.0206511559 actual$lfit[[1]]$residuals[673, ] -0.919405009 -0.0250046098 actual$lfit[[1]]$residuals[674, ] -0.503924294 0.2934561817 actual$lfit[[1]]$residuals[675, ] -0.229628521 0.1240600603 attr(actual$lfit[[1]]$fixDF, 'varFixFact') vs attr(expected$lfit[[1]]$fixDF, 'varFixFact') - 0.078395260407046391 + 0.078395260406849229 - -0.002929073613590517 + -0.002929073613597832 - -0.366749298899636034 + -0.366749298898715936 - 0.260197319357138690 + 0.260197319356478107 0.000000000000000000 - 0.018113680629799282 + 0.018113680629790248 - 0.000032211066084406 + 0.000032211066084762 - 0.000003970987334522 + 0.000003970987334503 0.000000000000000000 0.000000000000000000 and 6 more ... actual$lfit[[2]]$modelStruct$reStruct$id vs expected$lfit[[2]]$modelStruct$reStruct$id - 0.097201411417 + 0.097201407504 - -1.488208048908 + -1.488208046449 - 0.015734781969 + 0.015734782031 actual$lfit[[2]]$coefficients$fixed vs expected$lfit[[2]]$coefficients$fixed - 4.1040101437833 + 4.1040101436101 - -0.1449372339361 + -0.1449372339836 - -0.0094836503903 + -0.0094836503850 - -0.2111762451639 + -0.2111762451428 actual$lfit[[2]]$coefficients$random$id vs expected$lfit[[2]]$coefficients$random$id [,1] [,2] actual$lfit[[2]]$coefficients$random$id[1, ] -0.372750393 -0.0038360504 - actual$lfit[[2]]$coefficients$random$id[2, ] 0.064207387 0.0097090471 + expected$lfit[[2]]$coefficients$random$id[2, ] 0.064207386 0.0097090471 - actual$lfit[[2]]$coefficients$random$id[3, ] -0.378789436 -0.0119736773 + expected$lfit[[2]]$coefficients$random$id[3, ] -0.378789435 -0.0119736774 - actual$lfit[[2]]$coefficients$random$id[4, ] -0.094229692 -0.0616401123 + expected$lfit[[2]]$coefficients$random$id[4, ] -0.094229692 -0.0616401125 - actual$lfit[[2]]$coefficients$random$id[5, ] 0.578301737 0.1302432009 + expected$lfit[[2]]$coefficients$random$id[5, ] 0.578301735 0.1302432013 - actual$lfit[[2]]$coefficients$random$id[6, ] 0.517268733 -0.0345959923 + expected$lfit[[2]]$coefficients$random$id[6, ] 0.517268732 -0.0345959922 actual$lfit[[2]]$coefficients$random$id[7, ] -0.130827266 0.0009238044 - actual$lfit[[2]]$coefficients$random$id[8, ] -0.265257116 -0.0037871607 + expected$lfit[[2]]$coefficients$random$id[8, ] -0.265257115 -0.0037871607 - actual$lfit[[2]]$coefficients$random$id[9, ] 0.681407265 -0.0066776426 + expected$lfit[[2]]$coefficients$random$id[9, ] 0.681407264 -0.0066776425 actual$lfit[[2]]$coefficients$random$id[10, ] -0.025186302 -0.0061956650 and 159 more ... actual$lfit[[2]]$varFix vs expected$lfit[[2]]$varFix [,1] [,2] [,3] [,4] actual$lfit[[2]]$varFix[1, ] 3.179045e-02 -9.503504e-05 -4.657575e-04 -8.438683e-03 actual$lfit[[2]]$varFix[2, ] -9.503504e-05 9.687701e-05 5.903641e-07 3.045241e-06 actual$lfit[[2]]$varFix[3, ] -4.657575e-04 5.903641e-07 8.248870e-06 5.288696e-05 - actual$lfit[[2]]$varFix[4, ] -8.438683e-03 3.045241e-06 5.288696e-05 6.920768e-03 + expected$lfit[[2]]$varFix[4, ] -8.438683e-03 3.045241e-06 5.288696e-05 6.920767e-03 `actual$lfit[[2]]$sigma`: 0.31438755707 `expected$lfit[[2]]$sigma`: 0.31438755721 attr(actual$lfit[[2]]$apVar, 'Pars') vs attr(expected$lfit[[2]]$apVar, 'Pars') - -1.05992738453 + -1.05992738802 - -2.64291425437 + -2.64291425148 - 0.13927088527 + 0.13927088548 - -1.15712879595 + -1.15712879553 actual$lfit[[2]]$apVar vs expected$lfit[[2]]$apVar [,1] [,2] [,3] [,4] - actual$lfit[[2]]$apVar[1, ] 0.0055542083 0.0004330153 -0.0064840300 -0.0002747749 + expected$lfit[[2]]$apVar[1, ] 0.0056485316 0.0006100806 -0.0081489425 -0.0002861812 - actual$lfit[[2]]$apVar[2, ] 0.0004330153 0.0252933514 -0.0123371701 -0.0012529389 + expected$lfit[[2]]$apVar[2, ] 0.0006100806 0.0256331957 -0.0154930995 -0.0012746130 - actual$lfit[[2]]$apVar[3, ] -0.0064840300 -0.0123371701 0.1108653347 0.0008556348 + expected$lfit[[2]]$apVar[3, ] -0.0081489425 -0.0154930995 0.1404234471 0.0010572587 - actual$lfit[[2]]$apVar[4, ] -0.0002747749 -0.0012529389 0.0008556348 0.0008709795 + expected$lfit[[2]]$apVar[4, ] -0.0002861812 -0.0012746130 0.0010572587 0.0008723788 `actual$lfit[[2]]$logLik`: -433.10909545109371 `expected$lfit[[2]]$logLik`: -433.10909545109325 actual$lfit[[2]]$fitted vs expected$lfit[[2]]$fitted [,1] [,2] actual$lfit[[2]]$fitted[815, ] 3.303745 3.272430 actual$lfit[[2]]$fitted[816, ] 3.167236 3.131981 actual$lfit[[2]]$fitted[817, ] 3.220353 2.732040 - actual$lfit[[2]]$fitted[818, ] 3.367473 2.964814 + expected$lfit[[2]]$fitted[818, ] 3.367473 2.964815 actual$lfit[[2]]$fitted[819, ] 3.302394 2.895962 actual$lfit[[2]]$fitted[820, ] 3.465260 3.399463 actual$lfit[[2]]$fitted[821, ] 3.393037 3.315746 attr(actual$lfit[[2]]$residuals, 'std') vs attr(expected$lfit[[2]]$residuals, 'std') - 0.31438755707 + 0.31438755721 - 0.31438755707 + 0.31438755721 - 0.31438755707 + 0.31438755721 - 0.31438755707 + 0.31438755721 - 0.31438755707 + 0.31438755721 - 0.31438755707 + 0.31438755721 - 0.31438755707 + 0.31438755721 - 0.31438755707 + 0.31438755721 - 0.31438755707 + 0.31438755721 - 0.31438755707 + 0.31438755721 and 862 more ... actual$lfit[[2]]$residuals vs expected$lfit[[2]]$residuals [,1] [,2] - actual$lfit[[2]]$residuals[1, ] -0.7355097502 -0.3627593568 + expected$lfit[[2]]$residuals[1, ] -0.7355097503 -0.3627593577 - actual$lfit[[2]]$residuals[2, ] -0.3193188923 0.0554480427 + expected$lfit[[2]]$residuals[2, ] -0.3193188925 0.0554480418 - actual$lfit[[2]]$residuals[3, ] 0.0405516460 -0.0236557405 + expected$lfit[[2]]$residuals[3, ] 0.0405516458 -0.0236557405 - actual$lfit[[2]]$residuals[4, ] -0.0796067343 -0.1484926673 + expected$lfit[[2]]$residuals[4, ] -0.0796067345 -0.1484926672 - actual$lfit[[2]]$residuals[5, ] 0.2749968140 0.2011133428 + expected$lfit[[2]]$residuals[5, ] 0.2749968138 0.2011133429 - actual$lfit[[2]]$residuals[6, ] 0.1053943927 0.0214360972 + expected$lfit[[2]]$residuals[6, ] 0.1053943926 0.0214360973 - actual$lfit[[2]]$residuals[7, ] -0.8336790801 -0.4548896443 + expected$lfit[[2]]$residuals[7, ] -0.8336790803 -0.4548896449 - actual$lfit[[2]]$residuals[8, ] -0.4190755318 -0.0341228846 + expected$lfit[[2]]$residuals[8, ] -0.4190755319 -0.0341228851 - actual$lfit[[2]]$residuals[9, ] -0.4260592931 -0.0350745666 + expected$lfit[[2]]$residuals[9, ] -0.4260592932 -0.0350745671 - actual$lfit[[2]]$residuals[10, ] -0.1643919168 0.2382963548 + expected$lfit[[2]]$residuals[10, ] -0.1643919168 0.2382963544 and 862 more ... attr(actual$lfit[[2]]$fixDF, 'varFixFact') vs attr(expected$lfit[[2]]$fixDF, 'varFixFact') [,1] [,2] [,3] [,4] attr(actual$lfit[[2]]$fixDF, 'varFixFact')[1, ] 0.030579954 0.000000e+00 0.0000000000 0.00000000 attr(actual$lfit[[2]]$fixDF, 'varFixFact')[2, ] -0.006332438 9.840461e-03 0.0000000000 0.00000000 - attr(actual$lfit[[2]]$fixDF, 'varFixFact')[3, ] -0.143267929 2.024723e-04 0.0028008427 0.00000000 + attr(expected$lfit[[2]]$fixDF, 'varFixFact')[3, ] -0.143267928 2.024723e-04 0.0028008427 0.00000000 - attr(actual$lfit[[2]]$fixDF, 'varFixFact')[4, ] 0.101437265 -3.660535e-05 -0.0006357282 -0.08319115 + attr(expected$lfit[[2]]$fixDF, 'varFixFact')[4, ] 0.101437264 -3.660535e-05 -0.0006357282 -0.08319115 actual$Sigma_fit | expected$Sigma_fit [1] 0.95808822850600 - 0.95808822851100 [1] [2] 0.01943255019041 - 0.01943255018972 [2] [3] -0.18731197576854 - -0.18731197575381 [3] [4] -0.01918833841194 - -0.01918833842881 [4] [5] 0.01943255019041 - 0.01943255018972 [5] [6] 0.02578576390533 - 0.02578576390290 [6] [7] -0.00567774905940 - -0.00567774906014 [7] [8] -0.00668313018749 - -0.00668313018605 [8] [9] -0.18731197576854 - -0.18731197575381 [9] [10] -0.00567774905940 - -0.00567774906014 [10] ... ... ... and 6 more ... ── Failure ('test-longitudinalSubCopula.R:65:3'): all-continuous input is completely unaffected by biomarker_type (hard requirement) ── Expected `fit_explicit_cont` to be identical to `fit_direct`. Differences: actual$lfit[[1]]$modelStruct$reStruct$id vs expected$lfit[[1]]$modelStruct$reStruct$id - 0.84509379964197 + 0.84509379964548 - -1.00327391167456 + -1.00327391167261 - 0.04333172902067 + 0.04333172902034 actual$lfit[[1]]$coefficients$fixed vs expected$lfit[[1]]$coefficients$fixed - 1.0885147619297428 + 1.0885147619294580 - 0.2747350678480661 + 0.2747350678480704 - -0.0051877016786271 + -0.0051877016786222 - 0.2017491813194588 + 0.2017491813195650 actual$lfit[[1]]$coefficients$random$id vs expected$lfit[[1]]$coefficients$random$id [,1] [,2] actual$lfit[[1]]$coefficients$random$id[161, ] -1.040635202 -0.0909711424 actual$lfit[[1]]$coefficients$random$id[162, ] 0.973876894 0.0200552384 actual$lfit[[1]]$coefficients$random$id[163, ] 0.433022797 0.0969949712 - actual$lfit[[1]]$coefficients$random$id[164, ] 0.532608958 0.0933565212 + expected$lfit[[1]]$coefficients$random$id[164, ] 0.532608958 0.0933565213 actual$lfit[[1]]$coefficients$random$id[165, ] 1.137483762 -0.0198786154 actual$lfit[[1]]$coefficients$random$id[166, ] -0.009024028 0.0015074274 actual$lfit[[1]]$coefficients$random$id[167, ] -0.369366964 0.0095429293 actual$lfit[[1]]$varFix | expected$lfit[[1]]$varFix [1] 0.2083620895695153519 - 0.2083620895705378673 [1] [2] -0.0000638364496205299 - -0.0000638364496213727 [2] [3] -0.0030438308486345107 - -0.0030438308486493921 [3] [4] -0.0555033050486936769 - -0.0555033050489676730 [4] [5] -0.0000638364496205299 - -0.0000638364496213727 [5] [6] 0.0003281064792795349 - 0.0003281064792798844 [6] [7] 0.0000002237154358993 - 0.0000002237154359049 [7] [8] -0.0000008470606919916 - -0.0000008470606919322 [8] [9] -0.0030438308486345107 - -0.0030438308486493921 [9] [10] 0.0000002237154358993 - 0.0000002237154359049 [10] ... ... ... and 6 more ... `actual$lfit[[1]]$sigma`: 0.41960177746375 `expected$lfit[[1]]$sigma`: 0.41960177746343 attr(actual$lfit[[1]]$apVar, 'Pars') vs attr(expected$lfit[[1]]$apVar, 'Pars') - -0.02335536673607 + -0.02335536673334 - -1.86478882477458 + -1.86478882477353 - 0.23580154445233 + 0.23580154445009 - -0.86844916637804 + -0.86844916637882 actual$lfit[[1]]$apVar vs expected$lfit[[1]]$apVar [,1] [,2] [,3] [,4] - actual$lfit[[1]]$apVar[1, ] 3.584306e-03 3.351418e-05 -0.0018157337 -8.360875e-05 + expected$lfit[[1]]$apVar[1, ] 3.448214e-03 2.953078e-05 -0.0013875550 -7.883226e-05 - actual$lfit[[1]]$apVar[2, ] 3.351418e-05 1.279270e-02 -0.0020115679 -6.921956e-04 + expected$lfit[[1]]$apVar[2, ] 2.953078e-05 1.279161e-02 -0.0019334647 -6.918010e-04 - actual$lfit[[1]]$apVar[3, ] -1.815734e-03 -2.011568e-03 0.0800102072 4.692731e-04 + expected$lfit[[1]]$apVar[3, ] -1.387555e-03 -1.933465e-03 0.0756816596 4.386723e-04 - actual$lfit[[1]]$apVar[4, ] -8.360875e-05 -6.921956e-04 0.0004692731 8.767102e-04 + expected$lfit[[1]]$apVar[4, ] -7.883226e-05 -6.918010e-04 0.0004386723 8.764462e-04 `actual$lfit[[1]]$logLik`: -825.07004096653600 `expected$lfit[[1]]$logLik`: -825.07004096653554 actual$lfit[[1]]$fitted vs expected$lfit[[1]]$fitted [,1] [,2] actual$lfit[[1]]$fitted[518, ] 0.7362243 0.336168521 actual$lfit[[1]]$fitted[519, ] 1.0525535 1.488644215 actual$lfit[[1]]$fitted[520, ] 1.1691451 1.607235350 - actual$lfit[[1]]$fitted[521, ] 0.8141307 -0.304462119 + expected$lfit[[1]]$fitted[521, ] 0.8141307 -0.304462120 actual$lfit[[1]]$fitted[522, ] 1.0454943 0.436364260 actual$lfit[[1]]$fitted[523, ] 1.1846521 0.583483548 actual$lfit[[1]]$fitted[524, ] 1.3102702 0.716288527 attr(actual$lfit[[1]]$residuals, 'std') vs attr(expected$lfit[[1]]$residuals, 'std') - 0.41960177746375 + 0.41960177746343 - 0.41960177746375 + 0.41960177746343 - 0.41960177746375 + 0.41960177746343 - 0.41960177746375 + 0.41960177746343 - 0.41960177746375 + 0.41960177746343 - 0.41960177746375 + 0.41960177746343 - 0.41960177746375 + 0.41960177746343 - 0.41960177746375 + 0.41960177746343 - 0.41960177746375 + 0.41960177746343 - 0.41960177746375 + 0.41960177746343 and 862 more ... actual$lfit[[1]]$residuals vs expected$lfit[[1]]$residuals [,1] [,2] actual$lfit[[1]]$residuals[342, ] 1.480641607 0.2306116635 actual$lfit[[1]]$residuals[343, ] 0.855295967 -0.1715707403 actual$lfit[[1]]$residuals[344, ] 1.407028755 0.3575864719 - actual$lfit[[1]]$residuals[345, ] 0.799018118 0.4780299664 + expected$lfit[[1]]$residuals[345, ] 0.799018118 0.4780299663 actual$lfit[[1]]$residuals[346, ] 0.047599361 -0.2855780782 actual$lfit[[1]]$residuals[347, ] -0.070092924 -0.4165491969 actual$lfit[[1]]$residuals[348, ] 0.664335878 0.2806988718 actual$lfit[[1]]$residuals vs expected$lfit[[1]]$residuals [,1] [,2] actual$lfit[[1]]$residuals[669, ] 0.958913484 0.0666263357 actual$lfit[[1]]$residuals[670, ] -1.262516129 -0.1977719925 actual$lfit[[1]]$residuals[671, ] -1.283890873 -0.2605031558 - actual$lfit[[1]]$residuals[672, ] -0.997764393 -0.0206511559 + expected$lfit[[1]]$residuals[672, ] -0.997764393 -0.0206511558 actual$lfit[[1]]$residuals[673, ] -0.919405009 -0.0250046098 actual$lfit[[1]]$residuals[674, ] -0.503924294 0.2934561817 actual$lfit[[1]]$residuals[675, ] -0.229628521 0.1240600603 attr(actual$lfit[[1]]$fixDF, 'varFixFact') vs attr(expected$lfit[[1]]$fixDF, 'varFixFact') - 0.07839526040685475 + 0.07839526040704639 - -0.00292907361356393 + -0.00292907361359052 - -0.36674929889874214 + -0.36674929889963603 - 0.26019731935649182 + 0.26019731935713869 0.00000000000000000 - 0.01811368062978964 + 0.01811368062979928 - 0.00003221106608377 + 0.00003221106608441 - 0.00000397098733481 + 0.00000397098733452 0.00000000000000000 0.00000000000000000 and 6 more ... actual$Sigma_fit | expected$Sigma_fit [1] 0.954422905793598 - 0.954422905793760 [1] [2] 0.017659233452580 - 0.017659233452545 [2] [3] 0.017659233452580 - 0.017659233452545 [3] [4] 0.024036797582413 - 0.024036797582443 [4] [ FAIL 2 | WARN 10 | SKIP 64 | PASS 753 ] Error: ! Test failures. Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [18s/18s] 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/BJM.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 5:59.36, 341.48 + 12.34