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Type 'q()' to quit R. > # 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/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > Sys.setenv(R_TESTS="") > > library(testthat) > library(admixr2) > > test_check("admixr2") Starting 2 test processes. > test-adfweight.R: > loading into symengine environment... > test-adfweight.R: > pruning branches (`if`/`else`) of full model... > test-adfweight.R: v done > test-adfweight.R: > finding duplicate expressions in admixr2 sensitivity model... > test-covariate.R: admixr2: covariate 'CRCL': median 92 and iqr c(62, 118) are not consistent with a normal margin -- the quartiles centre on 90 instead. Matching the median and the IQR WIDTH; the quartiles will come out shifted. Give `sd =` if the paper reports one. > test-covariate.R: admixr2: covariate 'WT': median 70 and iqr c(60, 84) are not consistent with a normal margin -- the quartiles centre on 72 instead. Matching the median and the IQR WIDTH; the quartiles will come out shifted. Give `sd =` if the paper reports one. > test-adfweight.R: > loading into symengine environment... > test-adfweight.R: > pruning branches (`if`/`else`) of full model... > test-adfweight.R: v done > test-adfweight.R: > finding duplicate expressions in admixr2 sensitivity model... > test-adfweight.R: > loading into symengine environment... > test-adfweight.R: > pruning branches (`if`/`else`) of full model... > test-adfweight.R: v done > test-adfweight.R: > finding duplicate expressions in admixr2 sensitivity model... > test-adfweight.R: > loading into symengine environment... > test-adfweight.R: > pruning branches (`if`/`else`) of full model... > test-adfweight.R: v done > test-adfweight.R: > finding duplicate expressions in admixr2 sensitivity model... > test-adfweight.R: > loading into symengine environment... > test-adfweight.R: > pruning branches (`if`/`else`) of full model... > test-adfweight.R: v done > test-adfweight.R: > finding duplicate expressions in admixr2 sensitivity model... > test-adfweight.R: > loading into symengine environment... > test-adfweight.R: > pruning branches (`if`/`else`) of full model... > test-adfweight.R: v done > test-adfweight.R: > finding duplicate expressions in admixr2 sensitivity model... > test-adfweight.R: > loading into symengine environment... > test-adfweight.R: > pruning branches (`if`/`else`) of full model... > test-adfweight.R: v done > test-adfweight.R: > finding duplicate expressions in admixr2 sensitivity model... > test-adfweight.R: > loading into symengine environment... > test-adfweight.R: > pruning branches (`if`/`else`) of full model... > test-adfweight.R: v done > test-adfweight.R: > finding duplicate expressions in admixr2 sensitivity model... > test-adfweight.R: > loading into symengine environment... > test-adfweight.R: > pruning branches (`if`/`else`) of full model... > test-adfweight.R: v done > test-adfweight.R: > finding duplicate expressions in admixr2 sensitivity model... > test-adfweight.R: > loading into symengine environment... > test-adfweight.R: > pruning branches (`if`/`else`) of full model... > test-adfweight.R: v done > test-adfweight.R: > finding duplicate expressions in admixr2 sensitivity model... > test-utils.R: No admixr2 workers running. > test-utils.R: No admixr2 workers running. > test-utils.R: No admixr2 workers running. > test-utils.R: admixr2: tv finished on the gradient box constraint (grad_bounds = 5 from the starting value), not at an interior optimum. The reported estimate and SE are those of a constrained fit. Widen grad_bounds, or start closer to the expected value. [ FAIL 0 | WARN 0 | SKIP 169 | PASS 3539 ] ══ Skipped tests (169) ═════════════════════════════════════════════════════════ • On CRAN (169): 'test-adgh-nodes.R:315:3', 'test-adgh-nodes.R:368:3', 'test-covariate.R:919:3', 'test-covariate.R:996:3', 'test-covariate.R:1024:3', 'test-covariate.R:1051:3', 'test-covariate.R:1086:3', 'test-covariate.R:1144:3', 'test-covariate.R:1175:3', 'test-covariate.R:1205:3', 'test-covariate.R:1235:3', 'test-covariate.R:1261:3', 'test-covariate.R:1302:3', 'test-covariate.R:1342:3', 'test-covariate.R:1489:3', 'test-covariate.R:1803:3', 'test-covariate.R:1906:3', 'test-covariate.R:1924:3', 'test-covariate.R:1946:3', 'test-covariate.R:1975:3', 'test-covariate.R:2011:3', 'test-covariate.R:2034:3', 'test-covariate.R:2108:3', 'test-covariate.R:2134:3', 'test-covariate.R:2177:3', 'test-covariate.R:2204:3', 'test-covariate.R:2238:3', 'test-datagen.R:174:3', 'test-datagen.R:196:3', 'test-datagen.R:211:3', 'test-datagen.R:230:3', 'test-datagen.R:247:3', 'test-datagen.R:268:3', 'test-datagen.R:284:3', 'test-datagen.R:299:3', 'test-datagen.R:312:3', 'test-integration-adfo.R:10:3', 'test-integration-adfo.R:17:3', 'test-integration-adfo.R:24:3', 'test-integration-adfo.R:31:3', 'test-integration-adfo.R:37:3', 'test-integration-adfo.R:53:3', 'test-integration-adfo.R:69:3', 'test-integration-adgh-unpaired.R:80:3', 'test-integration-adgh-unpaired.R:90:3', 'test-integration-adgh.R:5:1', 'test-integration-batch-align.R:8:3', 'test-integration-beta.R:56:3', 'test-integration-beta.R:66:3', 'test-integration-beta.R:78:3', 'test-integration-beta.R:89:3', 'test-integration-beta.R:104:3', 'test-integration-beta.R:124:3', 'test-integration-beta.R:136:3', 'test-integration-cache-hit.R:10:1', 'test-integration-cold-session.R:29:3', 'test-integration-collapse-gradient.R:2:3', 'test-integration-cov.R:2:1', 'test-integration-covariate.R:9:1', 'test-integration-daemon-patch.R:18:1', 'test-integration-daemon-wipe.R:15:1', 'test-integration-datagen-roundtrip.R:30:3', 'test-integration-datagen-roundtrip.R:69:3', 'test-integration-edge-cases.R:9:1', 'test-integration-errmodel.R:72:3', 'test-integration-errmodel.R:94:3', 'test-integration-errmodel.R:100:3', 'test-integration-errmodel.R:110:3', 'test-integration-errmodel.R:139:3', 'test-integration-errmodel.R:146:3', 'test-integration-errmodel.R:172:3', 'test-integration-errmodel.R:196:3', 'test-integration-errmodel.R:208:3', 'test-integration-errmodel.R:238:3', 'test-integration-errmodel.R:263:3', 'test-integration-fixed-theta.R:13:1', 'test-integration-grad-branches.R:13:1', 'test-integration-grad.R:2:1', 'test-integration-gradbatch-multi.R:11:3', 'test-integration-iov.R:5:1', 'test-integration-irmc.R:2:1', 'test-integration-model-constant.R:8:1', 'test-integration-model-source.R:55:3', 'test-integration-model-source.R:71:3', 'test-integration-model-source.R:83:3', 'test-integration-model-source.R:96:3', 'test-integration-model-source.R:109:3', 'test-integration-model-source.R:121:3', 'test-integration-multi-output.R:8:1', 'test-integration-nll.R:2:1', 'test-integration-ordinal.R:72:3', 'test-integration-ordinal.R:82:3', 'test-integration-ordinal.R:90:3', 'test-integration-ordinal.R:128:3', 'test-integration-ordinal.R:167:3', 'test-integration-ordinal.R:179:3', 'test-integration-ordinal.R:214:3', 'test-integration-ordinal.R:238:3', 'test-integration-parallel.R:10:3', 'test-integration-parallel.R:37:3', 'test-integration-parallel.R:74:3', 'test-integration-pipeline.R:25:3', 'test-integration-pipeline.R:33:3', 'test-integration-pipeline.R:43:3', 'test-integration-pipeline.R:53:3', 'test-integration-pipeline.R:63:3', 'test-integration-pipeline.R:73:3', 'test-integration-pipeline.R:81:3', 'test-integration-pipeline.R:92:3', 'test-integration-pipeline.R:102:3', 'test-integration-pipeline.R:122:3', 'test-integration-pipeline.R:129:3', 'test-integration-pipeline.R:143:3', 'test-integration-pipeline.R:156:3', 'test-integration-pipeline.R:170:3', 'test-integration-pipeline.R:195:3', 'test-integration-pipeline.R:205:3', 'test-integration-pipeline.R:237:3', 'test-integration-pipeline.R:242:3', 'test-integration-pipeline.R:252:3', 'test-integration-pipeline.R:260:3', 'test-integration-pipeline.R:267:3', 'test-integration-pipeline.R:276:3', 'test-integration-pipeline.R:281:3', 'test-integration-plot.R:3:1', 'test-integration-projected-convergence.R:75:3', 'test-integration-projected-convergence.R:88:3', 'test-integration-projected-convergence.R:125:3', 'test-integration-projected-convergence.R:145:3', 'test-integration-projected-convergence.R:160:3', 'test-integration-projected-convergence.R:178:3', 'test-integration-projected-convergence.R:212:3', 'test-integration-realdata.R:90:3', 'test-integration-realdata.R:99:3', 'test-integration-realdata.R:110:3', 'test-integration-resid-moments.R:26:1', 'test-integration-rng.R:19:3', 'test-integration-roundtrip.R:35:3', 'test-integration-roundtrip.R:84:3', 'test-integration-sandwich.R:2:1', 'test-integration-sens-columns.R:14:1', 'test-integration-sens2.R:8:3', 'test-integration-sens2.R:19:3', 'test-integration-sens2.R:36:3', 'test-integration-sens2.R:56:3', 'test-integration-sens2.R:86:3', 'test-integration-sens2.R:101:3', 'test-integration-sens2.R:125:5', 'test-integration-sens2.R:167:5', 'test-integration-shi21.R:11:1', 'test-integration-simulate.R:2:1', 'test-integration-t-errmodel.R:24:1', 'test-integration-tbs-exact.R:2:1', 'test-integration-theta-sens.R:9:1', 'test-integration-worker-load.R:9:1', 'test-integration-xsession-cache.R:16:1', 'test-restart-output-var.R:24:3', 'test-sens-ui.R:107:3', 'test-sens-ui.R:139:3', 'test-adfweight.R:570:3', 'test-adfweight.R:608:3', 'test-study-api.R:135:3', 'test-study-api.R:167:3', 'test-study-api.R:191:3', 'test-study-api.R:367:3', 'test-study-api.R:398:3', 'test-study-api.R:420:3', 'test-study-api.R:446:3', 'test-study-api.R:467:3' [ FAIL 0 | WARN 0 | SKIP 169 | PASS 3539 ] > > proc.time() user system elapsed 25.00 1.12 133.06