Package: babelmixr2 Check: tests New result: ERROR Running ‘spelling.R’ [0s/0s] Running ‘testthat.R’ [119s/119s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(babelmixr2) Loading required package: nlmixr2 Loading required package: nlmixr2data > > test_check("babelmixr2") i mu2 item: Rx_pow_di(WT, 2) i writing monolix files i done i run Monolix manually and rerun nlmixr() i mu2 item: Rx_pow_di(WT, 2) i leaving alone monolix files because 'monolixTest-monolix.txt' is present > loading into symengine environment... > pruning branches (`if`/`else`) of full model... v done > loading into symengine environment... > pruning branches (`if`/`else`) of full model... v done > finding duplicate expressions in EBE model... [====|====|====|====|====|====|====|====|====|====] 0:00:00 > optimizing duplicate expressions in EBE model... [====|====|====|====|====|====|====|====|====|====] 0:00:00 > compiling EBE model... using C compiler: ‘gcc-14 (Debian 14.2.0-19) 14.2.0’ v done > Calculating residuals/tables v done > compress origData in nlmixr2 object, save 1336 > compress parHistData in nlmixr2 object, save 1624 Error : nonmem minimization not successful > loading into symengine environment... > pruning branches (`if`/`else`) of full model... v done > calculate jacobian > calculate sensitivities > calculate d(f)/d(eta) > finding duplicate expressions in inner model... > optimizing duplicate expressions in inner model... > finding duplicate expressions in EBE model... > optimizing duplicate expressions in EBE model... > compiling inner model... using C compiler: ‘gcc-14 (Debian 14.2.0-19) 14.2.0’ v done > finding duplicate expressions in FD model... [====|====|====|====|====|====|====|====|====|====] 0:00:00 > optimizing duplicate expressions in FD model... [====|====|====|====|====|====|====|====|====|====] 0:00:00 > compiling EBE model... using C compiler: ‘gcc-14 (Debian 14.2.0-19) 14.2.0’ v done > compiling events FD model... using C compiler: ‘gcc-14 (Debian 14.2.0-19) 14.2.0’ v done [====|====|====|====|====|====|====|====|====|====] 0:00:06 > compress origData in nlmixr2 object, save 27560 Updated original fit object f warning: eig_sym(): given matrix is not symmetric > loading into symengine environment... > pruning branches (`if`/`else`) of full model... v done i writing nonmem files i done i only exported NONMEM control stream/data > loading into symengine environment... > pruning branches (`if`/`else`) of full model... v done i writing nonmem files i done > loading into symengine environment... > pruning branches (`if`/`else`) of full model... v done > loading into symengine environment... > pruning branches (`if`/`else`) of full model... v done > loading into symengine environment... > pruning branches (`if`/`else`) of full model... v done i mu2 item: Rx_pow_di(WT, 2) > loading into symengine environment... > pruning branches (`if`/`else`) of full model... v done i writing nonmem files i done i only exported NONMEM control stream/data i mu2 item: Rx_pow_di(WT, 2) > loading into symengine environment... > pruning branches (`if`/`else`) of full model... v done i only exported NONMEM control stream/data Error in pknca_unit_conversion(result = result, units = data$units, allow_partial_missing_units = data$options$allow_partial_missing_units) : Units are provided for some but not all parameters; missing for: aucinf.obs, auclast, aumclast, cl.last, clast.obs, clast.pred, cmax, cmax.dn, half.life, lambda.z, lambda.z.time.first, mrt.last, tlast, tmax, vss.last This error can be converted to a warning using `PKNCA.options(allow_partial_missing_units = TRUE)` Error in pknca_unit_conversion(result = result, units = data$units, allow_partial_missing_units = data$options$allow_partial_missing_units) : Units are provided for some but not all parameters; missing for: aucinf.obs, auclast, aumclast, cl.last, clast.obs, clast.pred, cmax, cmax.dn, half.life, lambda.z, lambda.z.time.first, mrt.last, tlast, tmax, vss.last This error can be converted to a warning using `PKNCA.options(allow_partial_missing_units = TRUE)` [ FAIL 2 | WARN 19 | SKIP 7 | PASS 272 ] ══ Skipped tests (7) ═══════════════════════════════════════════════════════════ • On CRAN (7): 'test-as-nlmixr2.R:8:3', 'test-as-nlmixr2.R:66:3', 'test-bioavil-works.R:2:3', 'test-convert.R:2:3', 'test-convert.R:35:3', 'test-convert.R:215:3', 'test-convert.R:229:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-pknca.R:20:3'): est='pknca' ──────────────────────────────────── Error: Units are provided for some but not all parameters; missing for: aucinf.obs, auclast, aumclast, cl.last, clast.obs, clast.pred, cmax, cmax.dn, half.life, lambda.z, lambda.z.time.first, mrt.last, tlast, tmax, vss.last This error can be converted to a warning using `PKNCA.options(allow_partial_missing_units = TRUE)` Backtrace: ▆ 1. ├─base::suppressMessages(...) at test-pknca.R:20:3 2. │ └─base::withCallingHandlers(...) 3. ├─testthat::expect_s3_class(...) 4. │ └─testthat::quasi_label(enquo(object), arg = "object") 5. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 6. ├─nlmixr2est::nlmixr(...) 7. └─nlmixr2est:::nlmixr2.function(...) 8. └─nlmixr2est:::nlmixr2Est0(.env) ── Error ('test-pknca.R:145:3'): dvParam ─────────────────────────────────────── Error: Units are provided for some but not all parameters; missing for: aucinf.obs, auclast, aumclast, cl.last, clast.obs, clast.pred, cmax, cmax.dn, half.life, lambda.z, lambda.z.time.first, mrt.last, tlast, tmax, vss.last This error can be converted to a warning using `PKNCA.options(allow_partial_missing_units = TRUE)` Backtrace: ▆ 1. ├─base::suppressMessages(...) at test-pknca.R:145:3 2. │ └─base::withCallingHandlers(...) 3. ├─testthat::expect_s3_class(...) 4. │ └─testthat::quasi_label(enquo(object), arg = "object") 5. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 6. ├─nlmixr2est::nlmixr(...) 7. └─nlmixr2est:::nlmixr2.function(...) 8. └─nlmixr2est:::nlmixr2Est0(.env) [ FAIL 2 | WARN 19 | SKIP 7 | PASS 272 ] Error: Test failures Execution halted