Last updated on 2025-10-10 03:50:59 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.1.9 | 71.02 | 428.98 | 500.00 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.1.9 | 48.02 | 285.36 | 333.38 | OK | |
| r-devel-linux-x86_64-fedora-clang | 0.1.9 | 872.25 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 0.1.9 | 852.83 | ERROR | |||
| r-devel-windows-x86_64 | 0.1.9 | 84.00 | 557.00 | 641.00 | OK | |
| r-patched-linux-x86_64 | 0.1.9 | 67.87 | 404.14 | 472.01 | OK | |
| r-release-linux-x86_64 | 0.1.9 | 67.42 | 407.63 | 475.05 | OK | |
| r-release-macos-arm64 | 0.1.9 | 144.00 | OK | |||
| r-release-macos-x86_64 | 0.1.9 | 342.00 | OK | |||
| r-release-windows-x86_64 | 0.1.9 | 83.00 | 551.00 | 634.00 | OK | |
| r-oldrel-macos-arm64 | 0.1.9 | 147.00 | NOTE | |||
| r-oldrel-macos-x86_64 | 0.1.9 | 321.00 | NOTE | |||
| r-oldrel-windows-x86_64 | 0.1.9 | 102.00 | 705.00 | 807.00 | NOTE |
Version: 0.1.9
Check: tests
Result: ERROR
Running ‘spelling.R’
Running ‘testthat.R’ [8m/16m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(babelmixr2)
>
> test_check("babelmixr2")
i parameter labels from comments will be replaced by 'label()'
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: ‘clang version 21.1.3’
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: ‘clang version 21.1.3’
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: ‘clang version 21.1.3’
v done
> compiling events FD model...
using C compiler: ‘clang version 21.1.3’
v done
[====|====|====|====|====|====|====|====|====|====] 0:00:20
> 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 bblDatToPknca(model = env$ui, data = rawData, rxControl = rxControl) :
no dosing rows (EVID = 1 or 4) detected
Error : no rows in event table or input data
Error in nlmixr2Est(env, ...) :
Could not detect DV assignment for unit conversion
i volumeu detected from amtu and dvu as: mol*mL/ng
[ FAIL 8 | WARN 6 | SKIP 9 | PASS 280 ]
══ Skipped tests (9) ═══════════════════════════════════════════════════════════
• On CRAN (9): 'test-as-nlmixr2.R:8:3', 'test-as-nlmixr2.R:66:3',
'test-bioavil-works.R:2:3', 'test-convert.R:2:3', 'test-convert.R:35:3',
'test-convert.R:215:3', 'test-convert.R:229:3', 'test-fmeMcmc.R:4:3',
'test-psuedoOptim.R:3:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-units.R:5:3'): simplifyUnit ──────────────────────────────────
simplifyUnit("", "kg") (`actual`) not equal to "1/kg" (`expected`).
`actual`: "fraction/kg"
`expected`: "1/kg"
── Failure ('test-units.R:7:3'): simplifyUnit ──────────────────────────────────
simplifyUnit(NA, "kg") (`actual`) not equal to "1/kg" (`expected`).
`actual`: "fraction/kg"
`expected`: "1/kg"
── Failure ('test-units.R:9:3'): simplifyUnit ──────────────────────────────────
simplifyUnit("", "kg^2") (`actual`) not equal to "1/(kg*kg)" (`expected`).
`actual`: "fraction/(kg*kg)"
`expected`: "1/(kg*kg)"
── Failure ('test-units.R:15:3'): simplifyUnit ─────────────────────────────────
simplifyUnit(denominator = "mg") (`actual`) not equal to "1/mg" (`expected`).
`actual`: "fraction/mg"
`expected`: "1/mg"
── Failure ('test-units.R:74:3'): modelUnitConversion ──────────────────────────
`conversion` (`actual`) not equal to list(...) (`expected`).
`actual$clearanceu`: "mL/(kg*h)"
`expected$clearanceu`: "mL/(h*kg)"
── Failure ('test-units.R:91:3'): modelUnitConversion ──────────────────────────
`conversion` (`actual`) not equal to list(...) (`expected`).
`actual$clearanceu`: "mL/(kg*h)"
`expected$clearanceu`: "mL/(h*kg)"
`actual$cmtu`: "mg*kg/(g*mL)"
`expected$cmtu`: "kg*mg/(g*mL)"
── Failure ('test-units.R:104:3'): modelUnitConversion ─────────────────────────
`... <- NULL` did not throw the expected message.
── Failure ('test-units.R:109:3'): modelUnitConversion ─────────────────────────
`conversion` (`actual`) not equal to list(...) (`expected`).
`actual$clearanceu`: "mol*mL/(ng*h)"
`expected$clearanceu`: "mL*mol/(h*ng)"
`actual$volumeu`: "mol*mL/ng"
`expected$volumeu`: "mL*mol/ng"
[ FAIL 8 | WARN 6 | SKIP 9 | PASS 280 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.1.9
Check: tests
Result: ERROR
Running ‘spelling.R’
Running ‘testthat.R’ [9m/21m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(babelmixr2)
>
> test_check("babelmixr2")
i parameter labels from comments will be replaced by 'label()'
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 (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)’
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 (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)’
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 (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)’
v done
> compiling events FD model...
using C compiler: ‘gcc (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)’
v done
[====|====|====|====|====|====|====|====|====|====] 0:00:21
> 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 bblDatToPknca(model = env$ui, data = rawData, rxControl = rxControl) :
no dosing rows (EVID = 1 or 4) detected
Error : no rows in event table or input data
Error in nlmixr2Est(env, ...) :
Could not detect DV assignment for unit conversion
i volumeu detected from amtu and dvu as: mol*mL/ng
[ FAIL 8 | WARN 6 | SKIP 9 | PASS 280 ]
══ Skipped tests (9) ═══════════════════════════════════════════════════════════
• On CRAN (9): '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', 'test-fmeMcmc.R:4:3',
'test-psuedoOptim.R:3:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-units.R:5:3'): simplifyUnit ──────────────────────────────────
simplifyUnit("", "kg") (`actual`) not equal to "1/kg" (`expected`).
`actual`: "fraction/kg"
`expected`: "1/kg"
── Failure ('test-units.R:7:3'): simplifyUnit ──────────────────────────────────
simplifyUnit(NA, "kg") (`actual`) not equal to "1/kg" (`expected`).
`actual`: "fraction/kg"
`expected`: "1/kg"
── Failure ('test-units.R:9:3'): simplifyUnit ──────────────────────────────────
simplifyUnit("", "kg^2") (`actual`) not equal to "1/(kg*kg)" (`expected`).
`actual`: "fraction/(kg*kg)"
`expected`: "1/(kg*kg)"
── Failure ('test-units.R:15:3'): simplifyUnit ─────────────────────────────────
simplifyUnit(denominator = "mg") (`actual`) not equal to "1/mg" (`expected`).
`actual`: "fraction/mg"
`expected`: "1/mg"
── Failure ('test-units.R:74:3'): modelUnitConversion ──────────────────────────
`conversion` (`actual`) not equal to list(...) (`expected`).
`actual$clearanceu`: "mL/(kg*h)"
`expected$clearanceu`: "mL/(h*kg)"
── Failure ('test-units.R:91:3'): modelUnitConversion ──────────────────────────
`conversion` (`actual`) not equal to list(...) (`expected`).
`actual$clearanceu`: "mL/(kg*h)"
`expected$clearanceu`: "mL/(h*kg)"
`actual$cmtu`: "mg*kg/(g*mL)"
`expected$cmtu`: "kg*mg/(g*mL)"
── Failure ('test-units.R:104:3'): modelUnitConversion ─────────────────────────
`... <- NULL` did not throw the expected message.
── Failure ('test-units.R:109:3'): modelUnitConversion ─────────────────────────
`conversion` (`actual`) not equal to list(...) (`expected`).
`actual$clearanceu`: "mol*mL/(ng*h)"
`expected$clearanceu`: "mL*mol/(h*ng)"
`actual$volumeu`: "mol*mL/ng"
`expected$volumeu`: "mL*mol/ng"
[ FAIL 8 | WARN 6 | SKIP 9 | PASS 280 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.1.9
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘lixoftConnectors’
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64