Last updated on 2025-10-10 09:51:06 CEST.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| babelmixr2 | 2 | 3 | 8 |
| dparser | 13 | ||
| lbfgsb3c | 13 | ||
| lotri | 13 | ||
| monolix2rx | 2 | 11 | |
| n1qn1 | 13 | ||
| nlmixr2 | 13 | ||
| nlmixr2data | 13 | ||
| nlmixr2est | 2 | 11 | |
| nlmixr2extra | 13 | ||
| nlmixr2plot | 13 | ||
| nonmem2rx | 3 | 10 | |
| PreciseSums | 13 | ||
| rxode2 | 3 | 10 | |
| rxode2ll | 2 | 11 |
Current CRAN status: ERROR: 2, NOTE: 3, OK: 8
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
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: NOTE: 2, OK: 11
Version: 0.0.6
Check: installed package size
Result: NOTE
installed size is 6.0Mb
sub-directories of 1Mb or more:
libs 3.7Mb
theo 1.1Mb
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: NOTE: 2, OK: 11
Version: 4.1.1
Check: installed package size
Result: NOTE
installed size is 22.8Mb
sub-directories of 1Mb or more:
R 2.1Mb
libs 19.6Mb
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: NOTE: 3, OK: 10
Version: 0.1.8
Check: installed package size
Result: NOTE
installed size is 9.3Mb
sub-directories of 1Mb or more:
libs 5.3Mb
mods 3.3Mb
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64
Current CRAN status: OK: 13
Current CRAN status: NOTE: 3, OK: 10
Version: 4.1.1
Check: installed package size
Result: NOTE
installed size is 11.3Mb
sub-directories of 1Mb or more:
R 2.1Mb
include 1.3Mb
libs 6.0Mb
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64
Current CRAN status: NOTE: 2, OK: 11
Version: 2.0.13
Check: installed package size
Result: NOTE
installed size is 13.9Mb
sub-directories of 1Mb or more:
libs 13.8Mb
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64