Last updated on 2024-12-18 19:49:44 CET.
| Package | ERROR | OK |
|---|---|---|
| campsis | 1 | 12 |
| campsismod | 13 |
Current CRAN status: ERROR: 1, OK: 12
Version: 1.5.5
Check: tests
Result: ERROR
Running ‘testthat.R’ [214s/326s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> Sys.setenv("R_TESTS" = "")
> library(testthat)
> library(campsis)
Loading required package: campsismod
Attaching package: 'campsismod'
The following object is masked from 'package:utils':
find
The following objects are masked from 'package:base':
Position, as.data.frame, replace, sort, toString, write
Attaching package: 'campsis'
The following object is masked from 'package:stats':
simulate
The following objects are masked from 'package:base':
months, sample
> test_check("campsis")
Model:
KA=THETA_KA*exp(ETA_KA);
CL=THETA_CL*exp(ETA_CL);
V=THETA_V*exp(ETA_V)*BW/70;
S2=V;
ARM=ARM;
EVENT_RELATED=EVENT_RELATED;
d/dt(A_DEPOT)=-KA*A_DEPOT;
d/dt(A_CENTRAL)=-CL*A_CENTRAL/V+KA*A_DEPOT;
d/dt(A_OUTPUT)=CL*A_CENTRAL/V;
F=A_CENTRAL/S2;
CP=F;
OBS_CP=CP*(EPS_PROP+1);
Y=OBS_CP;
---:: stderr ::---------------------------------------------
------------------------------------------------------------
---:: stderr ::---------------------------------------------
------------------------------------------------------------
---:: stderr ::---------------------------------------------
------------------------------------------------------------
[ FAIL 5 | WARN 0 | SKIP 29 | PASS 578 ]
══ Skipped tests (29) ══════════════════════════════════════════════════════════
• On CRAN (3): 'testDefaultPlots.R:46:7', 'testDefaultPlots.R:73:7',
'testDefaultPlots.R:115:7'
• empty test (26): 'testSimulateEvents.R:8:1', 'testSimulateEvents.R:32:1',
'testSimulateEvents.R:55:1', 'testSimulateEvents.R:79:1',
'testSimulateEvents.R:112:1', 'testSimulateEventsLogic.R:8:1',
'testSimulateEventsLogic.R:41:1', 'testSimulateEventsLogic.R:79:1',
'testSimulateEventsLogic.R:125:1', 'testSimulateEventsLogic.R:148:1',
'testSimulateIOV.R:8:1', 'testSimulateIOV.R:47:1', 'testSimulateIOV.R:79:1',
'testSimulateIOV.R:129:1', 'testSimulateIOV.R:193:1',
'testSimulateIOV.R:241:1', 'testSimulateInfusion.R:8:1',
'testSimulateNocbLocf.R:8:1', 'testSimulateNocbLocf.R:49:1',
'testSimulateNocbLocf.R:89:1', 'testSimulateReplicates.R:9:1',
'testSimulateReplicates.R:26:1', 'testSimulateReplicates.R:50:1',
'testSimulateReplicates.R:103:1', 'testSimulateReplicates.R:139:1',
'testSimulateTTEModels.R:7:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('testSimulateScenarios.R:79:3'): Simulate scenarios - make few changes on model (rxode2/mrgsolve) ──
<purrr_error_indexed/rlang_error/error/condition>
Error in `(function (.x, .y, .f, ..., .progress = FALSE)
{
map2_("list", .x, .y, .f, ..., .progress = .progress)
})(.x = list(new("campsis_model", model = new("code_records",
list = list(new("main_record", comment = NA_character_, statements = new("model_statements",
list = list(new("equation", lhs = "KA", rhs = "THETA_KA*exp(ETA_KA)",
comment = NA_character_), new("equation", lhs = "CL",
rhs = "THETA_CL*exp(ETA_CL)", comment = NA_character_),
new("equation", lhs = "V2", rhs = "THETA_V2*exp(ETA_V2)",
comment = NA_character_), new("equation", lhs = "V3",
rhs = "THETA_V3*exp(ETA_V3)", comment = NA_character_),
new("equation", lhs = "Q", rhs = "THETA_Q*exp(ETA_Q)",
comment = NA_character_), new("equation", lhs = "S2",
rhs = "V2", comment = NA_character_)), type = "model_statement")),
new("ode_record", comment = NA_character_, statements = new("model_statements",
list = list(new("ode", lhs = "A_DEPOT", rhs = "-KA*A_DEPOT",
comment = NA_character_), new("ode", lhs = "A_CENTRAL",
rhs = "KA*A_DEPOT + Q*A_PERIPHERAL/V3 + (-CL/V2 - Q/V2)*A_CENTRAL",
comment = NA_character_), new("ode", lhs = "A_PERIPHERAL",
rhs = "-Q*A_PERIPHERAL/V3 + Q*A_CENTRAL/V2",
comment = NA_character_), new("ode", lhs = "A_OUTPUT",
rhs = "CL*A_CENTRAL/V2", comment = NA_character_),
new("equation", lhs = "F", rhs = "A_CENTRAL/S2",
comment = NA_character_)), type = "model_statement")),
new("error_record", comment = NA_character_, statements = new("model_statements",
list = list(new("equation", lhs = "CP", rhs = "F",
comment = NA_character_), new("equation", lhs = "OBS_CP",
rhs = "CP*(EPS_PROP + 1)", comment = NA_character_),
new("equation", lhs = "Y", rhs = "OBS_CP", comment = NA_character_)),
type = "model_statement"))), type = "code_record"),
parameters = new("parameters", varcov = structure(numeric(0), dim = c(0L,
0L)), list = list(new("theta", unit = NA_character_, name = "KA",
index = 1L, value = 1, fix = FALSE, label = NA_character_,
comment = NA_character_), new("theta", unit = NA_character_,
name = "CL", index = 2L, value = 5, fix = FALSE, label = NA_character_,
comment = NA_character_), new("theta", unit = NA_character_,
name = "V2", index = 3L, value = 80, fix = FALSE, label = NA_character_,
comment = NA_character_), new("theta", unit = NA_character_,
name = "V3", index = 4L, value = 20, fix = FALSE, label = NA_character_,
comment = NA_character_), new("theta", unit = NA_character_,
name = "Q", index = 5L, value = 4, fix = FALSE, label = NA_character_,
comment = NA_character_), new("omega", same = NA, index2 = 1L,
type = "var", name = "KA", index = 1L, value = 0.025,
fix = FALSE, label = NA_character_, comment = NA_character_),
new("omega", same = NA, index2 = 2L, type = "var", name = "CL",
index = 2L, value = 0.025, fix = FALSE, label = NA_character_,
comment = NA_character_), new("omega", same = NA,
index2 = 3L, type = "var", name = "V2", index = 3L,
value = 0.025, fix = FALSE, label = NA_character_,
comment = NA_character_), new("omega", same = NA,
index2 = 4L, type = "var", name = "V3", index = 4L,
value = 0.025, fix = FALSE, label = NA_character_,
comment = NA_character_), new("omega", same = NA,
index2 = 5L, type = "var", name = "Q", index = 5L,
value = 0.025, fix = FALSE, label = NA_character_,
comment = NA_character_), new("sigma", index2 = 1L,
type = "var", name = "PROP", index = 1L, value = 0.025,
fix = FALSE, label = NA_character_, comment = NA_character_)),
type = "parameter"), compartments = new("compartments",
properties = new("compartment_properties", list = list(),
type = "compartment_property"), list = list(new("compartment",
name = "DEPOT", index = 1L), new("compartment", name = "CENTRAL",
index = 2L), new("compartment", name = "PERIPHERAL",
index = 3L), new("compartment", name = "OUTPUT",
index = 4L)), type = "compartment"))), .y = 1L, .f = function (...)
{
NULL
NULL
...furrr_out <- ...furrr_fn(...)
...furrr_out
})`: ℹ In index: 1.
Caused by error:
ℹ In index: 1.
Caused by error in `rxCompile.rxModelVars()`:
! something went wrong in compilation
── Failure ('testSimulateTimeVaryingCovariates.R:24:3'): Body weight as a true time varying covariate (rxode2/mrgsolve) ──
`results1` not equal to `results2`.
Component "CP": Mean relative difference: 0.2275966
Backtrace:
▆
1. └─global outputRegressionTest(results, output = "CP", filename = regFilename)
2. └─testthat::expect_equal(results1, results2)
── Failure ('testSimulateTimeVaryingCovariates.R:24:3'): Body weight as a true time varying covariate (rxode2/mrgsolve) ──
`results1` not equal to `results2`.
Component "CP": Mean relative difference: 0.2275966
Backtrace:
▆
1. └─global outputRegressionTest(results, output = "CP", filename = regFilename)
2. └─testthat::expect_equal(results1, results2)
── Failure ('testSimulateWeirdCases.R:135:3'): Model advan1_trans1 must compile properly with mrgsolve v1.5.2 on Windows (rxode2/mrgsolve) ──
`results1` not equal to `results2`.
Component "CONC": Mean relative difference: 0.247621
Backtrace:
▆
1. └─global outputRegressionTest(results, output = "CONC", filename = regFilename)
2. └─testthat::expect_equal(results1, results2)
── Failure ('testSimulateWeirdCases.R:135:3'): Model advan1_trans1 must compile properly with mrgsolve v1.5.2 on Windows (rxode2/mrgsolve) ──
`results1` not equal to `results2`.
Component "CONC": Mean relative difference: 0.247621
Backtrace:
▆
1. └─global outputRegressionTest(results, output = "CONC", filename = regFilename)
2. └─testthat::expect_equal(results1, results2)
[ FAIL 5 | WARN 0 | SKIP 29 | PASS 578 ]
Deleting unused snapshots:
• testDefaultPlots/scatterplot-colour-scenario.svg
• testDefaultPlots/shadedplot-colour-arm-strat-wt.svg
• testDefaultPlots/shadedplot-colour-arm-wt-strat-wt.svg
• testDefaultPlots/spaghettiplot-colour-scenario.svg
• testSimulateReplicates/vpc-specified-outfun.svg
Error: Test failures
Execution halted
Error in unserialize(node$con) : error reading from connection
Calls: workRSOCK ... doTryCatch -> recvData -> recvData.SOCK0nodeError in unserialize(node$con) : error reading from connection
Calls: workRSOCK ... doTryCatch -> recvData -> recvData.SOCK0nodeError in unserialize(node$con) : error reading from connection
Calls: workRSOCK ... doTryCatch -> recvData -> recvData.SOCK0node -> unserialize
-> unserialize
-> unserialize
Execution halted
Execution halted
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Current CRAN status: OK: 13