run_amd() stops at covsearch on cluster

[gustafwellhagen]

Loading required package: altair
amd1 2025-02-05 INFO Starting tool amd
23:15:24
amd1 2025-02-05 WARNING IOVsearch will be skipped because
23:15:26 occasion is None.
amd1 2025-02-05 WARNING Allometry will be skipped because
23:15:26 allometric_variable is None and
could not be inferred through
.datainfo via "body weight"
descriptor.
amd1/modelfit 2025-02-05 INFO Dispatching workflow in <Local
23:15:27 directory context at
/crex/proj/pmgroup_active_storage/…
<Client:
'inproc://172.18.9.169/2920/1'
processes=1 threads=1, memory=6.25
GiB>
amd1/modelfit 2025-02-05 INFO End dispatch
23:15:39
amd1/modelsearch 2025-02-05 INFO Dispatching workflow in <Local
23:15:39 directory context at
/crex/proj/pmgroup_active_storage/…
<Client:
'inproc://172.18.9.169/2920/10'
processes=1 threads=1, memory=6.25
GiB>
amd1/modelsearch 2025-02-05 INFO Starting tool modelsearch
23:15:39
amd1/modelsearch 2025-02-05 INFO Input model OFV: -1779.317
23:15:39
amd1/modelsearch 2025-02-05 INFO Starting algorithm
23:15:39 'reduced_stepwise'
amd1/modelsearch/@mode2025-02-05 WARNING Expected result files do not exist,
lsearch_run16 23:27:12 copying everything
amd1/modelsearch/@mode2025-02-06 WARNING Expected result files do not exist,
lsearch_run1 00:51:52 copying everything
amd1/modelsearch/@mode2025-02-06 WARNING Expected result files do not exist,
lsearch_run11 02:05:01 copying everything
amd1/modelsearch 2025-02-06 INFO Finished algorithm
03:17:46 'reduced_stepwise'. Best model:
modelsearch_run2, OFV: -1902.276
amd1/modelsearch 2025-02-06 INFO Finishing tool modelsearch
03:17:46
amd1/modelsearch 2025-02-06 INFO End dispatch
03:17:46
amd1/structural_retrie2025-02-06 INFO Dispatching workflow in <Local
s 03:18:01 directory context at
/crex/proj/pmgroup_active_storage/…
<Client:
'inproc://172.18.9.169/2920/19'
processes=1 threads=1, memory=6.25
GiB>
amd1/structural_retrie2025-02-06 INFO End dispatch
s 03:24:33
amd1/iivsearch 2025-02-06 INFO Dispatching workflow in <Local
03:24:41 directory context at
/crex/proj/pmgroup_active_storage/…
<Client:
'inproc://172.18.9.169/2920/28'
processes=1 threads=1, memory=6.25
GiB>
amd1/iivsearch 2025-02-06 INFO Starting tool iivsearch
03:24:41
amd1/iivsearch 2025-02-06 INFO Input model OFV: -1903.546
03:24:41
amd1/iivsearch 2025-02-06 INFO Creating base model
03:24:41
amd1/iivsearch 2025-02-06 INFO Starting step
03:24:41 'td_exhaustive_no_of_etas'
amd1/iivsearch 2025-02-06 INFO Finished step
03:25:43 'td_exhaustive_no_of_etas'. Best
model: [CL,VC,D1], OFV: -1910.377
amd1/iivsearch 2025-02-06 INFO Starting step
03:25:43 'td_exhaustive_block_structure'
amd1/iivsearch 2025-02-06 INFO Finished step
03:27:44 'td_exhaustive_block_structure'.
Best model: [D1]+[CL,VC], OFV:
-1903.525
amd1/iivsearch 2025-02-06 WARNING Worse bic in final model
03:27:44 iivsearch_run5 than input,
selecting input model
amd1/iivsearch 2025-02-06 INFO Finishing tool iivsearch
03:27:44
amd1/iivsearch 2025-02-06 INFO End dispatch
03:27:44
amd1/iivsearch_retries2025-02-06 INFO Dispatching workflow in <Local
03:27:52 directory context at
/crex/proj/pmgroup_active_storage/…
<Client:
'inproc://172.18.9.169/2920/37'
processes=1 threads=1, memory=6.25
GiB>
amd1/iivsearch_retries2025-02-06 INFO End dispatch
03:30:23
amd1/ruvsearch 2025-02-06 INFO Dispatching workflow in <Local
03:30:31 directory context at
/crex/proj/pmgroup_active_storage/…
<Client:
'inproc://172.18.9.169/2920/46'
processes=1 threads=1, memory=6.25
GiB>
amd1/ruvsearch 2025-02-06 INFO Starting tool ruvsearch
03:30:31
amd1/ruvsearch 2025-02-06 INFO Input model OFV: -1903.546
03:30:31
amd1/ruvsearch 2025-02-06 INFO Starting iteration 1
03:30:31
amd1/ruvsearch 2025-02-06 INFO Best model after iteration OFV:
03:31:11 -2058.102
amd1/ruvsearch 2025-02-06 INFO Starting iteration 2
03:31:11
amd1/ruvsearch 2025-02-06 INFO Best model after iteration OFV:
03:31:41 -2058.102
amd1/ruvsearch 2025-02-06 INFO Finishing tool ruvsearch
03:31:41
amd1/ruvsearch 2025-02-06 INFO End dispatch
03:31:41
amd1/residual_retries 2025-02-06 INFO Dispatching workflow in <Local
03:31:49 directory context at
/crex/proj/pmgroup_active_storage/…
<Client:
'inproc://172.18.9.169/2920/55'
processes=1 threads=1, memory=6.25
GiB>
amd1/residual_retries 2025-02-06 INFO End dispatch
03:33:56
amd1/covsearch_explora2025-02-06 INFO Dispatching workflow in <Local
tory 03:34:08 directory context at
/crex/proj/pmgroup_active_storage/…
<Client:
'inproc://172.18.9.169/2920/64'
processes=1 threads=1, memory=6.25
GiB>
amd1/covsearch_explora2025-02-06 INFO Starting tool covsearch
tory 03:34:08
2025-02-06 03:36:44,611 - distributed.worker - ERROR - Compute Failed
Key: CL-run4-89869d6b-6005-4391-b21b-f3b2e002ef3b
State: executing
Task: <Task 'CL-run4-89869d6b-6005-4391-b21b-f3b2e002ef3b' task(...)>
Exception: "ValueError('Symbol theta1 is not defined')"
Traceback: ' File "/domus/h1/gustafw/.virtualenvs/r-reticulate/lib/python3.11/site-packages/pharmpy/tools/covsearch/tool.py", line 739, in task_add_covariate_effect\n model_with_added_effect = func(model_with_added_effect, allow_nested=True)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File "/domus/h1/gustafw/.virtualenvs/r-reticulate/lib/python3.11/site-packages/pharmpy/modeling/covariate_effect.py", line 484, in add_covariate_effect\n model = model.replace(parameters=pset, statements=sset)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File "/domus/h1/gustafw/.virtualenvs/r-reticulate/lib/python3.11/site-packages/pharmpy/model/model.py", line 353, in replace\n statements = Model._canonicalize_statements(\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File "/domus/h1/gustafw/.virtualenvs/r-reticulate/lib/python3.11/site-packages/pharmpy/model/model.py", line 222, in _canonicalize_statements\n raise ValueError(f'Symbol {symb} is not defined')\n'

2025-02-06 03:36:44,622 - distributed.worker - ERROR - Compute Failed
Key: backward-search-create_modelentry-forward-search-init-store_input_model-results
State: long-running
Task: <Task 'backward-search-create_modelentry-forward-search-init-store_input_model-results' task_results(...)>
Exception: "ValueError('Symbol theta1 is not defined')"
Traceback: ' File "/domus/h1/gustafw/.virtualenvs/r-reticulate/lib/python3.11/site-packages/pharmpy/tools/covsearch/tool.py", line 425, in task_greedy_forward_search\n return _greedy_search(\n ^^^^^^^^^^^^^^^\n File "/domus/h1/gustafw/.virtualenvs/r-reticulate/lib/python3.11/site-packages/pharmpy/tools/covsearch/tool.py", line 513, in _greedy_search\n nonsignificant_effects, all_candidates_so_far, best_candidate_so_far = perform_step_procedure(\n ^^^^^^^^^^^^^^^^^^^^^^^\n File "/domus/h1/gustafw/.virtualenvs/r-reticulate/lib/python3.11/site-packages/pharmpy/tools/covsearch/tool.py", line 593, in perform_step_procedure\n new_candidates = handle_effects(\n ^^^^^^^^^^^^^^^\n File "/domus/h1/gustafw/.virtualenvs/r-reticulate/lib/python3.11/site-packages/pharmpy/tools/covsearch/tool.py", line 419, in handle_effects\n new_candidate_modelentries = context.call_workflow(wf, f'{NAME_WF}-effects_addition-{step}')\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File "/domus/h1/gustafw/.virtualenvs/r-reticulate/lib/python3.11/site-packages/pharmpy/workflows/contexts/baseclass.py", line 252, in call_workflow\n res = call_workflow(workflow, unique_name, self)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File "/domus/h1/gustafw/.virtualenvs/r-reticulate/lib/python3.11/site-packages/pharmpy/workflows/dispatchers/local_dask/call.py", line 41, in call_workflow\n res: T = client.gather(futures) # pyright: ignore [reportGeneralTypeIssues]\n ^^^^^^^^^^^^^^^^^^^^^^\n File "/domus/h1/gustafw/.virtualenvs/r-reticulate/lib/python3.11/site-packages/distributed/client.py", line 2565, in gather\n return self.sync(\n ^^^^^^^^^^\n File "/domus/h1/gustafw/.virtualenvs/r-reticulate/lib/python3.11/site-packages/pharmpy/tools/covsearch/tool.py", line 739, in task_add_covariate_effect\n model_with_added_effect = func(model_with_added_effect, allow_nested=True)\n ^^^^^^^^^^^^^^^^^\n File "/domus/h1/gustafw/.virtualenvs/r-reticulate/lib/python3.11/site-packages/pharmpy/modeling/covariate_effect.py", line 484, in add_covariate_effect\n model = model.replace(parameters=pset, statements=sset)\n ^^^^^^^^^^^^^^^^^\n File "/domus/h1/gustafw/.virtualenvs/r-reticulate/lib/python3.11/site-packages/pharmpy/model/model.py", line 353, in replace\n statements = Model._canonicalize_statements(\n ^^^^^^^^^^^^^^^^^\n File "/domus/h1/gustafw/.virtualenvs/r-reticulate/lib/python3.11/site-packages/pharmpy/model/model.py", line 222, in _canonicalize_statements\n raise ValueError(f'Symbol {symb} is not defined')\n ^^^^^^^^^^^^^^^^^\n'

Full stack:
ValueError: Symbol theta1 is not defined
Run reticulate::py_last_error() for details.ValueErrorSymbol theta1 is not definedc(" File "/domus/h1/gustafw/.virtualenvs/r-reticulate/lib/python3.11/site-packages/pharmpy/tools/amd/run.py", line 552, in run_amd\n subresults = func(next_model, next_res)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^\n", " File "/domus/h1/gustafw/.virtualenvs/r-reticulate/lib/python3.11/site-packages/pharmpy/tools/amd/run.py", line 1128, in _run_mechanistic_exploratory_covariates\n res = run_tool(\n ^^^^^^^^^\n", " File "/domus/h1/gustafw/.virtualenvs/r-reticulate/lib/python3.11/site-packages/pharmpy/tools/run.py", line 189, in run_tool\n return run_tool_with_name(name, tool, args, kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
" File "/domus/h1/gustafw/.virtualenvs/r-reticulate/lib/python3.11/site-packages/pharmpy/tools/run.py", line 244, in run_tool_with_name\n res = execute_workflow(wf, dispatcher=dispatcher, context=ctx)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n", " File "/domus/h1/gustafw/.virtualenvs/r-reticulate/lib/python3.11/site-packages/pharmpy/workflows/execute.py", line 73, in execute_workflow\n res: T = dispatcher.run(workflow, context)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
" File "/domus/h1/gustafw/.virtualenvs/r-reticulate/lib/python3.11/site-packages/pharmpy/workflows/dispatchers/local_dask/run.py", line 85, in run\n res = client.get(dsk_optimized, 'results')\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n", " File "/domus/h1/gustafw/.virtualenvs/r-reticulate/lib/python3.11/site-packages/distributed/client.py", line 3492, in get\n results = self.gather(packed, asynchronous=asynchronous, direct=direct)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
" File "/domus/h1/gustafw/.virtualenvs/r-reticulate/lib/python3.11/site-packages/distributed/client.py", line 2565, in gather\n return self.sync(\n ^^^^^^^^^^\n", " File "/domus/h1/gustafw/.virtualenvs/r-reticulate/lib/python3.11/site-packages/pharmpy/tools/covsearch/tool.py", line 425, in task_greedy_forward_search\n return _greedy_search(\n ^^^^^^^^^^^^^^^^^\n", " File "/domus/h1/gustafw/.virtualenvs/r-reticulate/lib/python3.11/site-packages/pharmpy/tools/covsearch/tool.py", line 513, in _greedy_search\n nonsignificant_effects, all_candidates_so_far, best_candidate_so_far = perform_step_procedure(\n ^^^^^^^^^^^^^^^^^\n",
" File "/domus/h1/gustafw/.virtualenvs/r-reticulate/lib/python3.11/site-packages/pharmpy/tools/covsearch/tool.py", line 593, in perform_step_procedure\n new_candidates = handle_effects(\n ^^^^^^^^^^^^^^^^^\n", " File "/domus/h1/gustafw/.virtualenvs/r-reticulate/lib/python3.11/site-packages/pharmpy/tools/covsearch/tool.py", line 419, in handle_effects\n new_candidate_modelentries = context.call_workflow(wf, f'{NAME_WF}-effects_addition-{step}')\n ^^^^^^^^^^^^^^^^^\n", " File "/domus/h1/gustafw/.virtualenvs/r-reticulate/lib/python3.11/site-packages/pharmpy/workflows/contexts/baseclass.py", line 252, in call_workflow\n res = call_workflow(workflow, unique_name, self)\n ^^^^^^^^^^^^^^^^^\n",
" File "/domus/h1/gustafw/.virtualenvs/r-reticulate/lib/python3.11/site-packages/pharmpy/workflows/dispatchers/local_dask/call.py", line 41, in call_workflow\n res: T = client.gather(futures) # pyright: ignore [reportGeneralTypeIssues]\n ^^^^^^^^^^^^^^^^^\n", " File "/domus/h1/gustafw/.virtualenvs/r-reticulate/lib/python3.11/site-packages/pharmpy/tools/covsearch/tool.py", line 739, in task_add_covariate_effect\n model_with_added_effect = func(model_with_added_effect, allow_nested=True)\n ^^^^^^^^^^^^^^^^^\n",
" File "/domus/h1/gustafw/.virtualenvs/r-reticulate/lib/python3.11/site-packages/pharmpy/modeling/covariate_effect.py", line 484, in add_covariate_effect\n model = model.replace(parameters=pset, statements=sset)\n ^^^^^^^^^^^^^^^^^\n", " File "/domus/h1/gustafw/.virtualenvs/r-reticulate/lib/python3.11/site-packages/pharmpy/model/model.py", line 353, in replace\n statements = Model._canonicalize_statements(\n ^^^^^^^^^^^^^^^^^\n", " File "/domus/h1/gustafw/.virtualenvs/r-reticulate/lib/python3.11/site-packages/pharmpy/model/model.py", line 222, in _canonicalize_statements\n raise ValueError(f'Symbol {symb} is not defined')\n ^^^^^^^^^^^^^^^^^\n"
)Traceback (most recent call last):
File "/domus/h1/gustafw/.virtualenvs/r-reticulate/lib/python3.11/site-packages/pharmpy/tools/amd/run.py", line 552, in run_amd
subresults = func(next_model, next_res)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/domus/h1/gustafw/.virtualenvs/r-reticulate/lib/python3.11/site-packages/pharmpy/tools/amd/run.py", line 1128, in _run_mechanistic_exploratory_covariates
res = run_tool(
^^^^^^^^^
File "/domus/h1/gustafw/.virtualenvs/r-reticulate/lib/python3.11/site-packages/pharmpy/tools/run.py", line 189, in run_tool
return run_tool_with_name(name, tool, args, kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/domus/h1/gustafw/.virtualenvs/r-reticulate/lib/python3.11/site-packages/pharmpy/tools/run.py", line 244, in run_tool_with_name
res = execute_workflow(wf, dispatcher=dispatcher, context=ctx)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/domus/h1/gustafw/.virtualenvs/r-reticulate/lib/python3.11/site-packages/pharmpy/workflows/execute.py", line 73, in execute_workflow
res: T = dispatcher.run(workflow, context)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/domus/h1/gustafw/.virtualenvs/r-reticulate/lib/python3.11/site-packages/pharmpy/workflows/dispatchers/local_dask/run.py", line 85, in run
res = client.get(dsk_optimized, 'results')
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/domus/h1/gustafw/.virtualenvs/r-reticulate/lib/python3.11/site-packages/distributed/client.py", line 3492, in get
results = self.gather(packed, asynchronous=asynchronous, direct=direct)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/domus/h1/gustafw/.virtualenvs/r-reticulate/lib/python3.11/site-packages/distributed/client.py", line 2565, in gather
return self.sync(
^^^^^^^^^^
File "/domus/h1/gustafw/.virtualenvs/r-reticulate/lib/python3.11/site-packages/pharmpy/tools/covsearch/tool.py", line 425, in task_greedy_forward_search
return _greedy_search(
^^^^^^^^^^^^^^^^^
File "/domus/h1/gustafw/.virtualenvs/r-reticulate/lib/python3.11/site-packages/pharmpy/tools/covsearch/tool.py", line 513, in _greedy_search
nonsignificant_effects, all_candidates_so_far, best_candidate_so_far = perform_step_procedure(
^^^^^^^^^^^^^^^^^
File "/domus/h1/gustafw/.virtualenvs/r-reticulate/lib/python3.11/site-packages/pharmpy/tools/covsearch/tool.py", line 593, in perform_step_procedure
new_candidates = handle_effects(
^^^^^^^^^^^^^^^^^
File "/domus/h1/gustafw/.virtualenvs/r-reticulate/lib/python3.11/site-packages/pharmpy/tools/covsearch/tool.py", line 419, in handle_effects
new_candidate_modelentries = context.call_workflow(wf, f'{NAME_WF}-effects_addition-{step}')
^^^^^^^^^^^^^^^^^
File "/domus/h1/gustafw/.virtualenvs/r-reticulate/lib/python3.11/site-packages/pharmpy/workflows/contexts/baseclass.py", line 252, in call_workflow
res = call_workflow(workflow, unique_name, self)
^^^^^^^^^^^^^^^^^
File "/domus/h1/gustafw/.virtualenvs/r-reticulate/lib/python3.11/site-packages/pharmpy/workflows/dispatchers/local_dask/call.py", line 41, in call_workflow
res: T = client.gather(futures) # pyright: ignore [reportGeneralTypeIssues]
^^^^^^^^^^^^^^^^^
File "/domus/h1/gustafw/.virtualenvs/r-reticulate/lib/python3.11/site-packages/pharmpy/tools/covsearch/tool.py", line 739, in task_add_covariate_effect
model_with_added_effect = func(model_with_added_effect, allow_nested=True)
^^^^^^^^^^^^^^^^^
File "/domus/h1/gustafw/.virtualenvs/r-reticulate/lib/python3.11/site-packages/pharmpy/modeling/covariate_effect.py", line 484, in add_covariate_effect
model = model.replace(parameters=pset, statements=sset)
^^^^^^^^^^^^^^^^^
File "/domus/h1/gustafw/.virtualenvs/r-reticulate/lib/python3.11/site-packages/pharmpy/model/model.py", line 353, in replace
statements = Model._canonicalize_statements(
^^^^^^^^^^^^^^^^^
File "/domus/h1/gustafw/.virtualenvs/r-reticulate/lib/python3.11/site-packages/pharmpy/model/model.py", line 222, in _canonicalize_statements
raise ValueError(f'Symbol {symb} is not defined')
^^^^^^^^^^^^^^^^^
ValueError: Symbol theta1 is not defined
py_call_impl(callable, call_args$unnamed, call_args$named)c("python.builtin.ValueError", "python.builtin.Exception", "python.builtin.BaseException", "python.builtin.object", "error", "condition")list(call = list(run_amd(input = "new_PK_data_25-02-05.csv", modeltype = "basic_pk", administration = "oral", cl_init = 65, vc_init = 45, mat_init = 1, strategy = "default", search_space = search_space, allometric_variable = NULL, occasion = NULL), tryCatch({
mechanistic_covariates <- convert_input(mechanistic_covariates, "list")
seed <- convert_input(seed, "int")
func_out <- pharmpy$tools$run_amd(input, results = results, modeltype = modeltype, administration = administration, strategy = strategy, cl_init = cl_init, vc_init = vc_init, mat_init = mat_init, b_init = b_init, emax_init = emax_init, ec50_init = ec50_init, met_init = met_init, search_space = search_space, lloq_method = lloq_method, lloq_limit = lloq_limit, allometric_variable = allometric_variable, occasion = occasion, path = path, resume = resume, strictness = strictness, dv_types = dv_types,
mechanistic_covariates = mechanistic_covariates, retries_strategy = retries_strategy, seed = seed, parameter_uncertainty_method = parameter_uncertainty_method, ignore_datainfo_fallback = ignore_datainfo_fallback, _E = .E)
if ("pharmpy.workflows.results.Results" %in% class(func_out)) {
func_out <- reset_indices_results(func_out)
}
return(py_to_r(func_out))
}, error = function(cond) {
err <- reticulate::py_last_error()
if (is.null(err)) {
message(cond)
}
else if (err$type == "InputValidationError") {
message(err$value)
}
else {
message("Full stack:")
message(cond)
message(err)
message("pharmr version: ", packageVersion("pharmr"))
message("Pharmpy version: ", print_pharmpy_version())
message("This is a BUG. Please report it at https://github.com/pharmpy/pharmpy/issues. Thanks!")
}
return(NA)
}, warning = function(cond) {
err <- reticulate::py_last_error()
if (is.null(err)) {
message(cond)
}
else if (err$type == "InputValidationError") {
message(err$value)
}
else {
message("Full stack:")
message(cond)
message(err)
message("pharmr version: ", packageVersion("pharmr"))
message("Pharmpy version: ", print_pharmpy_version())
message("This is a BUG. Please report it at https://github.com/pharmpy/pharmpy/issues. Thanks!")
}
return(NA)
}), tryCatchList(expr, classes, parentenv, handlers), tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]]), doTryCatch(return(expr), name, parentenv, handler), tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), tryCatchOne(expr, names, parentenv, handlers[[1]]), doTryCatch(return(expr), name, parentenv, handler), pharmpy$tools$run_amd(input, results = results, modeltype = modeltype, administration = administration, strategy = strategy,
cl_init = cl_init, vc_init = vc_init, mat_init = mat_init, b_init = b_init, emax_init = emax_init, ec50_init = ec50_init, met_init = met_init, search_space = search_space, lloq_method = lloq_method, lloq_limit = lloq_limit, allometric_variable = allometric_variable, occasion = occasion, path = path, resume = resume, strictness = strictness, dv_types = dv_types, mechanistic_covariates = mechanistic_covariates, retries_strategy = retries_strategy, seed = seed, parameter_uncertainty_method = parameter_uncertainty_method,
ignore_datainfo_fallback = ignore_datainfo_fallback, _E = .E), py_call_impl(callable, call_args$unnamed, call_args$named)), parent = c(0, 1, 2, 3, 4, 3, 6, 7, 1, 9), visible = c(TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE), namespace = c("pharmr", "base", "base", "base", "base", "base", "base", "base", NA, "reticulate"), scope = c("::", "::", "local", "local", "local", "local", "local", "local", NA, ":::"), full_call = list(run_amd(input = "new_PK_data_25-02-05.csv", modeltype = "basic_pk",
administration = "oral", cl_init = 65, vc_init = 45, mat_init = 1, strategy = "default", search_space = search_space, allometric_variable = NULL, occasion = NULL), tryCatch({
mechanistic_covariates <- convert_input(mechanistic_covariates, "list")
seed <- convert_input(seed, "int")
func_out <- pharmpy$tools$run_amd(input, results = results, modeltype = modeltype, administration = administration, strategy = strategy, cl_init = cl_init, vc_init = vc_init, mat_init = mat_init, b_init = b_init, emax_init = emax_init, ec50_init = ec50_init, met_init = met_init, search_space = search_space, lloq_method = lloq_method, lloq_limit = lloq_limit, allometric_variable = allometric_variable, occasion = occasion, path = path, resume = resume, strictness = strictness, dv_types = dv_types,
mechanistic_covariates = mechanistic_covariates, retries_strategy = retries_strategy, seed = seed, parameter_uncertainty_method = parameter_uncertainty_method, ignore_datainfo_fallback = ignore_datainfo_fallback, _E = .E)
if ("pharmpy.workflows.results.Results" %in% class(func_out)) {
func_out <- reset_indices_results(func_out)
}
return(py_to_r(func_out))
}, error = function(cond) {
err <- reticulate::py_last_error()
if (is.null(err)) {
message(cond)
}
else if (err$type == "InputValidationError") {
message(err$value)
}
else {
message("Full stack:")
message(cond)
message(err)
message("pharmr version: ", packageVersion("pharmr"))
message("Pharmpy version: ", print_pharmpy_version())
message("This is a BUG. Please report it at https://github.com/pharmpy/pharmpy/issues. Thanks!")
}
return(NA)
}, warning = function(cond) {
err <- reticulate::py_last_error()
if (is.null(err)) {
message(cond)
}
else if (err$type == "InputValidationError") {
message(err$value)
}
else {
message("Full stack:")
message(cond)
message(err)
message("pharmr version: ", packageVersion("pharmr"))
message("Pharmpy version: ", print_pharmpy_version())
message("This is a BUG. Please report it at https://github.com/pharmpy/pharmpy/issues. Thanks!")
}
return(NA)
}), tryCatchList(expr, classes, parentenv, handlers), tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]]), doTryCatch(return(expr), name, parentenv, handler), tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), tryCatchOne(expr, names, parentenv, handlers[[1]]), doTryCatch(return(expr), name, parentenv, handler), pharmpy$tools$run_amd(input, results = results, modeltype = modeltype, administration = administration, strategy = strategy,
cl_init = cl_init, vc_init = vc_init, mat_init = mat_init, b_init = b_init, emax_init = emax_init, ec50_init = ec50_init, met_init = met_init, search_space = search_space, lloq_method = lloq_method, lloq_limit = lloq_limit, allometric_variable = allometric_variable, occasion = occasion, path = path, resume = resume, strictness = strictness, dv_types = dv_types, mechanistic_covariates = mechanistic_covariates, retries_strategy = retries_strategy, seed = seed, parameter_uncertainty_method = parameter_uncertainty_method,
ignore_datainfo_fallback = ignore_datainfo_fallback, _E = .E), py_call_impl(callable, call_args$unnamed, call_args$named)))
pharmr version: 1.5.0
'1.5.0'
Pharmpy version: 1.5.0
This is a BUG. Please report it at https://github.com/pharmpy/pharmpy/issues. Thanks!