R Under development (unstable) (2025-11-29 r89077 ucrt) -- "Unsuffered Consequences"
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> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
> 
> library(testthat)
> library(Certara.RDarwin)
> 
> test_check("Certara.RDarwin")
stparm(Cl = tvCl * exp( nCl + (Period==1)*nClPeriodx1 + (Period==2)*nClPeriodx2 ))
	fixef(tvCl= c(, 1, ))
	ranef(diag(nCl) = c(1))
	ranef(diag(nClPeriodx1) = c(1) , same(nClPeriodx2)) 
stparm(Cl = tvCl * exp( nCl + (Period==1)*nClPeriodPeriodx1 + (Period==2)*nClPeriodPeriodx2 ))
	fixef(tvCl= c(, 1, ))
	ranef(diag(nCl) = c(1))
	ranef(diag(nClPeriodPeriodx1) = c(1) , same(nClPeriodPeriodx2)) 
stparm(Cl = tvCl  * exp((Race==2)*dCldRace2) * exp((Race==3)*dCldRace3) * exp( nCl ))
	fixef(tvCl= c(, 1, ))
	
	fixef(dCldRace2= c(, 0, ))
	fixef(dCldRace3= c(, 0, ))
	ranef(diag(nCl) = c(1)) 
stparm(Cl = tvCl  * exp((Race==2)*dCldRace2) * exp((Race==3)*dCldRace3) * exp( nCl ))
	fixef(tvCl= c(, 1, ))
	
	fixef(dCldRace2= c(, 0, ))
	fixef(dCldRace3= c(, 0, ))
	ranef(diag(nCl) = c(1)) 
stparm(Cl = tvCl {Cl_Race[1]} * exp( nCl ))
	fixef(tvCl= c(, 1, ))
	{Cl_Race[2]}
	ranef(diag(nCl) = c(1)) 
stparm(Cl = tvCl {Cl_Race[1]} * exp( nCl ))
	fixef(tvCl= c(, 1, ))
	{Cl_Race[2]}
	ranef(diag(nCl) = c(1)) 
stparm(Cl = tvCl  * (WT/median(WT))^dCldWT * exp( nCl ))
	fixef(tvCl= c(, 1, ))
	fixef(dCldWT= c(, 0, ))
	ranef(diag(nCl) = c(1)) 
stparm(Cl = tvCl  * (WT/median(WT))^dCldWT * exp( nCl ))
	fixef(tvCl= c(, 1, ))
	fixef(dCldWT= c(, 0, ))
	ranef(diag(nCl) = c(1)) 
stparm(Cl = tvCl {Cl_WT[1]} * exp( nCl ))
	fixef(tvCl= c(, 1, ))
	{Cl_WT[2]}
	ranef(diag(nCl) = c(1)) 
stparm(Cl = tvCl {Cl_WT[1]} * exp( nCl ))
	fixef(tvCl= c(, 1, ))
	{Cl_WT[2]}
	ranef(diag(nCl) = c(1)) 
information stored in D:\temp\2025_12_01_01_25_17_20867\RtmpkxpGSr/template.txt and D:\temp\2025_12_01_01_25_17_20867\RtmpkxpGSr/tokens.json
PK1IVC 
 test() {
	cfMicro(A1, Cl / V)
	C = A1 / V
	dosepoint(A1, idosevar = A1Dose, infdosevar = A1InfDose, infratevar = A1InfRate)
	error(CEps = 0.1)
	observe(CObs = C * (1 + CEps))
	fcovariate(WT)
	stparm(Cl = tvCl  * WT^dCldWT * exp( nCl ))
	fixef(tvCl= c(, 1, ))
	fixef(dCldWT= c(, 0, ))
	ranef(diag(nCl) = c(1))
	stparm(V = tvV * exp( nV ))
	fixef(tvV= c(, 1, ))
	ranef(diag(nV) = c(1))

} 
PK2IVC 
 test() {
	cfMicro(A1, Cl / V, Cl2 / V, Cl2 / V2)
C = A1 / V
	dosepoint(A1, idosevar = A1Dose, infdosevar = A1InfDose, infratevar = A1InfRate)
	error(CEps = 0.1)
	observe(CObs = C * (1 + CEps))
	fcovariate(WT)
	stparm(Cl = tvCl  * WT^dCldWT * exp( nCl ))
	fixef(tvCl= c(, 1, ))
	fixef(dCldWT= c(, 0, ))
	ranef(diag(nCl) = c(1))
	stparm(V = tvV * exp( nV ))
	fixef(tvV= c(, 1, ))
	ranef(diag(nV) = c(1))
	stparm(Cl2 = tvCl2  * WT^dCl2dWT * exp( nCl2 ))
	fixef(tvCl2= c(, 1, ))
	fixef(dCl2dWT= c(, 0, ))
	ranef(diag(nCl2) = c(1))
	stparm(V2 = tvV2  * WT^dV2dWT * exp( nV2 ))
	fixef(tvV2= c(, 1, ))
	fixef(dV2dWT= c(, 0, ))
	ranef(diag(nV2) = c(1))

} 
PK3IVC 
 test() {
	cfMicro(A1, Cl / V, Cl2 / V, Cl2 / V2, Cl3 / V, Cl3 / V3)
	C = A1 / V
	dosepoint(A1, idosevar = A1Dose, infdosevar = A1InfDose, infratevar = A1InfRate)
	error(CEps = 0.1)
	observe(CObs = C * (1 + CEps))
	fcovariate(WT)
	stparm(Cl = tvCl  * WT^dCldWT * exp( nCl ))
	fixef(tvCl= c(, 1, ))
	fixef(dCldWT= c(, 0, ))
	ranef(diag(nCl) = c(1))
	stparm(V = tvV * exp( nV ))
	fixef(tvV= c(, 1, ))
	ranef(diag(nV) = c(1))
	stparm(Cl2 = tvCl2  * WT^dCl2dWT * exp( nCl2 ))
	fixef(tvCl2= c(, 1, ))
	fixef(dCl2dWT= c(, 0, ))
	ranef(diag(nCl2) = c(1))
	stparm(V2 = tvV2  * WT^dV2dWT * exp( nV2 ))
	fixef(tvV2= c(, 1, ))
	fixef(dV2dWT= c(, 0, ))
	ranef(diag(nV2) = c(1))
	stparm(Cl3 = tvCl3  * WT^dCl3dWT * exp( nCl3 ))
	fixef(tvCl3= c(, 1, ))
	fixef(dCl3dWT= c(, 0, ))
	ranef(diag(nCl3) = c(1))
	stparm(V3 = tvV3  * WT^dV3dWT * exp( nV3 ))
	fixef(tvV3= c(, 1, ))
	fixef(dV3dWT= c(, 0, ))
	ranef(diag(nV3) = c(1))

} 
Both EstArgs and SimArgs are not specified. Default EstArgs will be used.
information stored in D:\temp\2025_12_01_01_25_17_20867\RtmpkxpGSr/template_A1_main_mapped.txt and D:\temp\2025_12_01_01_25_17_20867\RtmpkxpGSr/tokens_A1_main_mapped.json
Both EstArgs and SimArgs are not specified. Default EstArgs will be used.
information stored in D:\temp\2025_12_01_01_25_17_20867\RtmpkxpGSr/template_A1_vs_AMT_main.txt and D:\temp\2025_12_01_01_25_17_20867\RtmpkxpGSr/tokens_A1_vs_AMT_main.json
Both EstArgs and SimArgs are not specified. Default EstArgs will be used.
information stored in D:\temp\2025_12_01_01_25_17_20867\RtmpkxpGSr/template_AMT_maps_to_Aa.txt and D:\temp\2025_12_01_01_25_17_20867\RtmpkxpGSr/tokens_AMT_maps_to_Aa.json
Both EstArgs and SimArgs are not specified. Default EstArgs will be used.
information stored in D:\temp\2025_12_01_01_25_17_20867\RtmpkxpGSr/template_secondary_A1_mapped.txt and D:\temp\2025_12_01_01_25_17_20867\RtmpkxpGSr/tokens_secondary_A1_mapped.json
Both EstArgs and SimArgs are not specified. Default EstArgs will be used.
information stored in D:\temp\2025_12_01_01_25_17_20867\RtmpkxpGSr/template_multi_model_diff_mains.txt and D:\temp\2025_12_01_01_25_17_20867\RtmpkxpGSr/tokens_multi_model_diff_mains.json
Both EstArgs and SimArgs are not specified. Default EstArgs will be used.
information stored in D:\temp\2025_12_01_01_25_17_20867\RtmpkxpGSr/template_AMT_generic_Rate.txt and D:\temp\2025_12_01_01_25_17_20867\RtmpkxpGSr/tokens_AMT_generic_Rate.json
Both EstArgs and SimArgs are not specified. Default EstArgs will be used.
information stored in D:\temp\2025_12_01_01_25_17_20867\RtmpkxpGSr/template_AMT_generic_Duration.txt and D:\temp\2025_12_01_01_25_17_20867\RtmpkxpGSr/tokens_AMT_generic_Duration.json
Both EstArgs and SimArgs are not specified. Default EstArgs will be used.
information stored in D:\temp\2025_12_01_01_25_17_20867\RtmpkxpGSr/template_A1_specific_Rate.txt and D:\temp\2025_12_01_01_25_17_20867\RtmpkxpGSr/tokens_A1_specific_Rate.json
Both EstArgs and SimArgs are not specified. Default EstArgs will be used.
information stored in D:\temp\2025_12_01_01_25_17_20867\RtmpkxpGSr/template_A1_specific_Duration.txt and D:\temp\2025_12_01_01_25_17_20867\RtmpkxpGSr/tokens_A1_specific_Duration.json
Both EstArgs and SimArgs are not specified. Default EstArgs will be used.
information stored in D:\temp\2025_12_01_01_25_17_20867\RtmpkxpGSr/template_multi_mixed_rate_dur_ext_mapped.txt and D:\temp\2025_12_01_01_25_17_20867\RtmpkxpGSr/tokens_multi_mixed_rate_dur_ext_mapped.json
Both EstArgs and SimArgs are not specified. Default EstArgs will be used.
information stored in D:\temp\2025_12_01_01_25_17_20867\RtmpkxpGSr/template_auto_map_cov_WT.txt and D:\temp\2025_12_01_01_25_17_20867\RtmpkxpGSr/tokens_auto_map_cov_WT.json
information stored in D:\temp\2025_12_01_01_25_17_20867\RtmpkxpGSr/template_cat_named_data_nopipe.txt and D:\temp\2025_12_01_01_25_17_20867\RtmpkxpGSr/tokens_cat_named_data_nopipe.json
information stored in D:\temp\2025_12_01_01_25_17_20867\RtmpkxpGSr/template_cat_unnamed_data_nopipe.txt and D:\temp\2025_12_01_01_25_17_20867\RtmpkxpGSr/tokens_cat_unnamed_data_nopipe.json
information stored in D:\temp\2025_12_01_01_25_17_20867\RtmpkxpGSr/template_occ_named_data_nopipe.txt and D:\temp\2025_12_01_01_25_17_20867\RtmpkxpGSr/tokens_occ_named_data_nopipe.json
information stored in D:\temp\2025_12_01_01_25_17_20867\RtmpkxpGSr/template_occ_unnamed_data_nopipe.txt and D:\temp\2025_12_01_01_25_17_20867\RtmpkxpGSr/tokens_occ_unnamed_data_nopipe.json
information stored in D:\temp\2025_12_01_01_25_17_20867\RtmpkxpGSr/template_cont_ign_data_nopipe.txt and D:\temp\2025_12_01_01_25_17_20867\RtmpkxpGSr/tokens_cont_ign_data_nopipe.json
Both EstArgs and SimArgs are not specified. Default EstArgs will be used.
information stored in D:\temp\2025_12_01_01_25_17_20867\RtmpkxpGSr/template_cat_map_override.txt and D:\temp\2025_12_01_01_25_17_20867\RtmpkxpGSr/tokens_cat_map_override.json
Both EstArgs and SimArgs are not specified. Default EstArgs will be used.
information stored in D:\temp\2025_12_01_01_25_17_20867\RtmpkxpGSr/template_cat_map_override.txt and D:\temp\2025_12_01_01_25_17_20867\RtmpkxpGSr/tokens_cat_map_override.json
For a space named Custom1 the main dosepoint is set to Aa
Both EstArgs and SimArgs are not specified. Default EstArgs will be used.
information stored in D:\temp\2025_12_01_01_25_17_20867\RtmpkxpGSr/template.txt and D:\temp\2025_12_01_01_25_17_20867\RtmpkxpGSr/tokensCustom.json
information stored in D:\temp\2025_12_01_01_25_17_20867\RtmpkxpGSr/template_test1_v4.txt and D:\temp\2025_12_01_01_25_17_20867\RtmpkxpGSr/tokens_test1_v4.json
Both EstArgs and SimArgs are not specified. Default EstArgs will be used.
information stored in D:\temp\2025_12_01_01_25_17_20867\RtmpkxpGSr/template.txt and D:\temp\2025_12_01_01_25_17_20867\RtmpkxpGSr/tokensSex.json
For method='QRPEM', stdErr must be 'Fisher-Score' or 'None'. Setting stdErr='Fisher-Score'.
information stored in D:\temp\2025_12_01_01_25_17_20867\RtmpkxpGSr/template.txt and D:\temp\2025_12_01_01_25_17_20867\RtmpkxpGSr/tokensZOGIGW.json
information stored in D:\temp\2025_12_01_01_25_17_20867\RtmpkxpGSr/template.txt and D:\temp\2025_12_01_01_25_17_20867\RtmpkxpGSr/tokensMixRatio.json
For method='QRPEM', stdErr must be 'Fisher-Score' or 'None'. Setting stdErr='Fisher-Score'.
information stored in D:\temp\2025_12_01_01_25_17_20867\RtmpkxpGSr/template.txt and D:\temp\2025_12_01_01_25_17_20867\RtmpkxpGSr/tokensCovs.json
information stored in D:\temp\2025_12_01_01_25_17_20867\RtmpkxpGSr/templateEllipsis.txt and D:\temp\2025_12_01_01_25_17_20867\RtmpkxpGSr/tokensEllipsis.json
information stored in D:\temp\2025_12_01_01_25_17_20867\RtmpkxpGSr/templateEllipsis.txt and D:\temp\2025_12_01_01_25_17_20867\RtmpkxpGSr/tokensEllipsis.json
information stored in D:\temp\2025_12_01_01_25_17_20867\RtmpkxpGSr/template.txt and D:\temp\2025_12_01_01_25_17_20867\RtmpkxpGSr/tokens.json
information stored in D:\temp\2025_12_01_01_25_17_20867\RtmpkxpGSr/template_expr_test.txt and D:\temp\2025_12_01_01_25_17_20867\RtmpkxpGSr/tokens_expr_test.json
Model setup: D:/temp/2025_12_01_01_25_17_20867/RtmpkxpGSr/test_setup.json
Template path: D:/temp/2025_12_01_01_25_17_20867/RtmpkxpGSr/test_template.txt
Tokens path: D:/temp/2025_12_01_01_25_17_20867/RtmpkxpGSr/test_tokens.json
Data path: D:/temp/2025_12_01_01_25_17_20867/RtmpkxpGSr/test_data.csv
Author: R Test Suite
Description: A basic 1-cpt PK model test
Both EstArgs and SimArgs are not specified. Default EstArgs will be used.
information stored in D:/temp/2025_12_01_01_25_17_20867/RtmpkxpGSr/test_template.txt and D:/temp/2025_12_01_01_25_17_20867/RtmpkxpGSr/test_tokens.json
For method='QRPEM', stdErr must be 'Fisher-Score' or 'None'. Setting stdErr='Fisher-Score'.
For method='QRPEM', stdErr must be 'Fisher-Score' or 'None'. Setting stdErr='Fisher-Score'.
For method='IT2S-EM', stdErr must be 'None'. Setting stdErr='None'.
For method='QRPEM', stdErr must be 'Fisher-Score' or 'None'. Setting stdErr='Fisher-Score'.
For method='QRPEM', stdErr must be 'Fisher-Score' or 'None'. Setting stdErr='Fisher-Score'.
For method='QRPEM', stdErr must be 'Fisher-Score' or 'None'. Setting stdErr='Fisher-Score'.
[ FAIL 0 | WARN 0 | SKIP 65 | PASS 142 ]

══ Skipped tests (65) ══════════════════════════════════════════════════════════
• On CRAN (65): 'test-2CatCovSearched.R:1:1', 'test-3CatCovSearched.R:1:1',
  'test-CatCovMultRelationsSearched.R:1:1', 'test-ContCovSearched.R:1:1',
  'test-Dosepoint.R:1:1', 'test-StParm.R:70:1', 'test-THETAD1_1_ETAD1_2.R:1:1',
  'test-THETAD1_2_ETAD1_1.R:1:1', 'test-THETAD1_2_ETAD1_2.R:1:1',
  'test-THETAR1_1_BW_2.R:1:1', 'test-THETAR1_1_ETAR1_1.R:1:1',
  'test-THETAR_Frozen_ETA_Frozen.R:1:1', 'test-Table.R:1:1',
  'test-add_Covariate.R:1:1', 'test-add_Covariate.R:73:1',
  'test-add_StParm.R:1:1', 'test-create_CustomSpace.R:1:1',
  'test-create_CustomSpace.R:38:1', 'test-gen_InputRow1.R:1:1',
  'test-gen_InputRow1.R:9:1', 'test-gen_InputRow1.R:14:1',
  'test-gen_InputRow1.R:19:1', 'test-gen_MAP.R:1:1', 'test-gen_MAP.R:54:1',
  'test-gen_MAP.R:115:1', 'test-gen_MAP.R:171:1', 'test-gen_MAP.R:239:1',
  'test-gen_MAP.R:327:1', 'test-gen_MAP.R:381:1', 'test-gen_MAP.R:488:1',
  'test-gen_MAP.R:542:1', 'test-gen_MAP.R:650:1', 'test-gen_MAP.R:749:1',
  'test-gen_MAP.R:1215:1', 'test-gen_MAP.R:1282:1', 'test-gen_MAP.R:1352:1',
  'test-gen_MAP.R:1408:1', 'test-gen_MAP.R:1467:1', 'test-gen_MAP.R:1526:1',
  'test-gen_MAP.R:1581:1', 'test-gen_MAPCustom.R:1:1',
  'test-get_PMLParametersSets.R:1:1', 'test-get_PMLParametersSets.R:167:1',
  'test-get_PMLParametersSets.R:229:1', 'test-get_PMLParametersSets.R:289:1',
  'test-get_PMLParametersSets.R:343:1', 'test-get_PMLParametersSets.R:438:1',
  'test-get_PMLParametersSets.R:609:1', 'test-get_PMLParametersSets.R:678:1',
  'test-modify_Omega.R:1:1', 'test-modify_StParmCustom.R:1:1',
  'test-output_NLMETemplate.R:1:1', 'test-output_NLMETemplate.R:80:1',
  'test-pyDarwinOptions.R:2:1', 'test-pyDarwinOptions.R:18:1',
  'test-pyDarwinOptions.R:33:1', 'test-pyDarwinOptions.R:46:1',
  'test-pyDarwinOptions.R:59:1', 'test-pyDarwinOptions.R:72:1',
  'test-pyDarwinOptions.R:89:1', 'test-pyDarwinOptions.R:108:1',
  'test-pyDarwinOptions.R:136:1', 'test-pyDarwinOptions.R:160:1',
  'test-specify_SimParams.R:1:1', 'test-specify_SimParams.R:16:1'

[ FAIL 0 | WARN 0 | SKIP 65 | PASS 142 ]
> 
> proc.time()
   user  system elapsed 
   7.87    0.85    8.75