Running ‘3comp_test.R’ [11s/16s]
  Comparing ‘3comp_test.Rout’ to ‘3comp_test.Rout.save’ ... OK
  Running ‘3compss_test.R’ [10s/13s]
  Comparing ‘3compss_test.Rout’ to ‘3compss_test.Rout.save’ ... OK
  Running ‘caco2_test.R’ [15s/20s]
  Comparing ‘caco2_test.Rout’ to ‘caco2_test.Rout.save’ ... OK
  Running ‘cheminfo_test.R’ [6s/8s]
  Comparing ‘cheminfo_test.Rout’ to ‘cheminfo_test.Rout.save’ ... OK
  Running ‘fetal_pbtk_testing.R’ [8s/9s]
  Comparing ‘fetal_pbtk_testing.Rout’ to ‘fetal_pbtk_testing.Rout.save’ ... OK
  Running ‘ionization_tests.R’ [3s/4s]
  Comparing ‘ionization_tests.Rout’ to ‘ionization_tests.Rout.save’ ... OK
  Running ‘ivive_test.R’ [10s/14s]
  Running ‘montecarlo_tests.R’ [19s/22s]
  Comparing ‘montecarlo_tests.Rout’ to ‘montecarlo_tests.Rout.save’ ... OK
  Running ‘other_tests.R’ [8s/11s]
  Comparing ‘other_tests.Rout’ to ‘other_tests.Rout.save’ ... OK
  Running ‘pbtk_test.R’ [8s/10s]
  Comparing ‘pbtk_test.Rout’ to ‘pbtk_test.Rout.save’ ... OK
  Running ‘solve_dermal_test.R’ [6s/8s]
  Comparing ‘solve_dermal_test.Rout’ to ‘solve_dermal_test.Rout.save’ ... OK
  Running ‘solve_gas_test.R’ [7s/9s]
  Comparing ‘solve_gas_test.Rout’ to ‘solve_gas_test.Rout.save’ ... OK
  Running ‘testthat.R’ [18s/21s]
  Running ‘unit_test.R’ [6s/7s]
  Comparing ‘unit_test.Rout’ to ‘unit_test.Rout.save’ ... OK
Running the tests in ‘tests/ivive_test.R’ failed.
Complete output:
  > # R CMD BATCH --no-timing --no-restore --no-save ivive_test.R ivive_test.Rout
  > 
  > # Get rid of anything in the workspace:
  > rm(list=ls()) 
  > 
  > library(httk)
  > 
  > # Reduce the number of samples used by Monte Carlo to decrease runtime for
  > # CRAN checks (never use predictions with only ten draws):
  > NSAMP <- 5
  > 
  > # From Honda et al. (2019) (currently only use mean conc's because steady-state 
  > # calculation does not give max):
  > #
  > # Default HTTK function arguments correspond to "Honda3"
  > #
  > #       in vivo Conc.	   Metabolic Clearance  In Vivo Conc.  In Vitro Conc.
  > #Honda1	Veinous (Plasma) Restrictive	        Free           Free
  > #Honda2	Veinous	         Restrictive	        Free	         Nominal
  > #Honda3	Veinous	         Restrictive	        Total	         Nominal
  > #Honda4	Target Tissue    Non-restrictive	    Total	         Nominal
  > #
  > # "Honda1" uses plasma concentration, restrictive clearance, and treats the 
  > # unbound invivo concentration as bioactive. For IVIVE, any input nominal 
  > # concentration in vitro should be converted to cfree.invitro using 
  > # \code{\link{armitage_eval}}, otherwise performance will be the same as 
  > # "Honda2". 
  > #
  > # Use \code{\link{show_honda.ivive()}} to print summary of Honda et al. (2019)
  > # results.
  > 
  > # Default HTTK: 
  > set.seed(12345)
  > Css0 <- calc_mc_css(chem.name="bisphenol a",
  +   output.units="uM",
  +   samples=NSAMP)
  Human plasma concentration returned in uM units for 0.95 quantile.
  Warning messages:
  1: In get_clint(dtxsid = dtxsid, chem.name = chem.name, chem.cas = chem.cas,  :
    Clint is provided as a distribution.
  2: In get_fup(dtxsid = dtxsid, chem.name = chem.name, chem.cas = chem.cas,  :
    Fraction unbound is provided as a distribution.
  3: In get_caco2(chem.cas = chem.cas, chem.name = chem.name, dtxsid = dtxsid,  :
    Default value of 1.6 used for Caco2 permeability.
  4: In (function (chem.name = NULL, chem.cas = NULL, dtxsid = NULL,  :
    calc_analytic_css deprecated argument daily.dose replaced with new argument dose, value given assigned to dose
  > set.seed(12345)
  > # This should be the same as calc_mc_oral_equiv:
  > signif(3/Css0,4) ==
  +   calc_mc_oral_equiv(3.0,chem.name="bisphenol a",
  +     samples=NSAMP)
  Human plasma concentration returned in uM units for 0.95 quantile.
  uM concentration converted to mgpkgpday dose for 0.95 quantile.
   95% 
  TRUE 
  Warning messages:
  1: In get_clint(dtxsid = dtxsid, chem.name = chem.name, chem.cas = chem.cas,  :
    Clint is provided as a distribution.
  2: In get_fup(dtxsid = dtxsid, chem.name = chem.name, chem.cas = chem.cas,  :
    Fraction unbound is provided as a distribution.
  3: In get_caco2(chem.cas = chem.cas, chem.name = chem.name, dtxsid = dtxsid,  :
    Default value of 1.6 used for Caco2 permeability.
  4: In (function (chem.name = NULL, chem.cas = NULL, dtxsid = NULL,  :
    calc_analytic_css deprecated argument daily.dose replaced with new argument dose, value given assigned to dose
  > 
  > # Honda1:
  > set.seed(12345)
  > Css1 <- calc_mc_css(chem.name="bisphenol a",
  +   calc.analytic.css.arg.list=list(
  +     restrictive.clearance = TRUE,
  +     bioactive.free.invivo = TRUE),
  +   output.units="uM",
  +   samples=NSAMP)
  Human plasma concentration returned in uM units for 0.95 quantile.
  Warning messages:
  1: In get_clint(dtxsid = dtxsid, chem.name = chem.name, chem.cas = chem.cas,  :
    Clint is provided as a distribution.
  2: In get_fup(dtxsid = dtxsid, chem.name = chem.name, chem.cas = chem.cas,  :
    Fraction unbound is provided as a distribution.
  3: In get_caco2(chem.cas = chem.cas, chem.name = chem.name, dtxsid = dtxsid,  :
    Default value of 1.6 used for Caco2 permeability.
  4: In (function (chem.name = NULL, chem.cas = NULL, dtxsid = NULL,  :
    calc_analytic_css deprecated argument daily.dose replaced with new argument dose, value given assigned to dose
  > temp <- armitage_eval(
  +   casrn.vector = c("80-05-7"), 
  +   this.FBSf = 0.1,
  +   this.well_number = 384, 
  +   nomconc = 3)
  Error in `[.data.table`(tcdata, IOC_Type_cell == "Base" & is.character(pKa_Accept) &  : 
    attempt access index 92/92 in VECTOR_ELT
  Calls: armitage_eval -> %>% -> [ -> [.data.table
  Execution halted