Last updated on 2025-12-28 01:48:41 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.7.4 | 41.67 | 586.48 | 628.15 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.7.4 | 29.80 | 375.86 | 405.66 | OK | |
| r-devel-linux-x86_64-fedora-clang | 2.7.4 | 73.00 | 905.67 | 978.67 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 2.7.4 | 75.00 | 936.08 | 1011.08 | OK | |
| r-devel-windows-x86_64 | 2.7.4 | 58.00 | 484.00 | 542.00 | ERROR | |
| r-patched-linux-x86_64 | 2.7.4 | 49.08 | 537.10 | 586.18 | OK | |
| r-release-linux-x86_64 | 2.7.4 | 40.35 | 538.80 | 579.15 | OK | |
| r-release-macos-arm64 | 2.7.4 | 12.00 | 125.00 | 137.00 | OK | |
| r-release-macos-x86_64 | 2.7.4 | 32.00 | 608.00 | 640.00 | OK | |
| r-release-windows-x86_64 | 2.7.4 | 56.00 | 596.00 | 652.00 | OK | |
| r-oldrel-macos-arm64 | 2.7.4 | 11.00 | 130.00 | 141.00 | NOTE | |
| r-oldrel-macos-x86_64 | 2.7.4 | 33.00 | 643.00 | 676.00 | NOTE | |
| r-oldrel-windows-x86_64 | 2.7.4 | 72.00 | 772.00 | 844.00 | OK |
Version: 2.7.4
Check: examples
Result: ERROR
Running examples in 'httk-Ex.R' failed
The error most likely occurred in:
> ### Name: armitage_eval
> ### Title: Armitage In Vitro Distribution Model
> ### Aliases: armitage_eval
>
> ### ** Examples
>
>
> library(httk)
>
> # Check to see if we have info on the chemical:
> "80-05-7" %in% get_cheminfo()
Warning in get_cheminfo() :
Excluding compounds that have one or more needed parameters missing in chem.physical_and_invitro.table.
For model 3compartmentss each chemical must have non-NA values for:Human.Clint, Human.Funbound.plasma, logP, MW
Warning in get_cheminfo() :
Excluding compounds without a 'fup' value (i.e. fup value = NA).
Warning in get_cheminfo() :
Excluding compounds with uncertain 'fup' confidence/credible intervals.
Warning in get_cheminfo() :
Excluding compounds that do not have a clint value or distribution of clint values.
Warning in get_cheminfo() :
Excluding volatile compounds defined as log.Henry >= -4.5.
Warning in get_cheminfo() :
Excluding compounds that are categorized in one or more of the following chemical classes: PFAS.
[1] TRUE
>
> #We do:
> temp <- armitage_eval(casrn.vector = c("80-05-7", "81-81-2"), this.FBSf = 0.1,
+ this.well_number = 384, nomconc = 10)
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
Flavor: r-devel-windows-x86_64
Version: 2.7.4
Check: tests
Result: ERROR
Running '3comp_test.R' [17s]
Comparing '3comp_test.Rout' to '3comp_test.Rout.save' ... OK
Running '3compss_test.R' [16s]
Comparing '3compss_test.Rout' to '3compss_test.Rout.save' ... OK
Running 'caco2_test.R' [23s]
Comparing 'caco2_test.Rout' to 'caco2_test.Rout.save' ... OK
Running 'cheminfo_test.R' [8s]
Comparing 'cheminfo_test.Rout' to 'cheminfo_test.Rout.save' ... OK
Running 'fetal_pbtk_testing.R' [12s]
Comparing 'fetal_pbtk_testing.Rout' to 'fetal_pbtk_testing.Rout.save' ... OK
Running 'ionization_tests.R' [3s]
Comparing 'ionization_tests.Rout' to 'ionization_tests.Rout.save' ... OK
Running 'ivive_test.R' [14s]
Running 'montecarlo_tests.R' [29s]
Comparing 'montecarlo_tests.Rout' to 'montecarlo_tests.Rout.save' ... OK
Running 'other_tests.R' [12s]
Comparing 'other_tests.Rout' to 'other_tests.Rout.save' ... OK
Running 'pbtk_test.R' [12s]
Comparing 'pbtk_test.Rout' to 'pbtk_test.Rout.save' ... OK
Running 'solve_dermal_test.R' [8s]
Comparing 'solve_dermal_test.Rout' to 'solve_dermal_test.Rout.save' ... OK
Running 'solve_gas_test.R' [10s]
Comparing 'solve_gas_test.Rout' to 'solve_gas_test.Rout.save' ... OK
Running 'testthat.R' [27s]
Running 'unit_test.R' [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
Flavor: r-devel-windows-x86_64
Version: 2.7.4
Check: installed package size
Result: NOTE
installed size is 5.1Mb
sub-directories of 1Mb or more:
data 2.1Mb
help 1.5Mb
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.