Last updated on 2025-07-26 19:49:55 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.7.0 | 44.21 | 762.69 | 806.90 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.7.0 | 29.52 | 480.76 | 510.28 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 2.7.0 | 1261.32 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 2.7.0 | 1239.17 | OK | |||
| r-devel-windows-x86_64 | 2.7.0 | 55.00 | 657.00 | 712.00 | OK | |
| r-patched-linux-x86_64 | 2.6.1 | 42.48 | 627.56 | 670.04 | OK | |
| r-release-linux-x86_64 | 2.6.1 | 33.15 | 624.12 | 657.27 | OK | |
| r-release-macos-arm64 | 2.6.1 | 229.00 | OK | |||
| r-release-macos-x86_64 | 2.7.0 | 556.00 | OK | |||
| r-release-windows-x86_64 | 2.7.0 | 57.00 | 679.00 | 736.00 | OK | |
| r-oldrel-macos-arm64 | 2.6.1 | 296.00 | NOTE | |||
| r-oldrel-macos-x86_64 | 2.7.0 | 566.00 | NOTE | |||
| r-oldrel-windows-x86_64 | 2.7.0 | 71.00 | 771.00 | 842.00 | NOTE |
Version: 2.7.0
Check: examples
Result: ERROR
Running examples in ‘httk-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: solve_dermal_pbtk
> ### Title: Solve_dermal_PBTK
> ### Aliases: solve_dermal_pbtk
> ### Keywords: Solve
>
> ### ** Examples
>
>
> # Dermal exposure to default dose
> out <- solve_dermal_pbtk(chem.name="bisphenola")
Warning in solve_dermal_pbtk(chem.name = "bisphenola") :
If route is not chosen, it is set to dermal by default.
Warning in solve_dermal_pbtk(chem.name = "bisphenola") :
Vvehicle not specified, so set to 0.1 L.
Warning in solve_dermal_pbtk(chem.name = "bisphenola") :
The initial.dose is automatically set to 1mg/kg.
Warning in get_clint(dtxsid = dtxsid, chem.name = chem.name, chem.cas = chem.cas, :
Clint is provided as a distribution.
Warning in apply_clint_adjustment(Clint.point, Fu_hep = Fu_hep, suppress.messages = suppress.messages) :
Clint adjusted for in vitro partitioning (Kilford, 2008), see calc_hep_fu.
Warning in get_fup(dtxsid = dtxsid, chem.name = chem.name, chem.cas = chem.cas, :
Fraction unbound is provided as a distribution.
Warning in apply_fup_adjustment(fup.point, fup.correction = fup.adjustment, :
Fup adjusted for in vivo lipid partitioning (Pearce, 2017), see calc_fup_correction.
Warning in parameterize_dermal_pbtk(chem.name = "bisphenola", species = "Human", :
Funbound.plasma recalculated with adjustment. Set adjusted.Funbound.plasma to FALSE to use original value.
Warning in available_rblood2plasma(chem.cas = chem.cas, species = species, :
Human in vivo measured Rblood2plasma used.
Warning in parameterize_dermal_pbtk(chem.name = "bisphenola", species = "Human", :
Since parameter Kvehicle2water is null, vehicle containing chemical is assumed to be water.
Warning in get_caco2(chem.cas = chem.cas, chem.name = chem.name, dtxsid = dtxsid, :
Default value of 1.6 used for Caco2 permeability.
None of the monitored components undergo unit conversions (i.e. conversion factor of 1).
AUC is area under the plasma concentration curve in uM*days units with Rblood2plasma = 0.77.
The model outputs are provided in the following units:
umol: Avehicle, Aplasma, Ain, Aexhaled, Atubules, Ametabolized
uM: Cgut, Cliver, Cven, Clung, Cart, Crest, Ckidney, Cplasma, Cskin_exposed, Cskin_unexposed, Cvehicle
uM*days: AUC
> # Dermal exposure to 20 mg/L in 0.01 L of octanol with wash-off after 8 hours
> # Since skin permeability happens quickly for bisphenol A, let's only look at 3 days.
> dose.conc <- 2 #mg/L
> Vvehicle <- 0.01 #L
> initial.dose <- dose.conc*Vvehicle
> out <- solve_dermal_pbtk(chem.name="bisphenola", initial.dose=initial.dose,
+ input.units="mg", Vvehicle=0.01,
+ Kskin2vehicle="octanol", dose.duration=8,
+ dose.duration.units="hr", days=3)
Warning in solve_dermal_pbtk(chem.name = "bisphenola", initial.dose = initial.dose, :
If route is not chosen, it is set to dermal by default.
Warning in solve_dermal_pbtk(chem.name = "bisphenola", initial.dose = initial.dose, :
Washoff occurs automatically if dose.duration is used.
Warning in get_clint(dtxsid = dtxsid, chem.name = chem.name, chem.cas = chem.cas, :
Clint is provided as a distribution.
Warning in apply_clint_adjustment(Clint.point, Fu_hep = Fu_hep, suppress.messages = suppress.messages) :
Clint adjusted for in vitro partitioning (Kilford, 2008), see calc_hep_fu.
Warning in get_fup(dtxsid = dtxsid, chem.name = chem.name, chem.cas = chem.cas, :
Fraction unbound is provided as a distribution.
Warning in apply_fup_adjustment(fup.point, fup.correction = fup.adjustment, :
Fup adjusted for in vivo lipid partitioning (Pearce, 2017), see calc_fup_correction.
Warning in parameterize_dermal_pbtk(chem.name = "bisphenola", species = "Human", :
Funbound.plasma recalculated with adjustment. Set adjusted.Funbound.plasma to FALSE to use original value.
Warning in available_rblood2plasma(chem.cas = chem.cas, species = species, :
Human in vivo measured Rblood2plasma used.
Warning in parameterize_dermal_pbtk(chem.name = "bisphenola", species = "Human", :
Since parameter Kvehicle2water is null, vehicle containing chemical is assumed to be water.
Warning in get_caco2(chem.cas = chem.cas, chem.name = chem.name, dtxsid = dtxsid, :
Default value of 1.6 used for Caco2 permeability.
None of the monitored components undergo unit conversions (i.e. conversion factor of 1).
AUC is area under the plasma concentration curve in uM*days units with Rblood2plasma = 0.77.
The model outputs are provided in the following units:
umol: Avehicle, Aplasma, Ain, Aexhaled, Atubules, Ametabolized
uM: Cgut, Cliver, Cven, Clung, Cart, Crest, Ckidney, Cplasma, Cskin_exposed, Cskin_unexposed, Cvehicle
uM*days: AUC
>
> # Now, try this again with an infinite dose.
> out <- solve_dermal_pbtk(chem.name="bisphenola", initial.dose=dose.conc,
+ input.units="mg/L", Vvehicle=0.01,
+ Kskin2vehicle="octanol", dose.duration=8,
+ dose.duration.units="hr", days=3,
+ InfiniteDose=TRUE)
Warning in solve_dermal_pbtk(chem.name = "bisphenola", initial.dose = dose.conc, :
If route is not chosen, it is set to dermal by default.
Warning in solve_dermal_pbtk(chem.name = "bisphenola", initial.dose = dose.conc, :
When InfiniteDose = TRUE, washoff is ignored, and Vvehicle is set to 0 L and ignored.
Warning in solve_dermal_pbtk(chem.name = "bisphenola", initial.dose = dose.conc, :
Washoff occurs automatically if dose.duration is used.
Warning in get_clint(dtxsid = dtxsid, chem.name = chem.name, chem.cas = chem.cas, :
Clint is provided as a distribution.
Warning in apply_clint_adjustment(Clint.point, Fu_hep = Fu_hep, suppress.messages = suppress.messages) :
Clint adjusted for in vitro partitioning (Kilford, 2008), see calc_hep_fu.
Warning in get_fup(dtxsid = dtxsid, chem.name = chem.name, chem.cas = chem.cas, :
Fraction unbound is provided as a distribution.
Warning in apply_fup_adjustment(fup.point, fup.correction = fup.adjustment, :
Fup adjusted for in vivo lipid partitioning (Pearce, 2017), see calc_fup_correction.
Warning in parameterize_dermal_pbtk(chem.name = "bisphenola", species = "Human", :
Funbound.plasma recalculated with adjustment. Set adjusted.Funbound.plasma to FALSE to use original value.
Warning in available_rblood2plasma(chem.cas = chem.cas, species = species, :
Human in vivo measured Rblood2plasma used.
Warning in parameterize_dermal_pbtk(chem.name = "bisphenola", species = "Human", :
Since parameter Kvehicle2water is null, vehicle containing chemical is assumed to be water.
Warning in get_caco2(chem.cas = chem.cas, chem.name = chem.name, dtxsid = dtxsid, :
Default value of 1.6 used for Caco2 permeability.
None of the monitored components undergo unit conversions (i.e. conversion factor of 1).
AUC is area under the plasma concentration curve in uM*days units with Rblood2plasma = 0.77.
The model outputs are provided in the following units:
uM: Cvehicle_infinite, Cgut, Cliver, Cven, Clung, Cart, Crest, Ckidney, Cplasma, Cskin_exposed, Cskin_unexposed, Cvehicle
umol: Aplasma, Ain, Aexhaled, Atubules, Ametabolized
uM*days: AUC
>
> # Now, try a scenario where 2 mg of chemical in 1 mL of water is applied
> # and washed off 8 hours later every day for 5 days
> num.days <- 5;
> time <- c(0:(num.days-1),(0:(num.days-1)) + 8/24); time <- sort(time) #in days
> Vvehicle <- rep(1e-3,length(time)) #convert mL to L
> Cvehicle <- rep(c(2,0),num.days)/Vvehicle # convert 2 mg to mg/L
> dosing.dermal <- cbind(time,Cvehicle,Vvehicle)
> out <- solve_dermal_pbtk(chem.name='bisphenola',
+ dosing.dermal=dosing.dermal)
Warning in solve_dermal_pbtk(chem.name = "bisphenola", dosing.dermal = dosing.dermal) :
If route is not chosen, it is set to dermal by default.
Warning in get_clint(dtxsid = dtxsid, chem.name = chem.name, chem.cas = chem.cas, :
Clint is provided as a distribution.
Warning in apply_clint_adjustment(Clint.point, Fu_hep = Fu_hep, suppress.messages = suppress.messages) :
Clint adjusted for in vitro partitioning (Kilford, 2008), see calc_hep_fu.
Warning in get_fup(dtxsid = dtxsid, chem.name = chem.name, chem.cas = chem.cas, :
Fraction unbound is provided as a distribution.
Warning in apply_fup_adjustment(fup.point, fup.correction = fup.adjustment, :
Fup adjusted for in vivo lipid partitioning (Pearce, 2017), see calc_fup_correction.
Warning in parameterize_dermal_pbtk(chem.name = "bisphenola", species = "Human", :
Funbound.plasma recalculated with adjustment. Set adjusted.Funbound.plasma to FALSE to use original value.
Warning in available_rblood2plasma(chem.cas = chem.cas, species = species, :
Human in vivo measured Rblood2plasma used.
Warning in parameterize_dermal_pbtk(chem.name = "bisphenola", species = "Human", :
Since parameter Kvehicle2water is null, vehicle containing chemical is assumed to be water.
Warning in get_caco2(chem.cas = chem.cas, chem.name = chem.name, dtxsid = dtxsid, :
Default value of 1.6 used for Caco2 permeability.
None of the monitored components undergo unit conversions (i.e. conversion factor of 1).
AUC is area under the plasma concentration curve in uM*days units with Rblood2plasma = 0.77.
The model outputs are provided in the following units:
umol: Avehicle, Aplasma, Ain, Aexhaled, Atubules, Ametabolized
uM: Cgut, Cliver, Cven, Clung, Cart, Crest, Ckidney, Cplasma, Cskin_exposed, Cskin_unexposed, Cvehicle
uM*days: AUC
>
> parameters <- parameterize_dermal_pbtk(chem.name='bisphenola',skin_depth=1)
Warning in get_clint(dtxsid = dtxsid, chem.name = chem.name, chem.cas = chem.cas, :
Clint is provided as a distribution.
Warning in apply_clint_adjustment(Clint.point, Fu_hep = Fu_hep, suppress.messages = suppress.messages) :
Clint adjusted for in vitro partitioning (Kilford, 2008), see calc_hep_fu.
Warning in get_fup(dtxsid = dtxsid, chem.name = chem.name, chem.cas = chem.cas, :
Fraction unbound is provided as a distribution.
Warning in apply_fup_adjustment(fup.point, fup.correction = fup.adjustment, :
Fup adjusted for in vivo lipid partitioning (Pearce, 2017), see calc_fup_correction.
Warning in parameterize_dermal_pbtk(chem.name = "bisphenola", skin_depth = 1) :
Funbound.plasma recalculated with adjustment. Set adjusted.Funbound.plasma to FALSE to use original value.
Warning in available_rblood2plasma(chem.cas = chem.cas, species = species, :
Human in vivo measured Rblood2plasma used.
Warning in parameterize_dermal_pbtk(chem.name = "bisphenola", skin_depth = 1) :
Since parameter Kvehicle2water is null, vehicle containing chemical is assumed to be water.
Warning in get_caco2(chem.cas = chem.cas, chem.name = chem.name, dtxsid = dtxsid, :
Default value of 1.6 used for Caco2 permeability.
> parameters$Fskin_exposed <- 0.25
> parameters$Vvehicle <- 1
> out <- solve_dermal_pbtk(parameters=parameters)
Warning in solve_dermal_pbtk(parameters = parameters) :
If route is not chosen, it is set to dermal by default.
Warning in solve_dermal_pbtk(parameters = parameters) :
Vvehicle not specified, so set to 0.1 L.
Warning in solve_dermal_pbtk(parameters = parameters) :
The initial.dose is automatically set to 1mg/kg.
None of the monitored components undergo unit conversions (i.e. conversion factor of 1).
Warning in (function (chem.name = NULL, chem.cas = NULL, dtxsid = NULL, :
Rblood2plasma not recalculated.
Set recalc.blood2plasma to TRUE if desired.
Warning in (function (chem.name = NULL, chem.cas = NULL, dtxsid = NULL, :
Clearance not recalculated.
Set recalc.clearance to TRUE if desired.
AUC is area under the plasma concentration curve in uM*days units with Rblood2plasma = 0.77.
The model outputs are provided in the following units:
umol: Avehicle, Aplasma, Ain, Aexhaled, Atubules, Ametabolized
uM: Cgut, Cliver, Cven, Clung, Cart, Crest, Ckidney, Cplasma, Cskin_exposed, Cskin_unexposed, Cvehicle
uM*days: AUC
>
> # Dermal is the default route:
> head(solve_dermal_pbtk(chem.name="bisphenola"))
Warning in solve_dermal_pbtk(chem.name = "bisphenola") :
If route is not chosen, it is set to dermal by default.
Warning in solve_dermal_pbtk(chem.name = "bisphenola") :
Vvehicle not specified, so set to 0.1 L.
Warning in solve_dermal_pbtk(chem.name = "bisphenola") :
The initial.dose is automatically set to 1mg/kg.
Warning in get_clint(dtxsid = dtxsid, chem.name = chem.name, chem.cas = chem.cas, :
Clint is provided as a distribution.
Warning in apply_clint_adjustment(Clint.point, Fu_hep = Fu_hep, suppress.messages = suppress.messages) :
Clint adjusted for in vitro partitioning (Kilford, 2008), see calc_hep_fu.
Warning in get_fup(dtxsid = dtxsid, chem.name = chem.name, chem.cas = chem.cas, :
Fraction unbound is provided as a distribution.
Warning in apply_fup_adjustment(fup.point, fup.correction = fup.adjustment, :
Fup adjusted for in vivo lipid partitioning (Pearce, 2017), see calc_fup_correction.
Warning in parameterize_dermal_pbtk(chem.name = "bisphenola", species = "Human", :
Funbound.plasma recalculated with adjustment. Set adjusted.Funbound.plasma to FALSE to use original value.
Warning in available_rblood2plasma(chem.cas = chem.cas, species = species, :
Human in vivo measured Rblood2plasma used.
Warning in parameterize_dermal_pbtk(chem.name = "bisphenola", species = "Human", :
Since parameter Kvehicle2water is null, vehicle containing chemical is assumed to be water.
Warning in get_caco2(chem.cas = chem.cas, chem.name = chem.name, dtxsid = dtxsid, :
Default value of 1.6 used for Caco2 permeability.
None of the monitored components undergo unit conversions (i.e. conversion factor of 1).
AUC is area under the plasma concentration curve in uM*days units with Rblood2plasma = 0.77.
The model outputs are provided in the following units:
umol: Avehicle, Aplasma, Ain, Aexhaled, Atubules, Ametabolized
uM: Cgut, Cliver, Cven, Clung, Cart, Crest, Ckidney, Cplasma, Cskin_exposed, Cskin_unexposed, Cvehicle
uM*days: AUC
time Avehicle Cgut Cliver Cven Clung Cart Crest
[1,] 0.00 306.6 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
[2,] 0.01 306.5 0.000901 0.000314 0.000199 0.001722 0.000179 0.000054
[3,] 0.02 306.4 0.003364 0.001763 0.000419 0.003757 0.000399 0.000251
[4,] 0.03 306.3 0.006527 0.004393 0.000640 0.005795 0.000620 0.000586
[5,] 0.04 306.3 0.009953 0.007928 0.000857 0.007806 0.000837 0.001046
[6,] 0.05 306.2 0.013450 0.012060 0.001070 0.009778 0.001051 0.001618
Ckidney Cplasma Aplasma Cskin_exposed Cskin_unexposed Cvehicle Ain
[1,] 0.000000 0.000000 0.000000 0.0000 0.000000 10.000 0.00000
[2,] 0.002595 0.000258 0.000388 0.3574 0.000136 9.997 0.08512
[3,] 0.007784 0.000544 0.000817 0.6543 0.000610 9.994 0.16990
[4,] 0.013320 0.000830 0.001246 0.9008 0.001379 9.992 0.25450
[5,] 0.018830 0.001113 0.001669 1.1060 0.002393 9.989 0.33890
[6,] 0.024250 0.001389 0.002084 1.2760 0.003603 9.986 0.42310
Aexhaled Atubules Ametabolized AUC
[1,] 0 0.000000 0.0e+00 0.0e+00
[2,] 0 0.000004 0.0e+00 1.0e-06
[3,] 0 0.000021 3.0e-06 5.0e-06
[4,] 0 0.000050 1.1e-05 1.2e-05
[5,] 0 0.000091 2.7e-05 2.2e-05
[6,] 0 0.000145 5.4e-05 3.4e-05
> head(solve_dermal_pbtk(chem.name="bisphenola", route="dermal"))
Warning in solve_dermal_pbtk(chem.name = "bisphenola", route = "dermal") :
Vvehicle not specified, so set to 0.1 L.
Warning in solve_dermal_pbtk(chem.name = "bisphenola", route = "dermal") :
The initial.dose is automatically set to 1mg/kg.
Warning in get_clint(dtxsid = dtxsid, chem.name = chem.name, chem.cas = chem.cas, :
Clint is provided as a distribution.
Warning in apply_clint_adjustment(Clint.point, Fu_hep = Fu_hep, suppress.messages = suppress.messages) :
Clint adjusted for in vitro partitioning (Kilford, 2008), see calc_hep_fu.
Warning in get_fup(dtxsid = dtxsid, chem.name = chem.name, chem.cas = chem.cas, :
Fraction unbound is provided as a distribution.
Warning in apply_fup_adjustment(fup.point, fup.correction = fup.adjustment, :
Fup adjusted for in vivo lipid partitioning (Pearce, 2017), see calc_fup_correction.
Warning in parameterize_dermal_pbtk(chem.name = "bisphenola", species = "Human", :
Funbound.plasma recalculated with adjustment. Set adjusted.Funbound.plasma to FALSE to use original value.
Warning in available_rblood2plasma(chem.cas = chem.cas, species = species, :
Human in vivo measured Rblood2plasma used.
Warning in parameterize_dermal_pbtk(chem.name = "bisphenola", species = "Human", :
Since parameter Kvehicle2water is null, vehicle containing chemical is assumed to be water.
Warning in get_caco2(chem.cas = chem.cas, chem.name = chem.name, dtxsid = dtxsid, :
Default value of 1.6 used for Caco2 permeability.
DLSODA- At T (=R1), too much accuracy requested
for precision of machine.. See TOLSF (=R2)
In above message, R1 = 9.96383e-06, R2 = nan
Warning in lsoda(y, times, func, parms, ...) :
Excessive precision requested. scale up `rtol' and `atol' e.g by the factor 10
Warning in lsoda(y, times, func, parms, ...) :
Returning early. Results are accurate, as far as they go
Error in (function (chem.name = NULL, chem.cas = NULL, dtxsid = NULL, :
Some of the requested variables to monitor (monitor.vars) are not in
the columns of the deSolve output object. These variables should
belong to either the states or outputs of the model.
Calls: head -> solve_dermal_pbtk -> do.call -> <Anonymous>
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
parameterize_steadystate 3.985 0 5.065
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 2.6.1
Check: installed package size
Result: NOTE
installed size is 6.5Mb
sub-directories of 1Mb or more:
data 2.2Mb
doc 1.7Mb
help 1.3Mb
Flavor: r-oldrel-macos-arm64
Version: 2.7.0
Check: installed package size
Result: NOTE
installed size is 7.9Mb
sub-directories of 1Mb or more:
data 3.1Mb
doc 2.0Mb
help 1.4Mb
Flavors: r-oldrel-macos-x86_64, r-oldrel-windows-x86_64