- using R Under development (unstable) (2025-08-10 r88559)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
Debian clang version 19.1.7 (3+b1)
Debian flang-new version 19.1.7 (3+b1)
- running under: Debian GNU/Linux 13 (trixie)
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- checking for file ‘httk/DESCRIPTION’ ... OK
- this is package ‘httk’ version ‘2.7.0’
- package encoding: UTF-8
- checking CRAN incoming feasibility ... [4s/7s] OK
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- checking package dependencies ... OK
- checking if this is a source package ... OK
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- checking for hidden files and directories ... OK
- checking for portable file names ... OK
- checking for sufficient/correct file permissions ... OK
- checking serialization versions ... OK
- checking whether package ‘httk’ can be installed ... OK
See the install log for details.
- used C compiler: ‘Debian clang version 19.1.7 (3+b1)’
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- checking for left-over files ... OK
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- checking package subdirectories ... OK
- checking code files for non-ASCII characters ... OK
- checking R files for syntax errors ... OK
- checking whether the package can be loaded ... [3s/4s] OK
- checking whether the package can be loaded with stated dependencies ... [3s/4s] OK
- checking whether the package can be unloaded cleanly ... [3s/4s] OK
- checking whether the namespace can be loaded with stated dependencies ... [3s/5s] OK
- checking whether the namespace can be unloaded cleanly ... [3s/4s] OK
- checking loading without being on the library search path ... [4s/5s] OK
- checking whether startup messages can be suppressed ... [4s/5s] OK
- checking use of S3 registration ... OK
- checking dependencies in R code ... OK
- checking S3 generic/method consistency ... OK
- checking replacement functions ... OK
- checking foreign function calls ... OK
- checking R code for possible problems ... [60s/75s] OK
- checking Rd files ... [13s/16s] OK
- checking Rd metadata ... OK
- checking Rd line widths ... OK
- checking Rd cross-references ... OK
- checking for missing documentation entries ... OK
- checking for code/documentation mismatches ... OK
- checking Rd \usage sections ... OK
- checking Rd contents ... OK
- checking for unstated dependencies in examples ... OK
- checking contents of ‘data’ directory ... OK
- checking data for non-ASCII characters ... [2s/2s] OK
- checking LazyData ... OK
- checking data for ASCII and uncompressed saves ... OK
- checking R/sysdata.rda ... OK
- checking line endings in C/C++/Fortran sources/headers ... OK
- checking pragmas in C/C++ headers and code ... OK
- checking compilation flags used ... OK
- checking compiled code ... OK
- checking installed files from ‘inst/doc’ ... OK
- checking files in ‘vignettes’ ... OK
- checking examples ... [99s/134s] 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.
DLSODA- At T (=R1), too much accuracy requested
for precision of machine.. See TOLSF (=R2)
In above message, R1 = 9.99855e-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: solve_dermal_pbtk -> do.call -> <Anonymous>
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
parameterize_steadystate 6.622 0.039 9.867
solve_1tri_pbtk 6.540 0.036 8.694
solve_1comp 5.962 0.074 8.744
parameterize_3comp2 4.705 0.004 5.298
calc_clearance_frac 4.508 0.076 5.643
calc_elimination_rate 4.082 0.044 6.097
calc_vdist 4.072 0.008 7.365
calc_half_life 3.951 0.039 5.230
calc_hepatic_clearance 3.567 0.008 5.905
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [253s/334s] OK
Running ‘1comp_test.R’ [24s/36s]
Comparing ‘1comp_test.Rout’ to ‘1comp_test.Rout.save’ ... OK
Running ‘3comp_test.R’ [17s/23s]
Comparing ‘3comp_test.Rout’ to ‘3comp_test.Rout.save’ ... OK
Running ‘3compss_test.R’ [14s/19s]
Comparing ‘3compss_test.Rout’ to ‘3compss_test.Rout.save’ ... OK
Running ‘adddata_test.R’ [8s/11s]
Comparing ‘adddata_test.Rout’ to ‘adddata_test.Rout.save’ ... OK
Running ‘caco2_test.R’ [23s/30s]
Comparing ‘caco2_test.Rout’ to ‘caco2_test.Rout.save’ ... OK
Running ‘cheminfo_test.R’ [9s/12s]
Comparing ‘cheminfo_test.Rout’ to ‘cheminfo_test.Rout.save’ ... OK
Running ‘fetal_pbtk_testing.R’ [11s/14s]
Comparing ‘fetal_pbtk_testing.Rout’ to ‘fetal_pbtk_testing.Rout.save’ ... OK
Running ‘ionization_tests.R’ [3s/5s]
Comparing ‘ionization_tests.Rout’ to ‘ionization_tests.Rout.save’ ... OK
Running ‘ivive_test.R’ [37s/47s]
Comparing ‘ivive_test.Rout’ to ‘ivive_test.Rout.save’ ... OK
Running ‘montecarlo_tests.R’ [28s/36s]
Comparing ‘montecarlo_tests.Rout’ to ‘montecarlo_tests.Rout.save’ ... OK
Running ‘other_tests.R’ [12s/15s]
Comparing ‘other_tests.Rout’ to ‘other_tests.Rout.save’ ... OK
Running ‘pbtk_test.R’ [12s/15s]
Comparing ‘pbtk_test.Rout’ to ‘pbtk_test.Rout.save’ ... OK
Running ‘solve_dermal_crude_test.R’ [10s/13s]
Running ‘solve_gas_test.R’ [10s/13s]
Comparing ‘solve_gas_test.Rout’ to ‘solve_gas_test.Rout.save’ ... OK
Running ‘testthat.R’ [27s/35s]
Running ‘unit_test.R’ [7s/9s]
Comparing ‘unit_test.Rout’ to ‘unit_test.Rout.save’ ... OK
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [175s/250s] OK
- checking PDF version of manual ... [19s/25s] OK
- checking HTML version of manual ... [14s/24s] OK
- checking for non-standard things in the check directory ... OK
- DONE
Status: 1 ERROR