- using R Under development (unstable) (2025-12-18 r89199)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
gcc-15 (Debian 15.2.0-11) 15.2.0
GNU Fortran (Debian 15.2.0-11) 15.2.0
- running under: Debian GNU/Linux forky/sid
- using session charset: UTF-8
- checking for file ‘httk/DESCRIPTION’ ... OK
- this is package ‘httk’ version ‘2.7.4’
- package encoding: UTF-8
- checking CRAN incoming feasibility ... [3s/5s] OK
- checking package namespace information ... OK
- checking package dependencies ... OK
- checking if this is a source package ... OK
- checking if there is a namespace ... OK
- checking for executable files ... OK
- 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: ‘gcc-15 (Debian 15.2.0-11) 15.2.0’
- checking package directory ... OK
- checking for future file timestamps ... OK
- checking ‘build’ directory ... OK
- checking DESCRIPTION meta-information ... OK
- checking top-level files ... OK
- checking for left-over files ... OK
- checking index information ... OK
- 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 ... [2s/3s] OK
- checking whether the package can be loaded with stated dependencies ... [2s/2s] OK
- checking whether the package can be unloaded cleanly ... [2s/3s] OK
- checking whether the namespace can be loaded with stated dependencies ... [2s/2s] OK
- checking whether the namespace can be unloaded cleanly ... [3s/3s] OK
- checking loading without being on the library search path ... [3s/3s] OK
- checking whether startup messages can be suppressed ... [3s/4s] 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 ... [38s/52s] OK
- checking Rd files ... [10s/12s] 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 ... [1s/1s] 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 ... [3s/4s] ERROR
Running examples in ‘httk-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### 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
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [138s/167s] ERROR
Running ‘3comp_test.R’ [11s/14s]
Comparing ‘3comp_test.Rout’ to ‘3comp_test.Rout.save’ ... OK
Running ‘3compss_test.R’ [11s/13s]
Comparing ‘3compss_test.Rout’ to ‘3compss_test.Rout.save’ ... OK
Running ‘caco2_test.R’ [15s/17s]
Comparing ‘caco2_test.Rout’ to ‘caco2_test.Rout.save’ ... OK
Running ‘cheminfo_test.R’ [6s/9s]
Comparing ‘cheminfo_test.Rout’ to ‘cheminfo_test.Rout.save’ ... OK
Running ‘fetal_pbtk_testing.R’ [7s/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’ [11s/12s]
Running ‘montecarlo_tests.R’ [20s/24s]
Comparing ‘montecarlo_tests.Rout’ to ‘montecarlo_tests.Rout.save’ ... OK
Running ‘other_tests.R’ [9s/11s]
Comparing ‘other_tests.Rout’ to ‘other_tests.Rout.save’ ... OK
Running ‘pbtk_test.R’ [9s/11s]
Comparing ‘pbtk_test.Rout’ to ‘pbtk_test.Rout.save’ ... OK
Running ‘solve_dermal_test.R’ [6s/7s]
Comparing ‘solve_dermal_test.Rout’ to ‘solve_dermal_test.Rout.save’ ... OK
Running ‘solve_gas_test.R’ [7s/8s]
Comparing ‘solve_gas_test.Rout’ to ‘solve_gas_test.Rout.save’ ... OK
Running ‘testthat.R’ [18s/21s]
Running ‘unit_test.R’ [5s/6s]
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
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [26s/36s] OK
- checking PDF version of manual ... [14s/20s] OK
- checking HTML version of manual ... [16s/25s] OK
- checking for non-standard things in the check directory ... OK
- DONE
Status: 2 ERRORs