* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/httk.Rcheck’ * using R Under development (unstable) (2025-04-24 r88177) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3) GNU Fortran (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3) * running under: Fedora Linux 40 (Workstation Edition) * using session charset: UTF-8 * checking for file ‘httk/DESCRIPTION’ ... OK * this is package ‘httk’ version ‘2.6.0’ * package encoding: UTF-8 * 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 whether package ‘httk’ can be installed ... [27s/27s] OK * used C compiler: ‘gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)’ * checking package directory ... 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 ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... 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 ... [36s/36s] OK * checking Rd files ... 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 ... 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 compilation flags used ... OK * checking compiled code ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [62s/63s] OK * checking examples with --run-donttest ... [11m/11m] ERROR Running examples in ‘httk-Ex.R’ failed The error most likely occurred in: > ### Name: solve_fetal_pbtk > ### Title: Solve_fetal_PBTK > ### Aliases: solve_fetal_pbtk > ### Keywords: Solve > > ### ** Examples > > > ## No test: > out = solve_fetal_pbtk(chem.name = 'bisphenol a', daily.dose = 1, + doses.per.day = 3) None of the monitored components undergo unit conversions (i.e. conversion factor of 1). AUC is area under the maternal plasma concentration curve in uM*days units. fAUC is area under the fetal plasma concentration curve in uM*days units. The model outputs are provided in the following units: umol: Agutlumen, Atubules, Ametabolized, Aplacenta uM: Cgut, Cliver, Cven, Clung, Cart, Cadipose, Crest, Ckidney, Cplasma, Cplacenta, Cfliver, Cfven, Cfart, Cfgut, Cflung, Cfrest, Cfthyroid, Cfkidney, Cfbrain, Cfplasma unitless: Rblood2plasma, Rfblood2plasma uM*days: AUC, fAUC > > # With adjustement to fraction unbound plasma for fetus: > fetal_parms_fup_adjusted <- + parameterize_fetal_pbtk(chem.name = "triclosan") > head(solve_fetal_pbtk(parameters = fetal_parms_fup_adjusted)) None of the monitored components undergo unit conversions (i.e. conversion factor of 1). Warning in solve_model(chem.name = chem.name, chem.cas = chem.cas, dtxsid = dtxsid, : Rblood2plasma not recalculated. Set recalc.blood2plasma to TRUE if desired. Warning in solve_model(chem.name = chem.name, chem.cas = chem.cas, dtxsid = dtxsid, : Clearance not recalculated. Set recalc.clearance to TRUE if desired. AUC is area under the maternal plasma concentration curve in uM*days units. fAUC is area under the fetal plasma concentration curve in uM*days units. The model outputs are provided in the following units: umol: Agutlumen, Atubules, Ametabolized, Aplacenta uM: Cgut, Cliver, Cven, Clung, Cart, Cadipose, Crest, Ckidney, Cplasma, Cplacenta, Cfliver, Cfven, Cfart, Cfgut, Cflung, Cfrest, Cfthyroid, Cfkidney, Cfbrain, Cfplasma unitless: Rblood2plasma, Rfblood2plasma uM*days: AUC, fAUC time Agutlumen Cgut Cliver Cven Clung Cart Cadipose [1,] 91.0000 1.361e+02 0.0000 0.0000000 0.000e+00 0.000e+00 0.0000000 0.000 [2,] 91.0001 1.360e+02 0.1074 0.0009451 3.520e-06 6.600e-07 0.0000002 0.000 [3,] 92.0000 1.844e-02 3.1320 6.1810000 5.580e-01 4.043e-01 0.5580000 4.194 [4,] 93.0000 2.500e-06 3.1180 6.1560000 5.559e-01 4.027e-01 0.5559000 4.182 [5,] 94.0000 0.000e+00 3.1080 6.1340000 5.541e-01 4.012e-01 0.5541000 4.167 [6,] 95.0000 0.000e+00 3.0970 6.1130000 5.522e-01 3.998e-01 0.5522000 4.153 Crest Ckidney Cplasma Atubules Ametabolized Rblood2plasma AUC [1,] 0.000 0.000e+00 0.000e+00 0.0000 0.00000 0.6923 0.0000 [2,] 0.000 3.000e-08 5.090e-06 0.0000 0.00000 0.6923 0.0000 [3,] 1.050 4.819e+00 8.059e-01 0.2778 0.07541 0.6924 0.8207 [4,] 1.046 4.799e+00 8.027e-01 0.5506 0.14490 0.6925 1.6250 [5,] 1.042 4.782e+00 7.999e-01 0.8228 0.21420 0.6927 2.4260 [6,] 1.038 4.766e+00 7.971e-01 1.0950 0.28330 0.6928 3.2250 fAUC Aplacenta Cplacenta Cfliver Cfven Cfart Cfgut Cflung Cfrest [1,] 0.0000 0.00000 0.0000 0.000 0.0000 0.0000 0.000 0.0000 0.000 [2,] 0.0000 0.00000 0.0000 0.000 0.0000 0.0000 0.000 0.0000 0.000 [3,] 0.6601 0.03818 0.3498 5.897 0.4888 0.4888 3.104 0.3954 1.824 [4,] 1.3140 0.03884 0.3484 5.873 0.4861 0.4861 3.092 0.3938 1.817 [5,] 1.9650 0.03953 0.3472 5.853 0.4836 0.4836 3.081 0.3924 1.811 [6,] 2.6140 0.04022 0.3460 5.832 0.4812 0.4812 3.070 0.3910 1.804 Cfthyroid Cfkidney Cfbrain Cfplasma Rfblood2plasma [1,] 0.000 0.000 0.000 0.0000 0.7471 [2,] 0.000 0.000 0.000 0.0000 0.7471 [3,] 2.959 4.660 1.043 0.6552 0.7460 [4,] 2.947 4.641 1.039 0.6525 0.7449 [5,] 2.937 4.625 1.035 0.6502 0.7438 [6,] 2.927 4.609 1.032 0.6479 0.7427 > > # Without adjustement to fraction unbound plasma for fetus: > fetal_parms_fup_unadjusted <- + parameterize_fetal_pbtk(chem.name = "triclosan", + fetal_fup_adjustment = FALSE) > head(solve_fetal_pbtk(parameters = fetal_parms_fup_unadjusted)) None of the monitored components undergo unit conversions (i.e. conversion factor of 1). Warning in solve_model(chem.name = chem.name, chem.cas = chem.cas, dtxsid = dtxsid, : Rblood2plasma not recalculated. Set recalc.blood2plasma to TRUE if desired. Warning in solve_model(chem.name = chem.name, chem.cas = chem.cas, dtxsid = dtxsid, : Clearance not recalculated. Set recalc.clearance to TRUE if desired. AUC is area under the maternal plasma concentration curve in uM*days units. fAUC is area under the fetal plasma concentration curve in uM*days units. The model outputs are provided in the following units: umol: Agutlumen, Atubules, Ametabolized, Aplacenta uM: Cgut, Cliver, Cven, Clung, Cart, Cadipose, Crest, Ckidney, Cplasma, Cplacenta, Cfliver, Cfven, Cfart, Cfgut, Cflung, Cfrest, Cfthyroid, Cfkidney, Cfbrain, Cfplasma unitless: Rblood2plasma, Rfblood2plasma uM*days: AUC, fAUC time Agutlumen Cgut Cliver Cven Clung Cart Cadipose [1,] 91.0000 1.361e+02 0.0000 0.0000000 0.000e+00 0.000e+00 0.0000000 0.000 [2,] 91.0001 1.360e+02 0.1074 0.0009451 3.520e-06 6.600e-07 0.0000002 0.000 [3,] 92.0000 1.844e-02 3.1320 6.1810000 5.580e-01 4.043e-01 0.5580000 4.194 [4,] 93.0000 2.500e-06 3.1180 6.1560000 5.559e-01 4.027e-01 0.5559000 4.182 [5,] 94.0000 0.000e+00 3.1070 6.1340000 5.540e-01 4.012e-01 0.5540000 4.167 [6,] 95.0000 0.000e+00 3.0970 6.1120000 5.522e-01 3.998e-01 0.5522000 4.153 Crest Ckidney Cplasma Atubules Ametabolized Rblood2plasma AUC fAUC [1,] 0.000 0.000e+00 0.000e+00 0.0000 0.0000 0.6923 0.0000 0.000 [2,] 0.000 3.000e-08 5.090e-06 0.0000 0.0000 0.6923 0.0000 0.000 [3,] 1.050 4.819e+00 8.059e-01 0.2778 0.0754 0.6924 0.8207 0.806 [4,] 1.046 4.799e+00 8.027e-01 0.5506 0.1449 0.6925 1.6250 1.603 [5,] 1.042 4.782e+00 7.998e-01 0.8228 0.2142 0.6927 2.4260 2.398 [6,] 1.038 4.766e+00 7.970e-01 1.0950 0.2833 0.6928 3.2240 3.189 Aplacenta Cplacenta Cfliver Cfven Cfart Cfgut Cflung Cfrest Cfthyroid [1,] 0.00000 0.0000 0.000 0.0000 0.0000 0.000 0.0000 0.000 0.000 [2,] 0.00000 0.0000 0.000 0.0000 0.0000 0.000 0.0000 0.000 0.000 [3,] 0.03818 0.3498 6.166 0.5820 0.5820 3.128 0.4038 1.910 2.815 [4,] 0.03884 0.3484 6.141 0.5787 0.5787 3.116 0.4021 1.902 2.803 [5,] 0.03953 0.3472 6.120 0.5757 0.5757 3.105 0.4007 1.896 2.793 [6,] 0.04021 0.3460 6.098 0.5728 0.5728 3.094 0.3993 1.889 2.783 Cfkidney Cfbrain Cfplasma Rfblood2plasma [1,] 0.000 0.000 0.0000 0.7295 [2,] 0.000 0.000 0.0000 0.7295 [3,] 4.812 1.110 0.7991 0.7283 [4,] 4.792 1.105 0.7959 0.7271 [5,] 4.775 1.101 0.7931 0.7259 [6,] 4.758 1.098 0.7903 0.7248 > > # The following will not work because Diquat dibromide monohydrate's > # Henry's Law Constant (-3.912) is higher than that of Acetone (~-4.5): > try(head(solve_fetal_pbtk(chem.cas = "6385-62-2"))) Error in check_model(chem.cas = chem.cas, chem.name = chem.name, dtxsid = dtxsid, : Chemical CAS: 6385-62-2, DTXSID: DTXSID7031248, named: Diquat dibromide monohydrate is outside the physico-chemical property domain for model pbtk. See help(get_cheminfo). > # However, we can turn off checking for phys-chem properties, since we know > # that Diquat dibromide monohydrate is not too volatile: > head(solve_fetal_pbtk(chem.cas = "6385-62-2", physchem.exclude = FALSE)) DINTDY- T (=R1) illegal In above message, R1 = 262.33 T not in interval TCUR - HU (= R1) to TCUR (=R2) In above message, R1 = 262.319, R2 = 262.33 DLSODA- Trouble in DINTDY. ITASK = I1, TOUT = R1 In above message, I1 = 1 In above message, R1 = 262.33 Error in lsoda(y, times, func, parms, ...) : illegal input detected before taking any integration steps - see written message Calls: head -> solve_fetal_pbtk -> solve_model -> ode -> lsoda Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘1comp_test.R’ [29s/29s] Comparing ‘1comp_test.Rout’ to ‘1comp_test.Rout.save’ ... OK Running ‘3comp_test.R’ [21s/22s] Comparing ‘3comp_test.Rout’ to ‘3comp_test.Rout.save’ ... OK Running ‘3compss_test.R’ Comparing ‘3compss_test.Rout’ to ‘3compss_test.Rout.save’ ... OK Running ‘adddata_test.R’ Comparing ‘adddata_test.Rout’ to ‘adddata_test.Rout.save’ ... OK Running ‘caco2_test.R’ [18s/18s] Comparing ‘caco2_test.Rout’ to ‘caco2_test.Rout.save’ ... OK Running ‘cheminfo_test.R’ Comparing ‘cheminfo_test.Rout’ to ‘cheminfo_test.Rout.save’ ... OK Running ‘fetal_pbtk_testing.R’ [13s/14s] Comparing ‘fetal_pbtk_testing.Rout’ to ‘fetal_pbtk_testing.Rout.save’ ... OK Running ‘ivive_test.R’ [23s/23s] Comparing ‘ivive_test.Rout’ to ‘ivive_test.Rout.save’ ... OK Running ‘montecarlo_tests.R’ [46s/46s] Comparing ‘montecarlo_tests.Rout’ to ‘montecarlo_tests.Rout.save’ ... OK Running ‘other_tests.R’ [23s/23s] Comparing ‘other_tests.Rout’ to ‘other_tests.Rout.save’ ... OK Running ‘pbtk_test.R’ [18s/18s] Comparing ‘pbtk_test.Rout’ to ‘pbtk_test.Rout.save’ ... OK Running ‘solve_gas_test.R’ [11s/11s] Comparing ‘solve_gas_test.Rout’ to ‘solve_gas_test.Rout.save’ ... OK Running ‘testthat.R’ [16s/16s] Running ‘unit_test.R’ Comparing ‘unit_test.Rout’ to ‘unit_test.Rout.save’ ... OK [243s/244s] OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [152s/152s] OK * checking PDF version of manual ... [16s/16s] OK * checking for non-standard things in the check directory ... NOTE Found the following files/directories: ‘PBTKmodel.jan’ ‘PBTKmodel.xml’ ‘input_param_data_files’ * checking for detritus in the temp directory ... OK * checking for new files in some other directories ... OK * DONE Status: 1 ERROR, 1 NOTE See ‘/data/blackswan/ripley/R/packages/tests-devel/httk.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 21:14.38, 1224.39 + 43.77