* using log directory ‘/home/hornik/tmp/CRAN_special_valgrind/httk.Rcheck’ * using R Under development (unstable) (2025-08-26 r88710) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc-14 (Debian 14.2.0-19) 14.2.0 GNU Fortran (Debian 14.2.0-19) 14.2.0 * running under: Debian GNU/Linux forky/sid * using session charset: UTF-8 * using option ‘--use-valgrind’ * checking for file ‘httk/DESCRIPTION’ ... OK * this is package ‘httk’ version ‘2.7.2’ * 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 serialization versions ... OK * checking whether package ‘httk’ can be installed ... [24s/25s] OK * used C compiler: ‘gcc-14 (Debian 14.3.0-5) 14.3.0’ * 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/2s] OK * checking whether the package can be loaded with stated dependencies ... [2s/2s] OK * checking whether the package can be unloaded cleanly ... [2s/2s] OK * checking whether the namespace can be loaded with stated dependencies ... [2s/2s] OK * checking whether the namespace can be unloaded cleanly ... [2s/2s] OK * checking loading without being on the library search path ... [2s/2s] OK * checking whether startup messages can be suppressed ... [2s/2s] 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 ... [29s/30s] OK * checking Rd files ... [6s/7s] 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 ... [30m/30m] ERROR Running examples in ‘httk-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: solve_fetal_pbtk > ### Title: Solve_fetal_PBTK > ### Aliases: solve_fetal_pbtk > ### Keywords: Solve > > ### ** Examples > > > out = solve_fetal_pbtk(chem.name = 'bisphenol a', daily.dose = 1, + doses.per.day = 3) Execution halted ==79723== ==79723== HEAP SUMMARY: ==79723== in use at exit: 326,971,328 bytes in 56,833 blocks ==79723== total heap usage: 60,267,252 allocs, 60,210,419 frees, 18,706,338,808 bytes allocated ==79723== ==79723== LEAK SUMMARY: ==79723== definitely lost: 0 bytes in 0 blocks ==79723== indirectly lost: 0 bytes in 0 blocks ==79723== possibly lost: 0 bytes in 0 blocks ==79723== still reachable: 326,971,328 bytes in 56,833 blocks ==79723== suppressed: 0 bytes in 0 blocks ==79723== Rerun with --leak-check=full to see details of leaked memory ==79723== ==79723== For lists of detected and suppressed errors, rerun with: -s ==79723== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 0 from 0) Examples with CPU (user + system) or elapsed time > 5s user system elapsed parameterize_steadystate 151.347 0.204 151.449 solve_1tri_pbtk 141.436 0.148 141.470 solve_1comp 129.406 0.172 129.478 parameterize_3comp2 105.169 0.172 105.269 parameterize_pfas1comp 88.455 0.144 88.508 calc_elimination_rate 88.211 0.192 88.327 calc_half_life 87.121 0.192 87.248 monte_carlo 71.190 0.076 71.245 calc_total_clearance 69.700 0.160 69.821 parameterize_sumclearances 67.841 0.080 67.874 get_physchem_param 54.166 0.128 54.251 calc_tkstats 53.707 0.200 53.887 calc_analytic_css 53.170 0.080 53.206 solve_3comp 50.444 0.068 50.475 parameterize_gas_pbtk 49.956 0.036 49.970 parameterize_pbtk 49.640 0.060 49.662 predict_partitioning_schmitt 49.425 0.068 49.475 parameterize_3comp 43.391 0.060 43.426 calc_clearance_frac 38.233 0.068 38.282 calc_hep_clearance 37.949 0.040 37.959 calc_rblood2plasma 26.263 0.140 26.388 solve_dermal_pbtk 20.949 0.020 20.949 armitage_eval 18.284 0.077 18.358 parameterize_schmitt 17.476 0.044 17.512 lump_tissues 17.095 0.040 17.131 calc_vdist 16.222 0.012 16.226 httkpop_mc 8.645 0.016 8.661 convert_units 5.772 0.008 5.780 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [0m/30m] ERROR Running ‘3comp_test.R’ [343s/343s] Comparing ‘3comp_test.Rout’ to ‘3comp_test.Rout.save’ ...1,5d0 < ==87414== Memcheck, a memory error detector < ==87414== Copyright (C) 2002-2024, and GNU GPL'd, by Julian Seward et al. < ==87414== Using Valgrind-3.24.0 and LibVEX; rerun with -h for copyright info < ==87414== Command: /home/hornik/tmp/R-d-gcc-valg/bin/exec/R -f 3comp_test.R --restore --save --no-readline --vanilla < ==87414== 187,204d181 < > proc.time() < user system elapsed < 337.303 0.917 337.160 < ==87414== < ==87414== HEAP SUMMARY: < ==87414== in use at exit: 334,238,427 bytes in 56,819 blocks < ==87414== total heap usage: 9,075,246 allocs, 9,018,427 frees, 3,024,389,740 bytes allocated < ==87414== < ==87414== LEAK SUMMARY: < ==87414== definitely lost: 0 bytes in 0 blocks < ==87414== indirectly lost: 0 bytes in 0 blocks < ==87414== possibly lost: 384 bytes in 1 blocks < ==87414== still reachable: 334,238,043 bytes in 56,818 blocks < ==87414== suppressed: 0 bytes in 0 blocks < ==87414== Rerun with --leak-check=full to see details of leaked memory < ==87414== < ==87414== For lists of detected and suppressed errors, rerun with: -s < ==87414== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 0 from 0) Running ‘3compss_test.R’ [303s/303s] Comparing ‘3compss_test.Rout’ to ‘3compss_test.Rout.save’ ...1,5d0 < ==88681== Memcheck, a memory error detector < ==88681== Copyright (C) 2002-2024, and GNU GPL'd, by Julian Seward et al. < ==88681== Using Valgrind-3.24.0 and LibVEX; rerun with -h for copyright info < ==88681== Command: /home/hornik/tmp/R-d-gcc-valg/bin/exec/R -f 3compss_test.R --restore --save --no-readline --vanilla < ==88681== 95,112d89 < > proc.time() < user system elapsed < 297.629 0.930 297.473 < ==88681== < ==88681== HEAP SUMMARY: < ==88681== in use at exit: 316,929,126 bytes in 53,503 blocks < ==88681== total heap usage: 8,461,132 allocs, 8,407,629 frees, 2,851,937,143 bytes allocated < ==88681== < ==88681== LEAK SUMMARY: < ==88681== definitely lost: 0 bytes in 0 blocks < ==88681== indirectly lost: 0 bytes in 0 blocks < ==88681== possibly lost: 0 bytes in 0 blocks < ==88681== still reachable: 316,929,126 bytes in 53,503 blocks < ==88681== suppressed: 0 bytes in 0 blocks < ==88681== Rerun with --leak-check=full to see details of leaked memory < ==88681== < ==88681== For lists of detected and suppressed errors, rerun with: -s < ==88681== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 0 from 0) Running ‘caco2_test.R’ [470s/470s] Comparing ‘caco2_test.Rout’ to ‘caco2_test.Rout.save’ ...1,5d0 < ==104330== Memcheck, a memory error detector < ==104330== Copyright (C) 2002-2024, and GNU GPL'd, by Julian Seward et al. < ==104330== Using Valgrind-3.24.0 and LibVEX; rerun with -h for copyright info < ==104330== Command: /home/hornik/tmp/R-d-gcc-valg/bin/exec/R -f caco2_test.R --restore --save --no-readline --vanilla < ==104330== 114,131d108 < > proc.time() < user system elapsed < 464.206 1.396 464.343 < ==104330== < ==104330== HEAP SUMMARY: < ==104330== in use at exit: 303,803,521 bytes in 55,175 blocks < ==104330== total heap usage: 11,122,415 allocs, 11,067,240 frees, 3,661,525,966 bytes allocated < ==104330== < ==104330== LEAK SUMMARY: < ==104330== definitely lost: 0 bytes in 0 blocks < ==104330== indirectly lost: 0 bytes in 0 blocks < ==104330== possibly lost: 0 bytes in 0 blocks < ==104330== still reachable: 303,803,521 bytes in 55,175 blocks < ==104330== suppressed: 0 bytes in 0 blocks < ==104330== Rerun with --leak-check=full to see details of leaked memory < ==104330== < ==104330== For lists of detected and suppressed errors, rerun with: -s < ==104330== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 0 from 0) Running ‘cheminfo_test.R’ [180s/180s] Comparing ‘cheminfo_test.Rout’ to ‘cheminfo_test.Rout.save’ ...1,5d0 < ==122100== Memcheck, a memory error detector < ==122100== Copyright (C) 2002-2024, and GNU GPL'd, by Julian Seward et al. < ==122100== Using Valgrind-3.24.0 and LibVEX; rerun with -h for copyright info < ==122100== Command: /home/hornik/tmp/R-d-gcc-valg/bin/exec/R -f cheminfo_test.R --restore --save --no-readline --vanilla < ==122100== 266,283d260 < > proc.time() < user system elapsed < 175.502 0.519 175.148 < ==122100== < ==122100== HEAP SUMMARY: < ==122100== in use at exit: 300,702,191 bytes in 52,837 blocks < ==122100== total heap usage: 1,520,235 allocs, 1,467,398 frees, 1,078,277,401 bytes allocated < ==122100== < ==122100== LEAK SUMMARY: < ==122100== definitely lost: 0 bytes in 0 blocks < ==122100== indirectly lost: 0 bytes in 0 blocks < ==122100== possibly lost: 384 bytes in 1 blocks < ==122100== still reachable: 300,701,807 bytes in 52,836 blocks < ==122100== suppressed: 0 bytes in 0 blocks < ==122100== Rerun with --leak-check=full to see details of leaked memory < ==122100== < ==122100== For lists of detected and suppressed errors, rerun with: -s < ==122100== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 0 from 0) Running ‘fetal_pbtk_testing.R’ [217s/217s] Comparing ‘fetal_pbtk_testing.Rout’ to ‘fetal_pbtk_testing.Rout.save’ ...1,5d0 < ==123183== Memcheck, a memory error detector < ==123183== Copyright (C) 2002-2024, and GNU GPL'd, by Julian Seward et al. < ==123183== Using Valgrind-3.24.0 and LibVEX; rerun with -h for copyright info < ==123183== Command: /home/hornik/tmp/R-d-gcc-valg/bin/exec/R -f fetal_pbtk_testing.R --restore --save --no-readline --vanilla < ==123183== 205,222d199 < > proc.time() < user system elapsed < 211.951 0.697 211.661 < ==123183== < ==123183== HEAP SUMMARY: < ==123183== in use at exit: 317,173,875 bytes in 56,251 blocks < ==123183== total heap usage: 4,562,746 allocs, 4,506,495 frees, 1,814,470,049 bytes allocated < ==123183== < ==123183== LEAK SUMMARY: < ==123183== definitely lost: 0 bytes in 0 blocks < ==123183== indirectly lost: 0 bytes in 0 blocks < ==123183== possibly lost: 384 bytes in 1 blocks < ==123183== still reachable: 317,173,491 bytes in 56,250 blocks < ==123183== suppressed: 0 bytes in 0 blocks < ==123183== Rerun with --leak-check=full to see details of leaked memory < ==123183== < ==123183== For lists of detected and suppressed errors, rerun with: -s < ==123183== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 0 from 0) Running ‘ionization_tests.R’ [61s/61s] Comparing ‘ionization_tests.Rout’ to ‘ionization_tests.Rout.save’ ...1,5d0 < ==124250== Memcheck, a memory error detector < ==124250== Copyright (C) 2002-2024, and GNU GPL'd, by Julian Seward et al. < ==124250== Using Valgrind-3.24.0 and LibVEX; rerun with -h for copyright info < ==124250== Command: /home/hornik/tmp/R-d-gcc-valg/bin/exec/R -f ionization_tests.R --restore --save --no-readline --vanilla < ==124250== 177,194d171 < > proc.time() < user system elapsed < 57.022 0.282 56.471 < ==124250== < ==124250== HEAP SUMMARY: < ==124250== in use at exit: 217,802,327 bytes in 47,837 blocks < ==124250== total heap usage: 229,878 allocs, 182,041 frees, 416,355,599 bytes allocated < ==124250== < ==124250== LEAK SUMMARY: < ==124250== definitely lost: 0 bytes in 0 blocks < ==124250== indirectly lost: 0 bytes in 0 blocks < ==124250== possibly lost: 0 bytes in 0 blocks < ==124250== still reachable: 217,802,327 bytes in 47,837 blocks < ==124250== suppressed: 0 bytes in 0 blocks < ==124250== Rerun with --leak-check=full to see details of leaked memory < ==124250== < ==124250== For lists of detected and suppressed errors, rerun with: -s < ==124250== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 0 from 0) Running ‘ivive_test.R’ [231s/231s] Running ‘montecarlo_tests.R’ [0s/15s] Running ‘other_tests.R’ 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) Execution halted ==124506== ==124506== HEAP SUMMARY: ==124506== in use at exit: 333,340,481 bytes in 56,803 blocks ==124506== total heap usage: 5,988,961 allocs, 5,932,158 frees, 2,388,267,126 bytes allocated ==124506== ==124506== LEAK SUMMARY: ==124506== definitely lost: 0 bytes in 0 blocks ==124506== indirectly lost: 0 bytes in 0 blocks ==124506== possibly lost: 0 bytes in 0 blocks ==124506== still reachable: 333,340,481 bytes in 56,803 blocks ==124506== suppressed: 0 bytes in 0 blocks ==124506== Rerun with --leak-check=full to see details of leaked memory ==124506== ==124506== For lists of detected and suppressed errors, rerun with: -s ==124506== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 0 from 0) Running the tests in ‘tests/montecarlo_tests.R’ failed. Complete output: > # R CMD BATCH --no-timing --no-restore --no-save montecarlo_tests.R montecarlo_tests.Rout > > # Get rid of anything in the workspace: > rm(list=ls()) > > library(httk) ==126283== ==126283== Process terminating with default action of signal 15 (SIGTERM) * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [97s/98s] OK * checking PDF version of manual ... [17s/17s] OK * checking HTML version of manual ... [7s/8s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... NOTE Found the following files/directories: ‘vgdb-pipe-from-vgdb-to-126377-by-hornik-on-???’ ‘vgdb-pipe-shared-mem-vgdb-126377-by-hornik-on-???’ ‘vgdb-pipe-to-vgdb-from-126377-by-hornik-on-???’ * DONE Status: 2 ERRORs, 1 NOTE