* using log directory ‘/srv/hornik/tmp/CRAN/httk.Rcheck’ * using R Under development (unstable) (2024-08-23 r87049) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 18.1.8 (9) Debian flang-new version 18.1.8 (9) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘httk/DESCRIPTION’ ... OK * this is package ‘httk’ version ‘2.4.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [8s/15s] NOTE Maintainer: ‘John Wambaugh ’ Found the following (possibly) invalid URLs: URL: https://gaftp.epa.gov/comptox/High_Throughput_Screening_Data/Previous_Data/ToxCast_Data_Release_Oct_2015/MySQL_Data/ From: man/wambaugh2019.tox21.Rd Status: Error Message: server certificate verification failed. CAfile: /etc/ssl/certs/ca-certificates.crt CRLfile: none (Status without verification: OK) URL: https://www.corning.com/catalog/cls/documents/application-notes/CLS-AN-209.pdf From: man/well_param.Rd Status: 403 Message: Forbidden URL: https://www.sciencedirect.com/science/article/pii/S2468111320300463 From: man/load_pradeep2020.Rd man/pradeep2020.Rd Status: 403 Message: Forbidden * 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 ... [14s/14s] OK * used C compiler: ‘Debian clang version 18.1.8 (9)’ * 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 ... [1s/1s] OK * checking whether the package can be loaded with stated dependencies ... [1s/1s] OK * checking whether the package can be unloaded cleanly ... [1s/1s] OK * checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK * checking whether the namespace can be unloaded cleanly ... [1s/1s] OK * checking loading without being on the library search path ... [1s/1s] OK * checking whether startup messages can be suppressed ... [1s/1s] 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 ... [19s/19s] OK * checking Rd files ... [3s/3s] 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 ... [0s/0s] 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 ... [34s/34s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [102s/102s] OK Running ‘1comp_test.R’ [10s/10s] Comparing ‘1comp_test.Rout’ to ‘1comp_test.Rout.save’ ...163,167d162 < MA : 19 < MW : 440.4 < Pow : 0.8903 < Rblood2plasma : 0.8419 < Vdist : 0.7338 172a168 > MA : 19 173a170 > MW : 440.4 176a174,176 > Pow : 0.8903 > Rblood2plasma : 0.8419 > Vdist : 0.7338 Running ‘3comp_test.R’ [10s/10s] Comparing ‘3comp_test.Rout’ to ‘3comp_test.Rout.save’ ...319a320 > hematocrit : 0.44 320a322 > kgutabs : 0.3711 323a326 > liver.density : 1.05 324a328 > million.cells.per.gliver : 110 325a330,331 > pKa_Accept : 8.09 > pKa_Donor : 2.81 335,340d340 < hematocrit : 0.44 < kgutabs : 0.3711 < liver.density : 1.05 < million.cells.per.gliver : 110 < pKa_Accept : 8.09 < pKa_Donor : 2.81 Running ‘3compss_test.R’ [4s/4s] Comparing ‘3compss_test.Rout’ to ‘3compss_test.Rout.save’ ...78a79,81 > hepatic.bioavailability : 1 > liver.density : 1.05 > million.cells.per.gliver : 110 84,86d86 < hepatic.bioavailability : 1 < liver.density : 1.05 < million.cells.per.gliver : 110 Running ‘adddata_test.R’ [3s/3s] Comparing ‘adddata_test.Rout’ to ‘adddata_test.Rout.save’ ... OK Running ‘caco2_test.R’ [9s/9s] Comparing ‘caco2_test.Rout’ to ‘caco2_test.Rout.save’ ... OK Running ‘cheminfo_test.R’ [3s/3s] Comparing ‘cheminfo_test.Rout’ to ‘cheminfo_test.Rout.save’ ... OK Running ‘fetal_pbtk_testing.R’ [6s/6s] Comparing ‘fetal_pbtk_testing.Rout’ to ‘fetal_pbtk_testing.Rout.save’ ...66,68c66,68 < [3,] 93 3.172e-06 6.016 8.701 1.608 3.376 1.608 2.670 2.323 9.240 < [4,] 94 1.000e-09 5.846 8.454 1.562 3.281 1.562 2.595 2.257 8.978 < [5,] 95 2.000e-09 5.680 8.215 1.517 3.188 1.517 2.521 2.193 8.724 --- > [3,] 93 3.170e-06 6.016 8.701 1.608 3.376 1.608 2.670 2.323 9.240 > [4,] 94 0.000e+00 5.846 8.454 1.562 3.281 1.562 2.595 2.257 8.978 > [5,] 95 0.000e+00 5.680 8.215 1.517 3.188 1.517 2.521 2.193 8.724 106,108c106,108 < [3,] 93 3.172e-06 6.016 8.701 1.608 3.376 1.608 2.670 2.323 9.240 < [4,] 94 1.000e-09 5.846 8.454 1.562 3.281 1.562 2.595 2.257 8.978 < [5,] 95 2.000e-09 5.680 8.215 1.517 3.188 1.517 2.521 2.193 8.724 --- > [3,] 93 3.170e-06 6.016 8.701 1.608 3.376 1.608 2.670 2.323 9.240 > [4,] 94 0.000e+00 5.846 8.454 1.562 3.281 1.562 2.595 2.257 8.978 > [5,] 95 0.000e+00 5.680 8.215 1.517 3.188 1.517 2.521 2.193 8.724 140a141,144 > adipose_density : 0.95 > amnf_density : 1.01 > arterial_blood_fraction : 0.16 > brain_density : 1.04 150a155,162 > fblood_weight_ratio : 80 > fBW_gompertz_theta0 : 0.0018282 > fBW_gompertz_theta1 : 1.1735 > fBW_gompertz_theta2 : 0.077577 > ffmx_density : 1.1 > fhematocrit_cubic_theta1 : 4.5061 > fhematocrit_cubic_theta2 : -0.18487 > fhematocrit_cubic_theta3 : 0.0026766 155a168,171 > gut_density : 1.04 > hematocrit_quadratic_theta0 : 39.192 > hematocrit_quadratic_theta1 : -0.10562 > hematocrit_quadratic_theta2 : -0.00071045 166a183,184 > kgutabs : 0.3711 > kidney_density : 1.05 173a192,193 > liver_density : 1.05 > lung_density : 1.05 174a195 > million.cells.per.gliver : 110 175a197,201 > pH_Plasma_fet : 7.28 > pH_Plasma_mat : 7.38 > pKa_Accept : NA > pKa_Donor : 9.46 > placenta_density : 1.02 176a203 > pre_pregnant_BW : 61.1 220a248,249 > term : 40 > thyroid_density : 1.05 223a253 > venous_blood_fraction : 0.595 256,285d285 < adipose_density : 0.95 < amnf_density : 1.01 < arterial_blood_fraction : 0.16 < brain_density : 1.04 < fBW_gompertz_theta0 : 0.0018282 < fBW_gompertz_theta1 : 1.1735 < fBW_gompertz_theta2 : 0.077577 < fblood_weight_ratio : 80 < ffmx_density : 1.1 < fhematocrit_cubic_theta1 : 4.5061 < fhematocrit_cubic_theta2 : -0.18487 < fhematocrit_cubic_theta3 : 0.0026766 < gut_density : 1.04 < hematocrit_quadratic_theta0 : 39.192 < hematocrit_quadratic_theta1 : -0.10562 < hematocrit_quadratic_theta2 : -0.00071045 < kgutabs : 0.3711 < kidney_density : 1.05 < liver_density : 1.05 < lung_density : 1.05 < million.cells.per.gliver : 110 < pH_Plasma_fet : 7.28 < pH_Plasma_mat : 7.38 < pKa_Accept : NA < pKa_Donor : 9.46 < placenta_density : 1.02 < pre_pregnant_BW : 61.1 < term : 40 < thyroid_density : 1.05 < venous_blood_fraction : 0.595 Running ‘ivive_test.R’ [11s/11s] Comparing ‘ivive_test.Rout’ to ‘ivive_test.Rout.save’ ... OK Running ‘montecarlo_tests.R’ [20s/20s] Comparing ‘montecarlo_tests.Rout’ to ‘montecarlo_tests.Rout.save’ ... OK Running ‘other_tests.R’ [10s/10s] Comparing ‘other_tests.Rout’ to ‘other_tests.Rout.save’ ... OK Running ‘pbtk_test.R’ [8s/8s] Comparing ‘pbtk_test.Rout’ to ‘pbtk_test.Rout.save’ ...219a220 > hematocrit : 0.44 220a222 > kgutabs : 0.3711 225a228 > liver.density : 1.05 226a230 > million.cells.per.gliver : 110 227a232,233 > pKa_Accept : 8.09 > pKa_Donor : 2.81 242,247d247 < hematocrit : 0.44 < kgutabs : 0.3711 < liver.density : 1.05 < million.cells.per.gliver : 110 < pKa_Accept : 8.09 < pKa_Donor : 2.81 Running ‘solve_gas_test.R’ [5s/5s] Comparing ‘solve_gas_test.Rout’ to ‘solve_gas_test.Rout.save’ ...133a134 > hematocrit : 0.44 135a137 > kgutabs : 0.3711 138a141 > km : 1 141a145,146 > kUrtc : 11 > liver.density : 1.05 142a148 > million.cells.per.gliver : 110 143a150,151 > pKa_Accept : NA > pKa_Donor : NA 157a166 > vmax : 0 161,169d169 < hematocrit : 0.44 < kUrtc : 11 < kgutabs : 0.3711 < km : 1 < liver.density : 1.05 < million.cells.per.gliver : 110 < pKa_Accept : NA < pKa_Donor : NA < vmax : 0 Running ‘unit_test.R’ [3s/3s] 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 ... [72s/72s] OK * checking PDF version of manual ... [7s/7s] OK * checking HTML version of manual ... [5s/5s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 NOTE