* using log directory ‘/srv/hornik/tmp/CRAN/httk.Rcheck’ * using R Under development (unstable) (2023-12-04 r85659) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 17.0.5 (1) Debian flang-new version 17.0.5 (1) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘httk/DESCRIPTION’ ... OK * this is package ‘httk’ version ‘2.3.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [7s/12s] NOTE Maintainer: ‘John Wambaugh ’ Found the following (possibly) invalid URLs: URL: https://clowder.edap-cluster.com/datasets/6364026ee4b04f6bb1409eda?space=62bb560ee4b07abf29f88fef From: inst/doc/V2_IntrotoIVIVE.html Status: 404 Message: Not Found 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: none CRLfile: none (Status without verification: OK) URL: https://github.com/HumanExposure/SEEM3RPackage/tree/main/SEEM3/data From: inst/doc/V2_IntrotoIVIVE.html Status: 404 Message: Not Found URL: https://www.epa.gov/chemical-research/computational-toxicology-communities-practice-high-throughput-toxicokinetic-httk From: man/httk-package.Rd Status: 403 Message: Forbidden URL: https://www.epa.gov/chemical-research/exploring-toxcast-data From: inst/doc/V1_IntroToHTTK.html inst/doc/V2_IntrotoIVIVE.html Status: 403 Message: Forbidden URL: https://www.epa.gov/chemical-research/rapid-chemical-exposure-and-dose-research From: DESCRIPTION man/httk-package.Rd Status: 403 Message: Forbidden URL: https://www.epa.gov/chemical-research/toxicology-testing-21st-century-tox21 From: man/dawson2021.Rd man/pradeep2020.Rd man/sipes2017.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 17.0.5 (1)’ * 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 ... NOTE Problems with news in ‘NEWS.md’: No news entries found. * checking R 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 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] NOTE checkRd: (-1) convert_units.Rd:76: Lost braces in \itemize; meant \describe ? checkRd: (-1) convert_units.Rd:77: Lost braces in \itemize; meant \describe ? checkRd: (-1) convert_units.Rd:78: Lost braces in \itemize; meant \describe ? checkRd: (-1) httk-package.Rd:14: Lost braces 14 | \doi{10.1080/17425255.2021.1935867}{Breen et al. (2021): High-throughput PBTK models for in vitro to in vivo extrapolation} | ^ checkRd: (-1) httk-package.Rd:16: Lost braces 16 | \doi{10.18637/jss.v079.i04}{Pearce et al. (2017): httk: R Package for High-Throughput Toxicokinetics} | ^ checkRd: (-1) httk-package.Rd:18: Lost braces 18 | \doi{10.1021/es501955g}{Armitage et al. (2014): Application of mass balance models and the chemical activity concept to facilitate the use of in vitro toxicity data for risk assessment} | ^ checkRd: (-1) httk-package.Rd:20: Lost braces 20 | \doi{10.1093/toxsci/kfv171}{Incorporating High-Throughput Exposure Predictions with Dosimetry-Adjusted In Vitro Bioactivity to Inform Chemical Toxicity Testing} | ^ checkRd: (-1) httk-package.Rd:22: Lost braces 22 | \doi{10.1093/toxsci/kfv118}{Wambaugh et al. (2015): Toxicokinetic Triage for Environmental Chemicals} | ^ checkRd: (-1) httk-package.Rd:24: Lost braces 24 | \doi{10.1007/s10928-017-9548-7}{Pearce et al. (2017): Evaluation and calibration of high-throughput predictions of chemical distribution to tissues} | ^ checkRd: (-1) httk-package.Rd:26: Lost braces 26 | \doi{10.1016/j.envint.2017.06.004}{Ring et al. (2017): Identifying populations sensitive to environmental chemicals by simulating toxicokinetic variability} | ^ checkRd: (-1) httk-package.Rd:28: Lost braces 28 | \doi{10.1021/acs.est.7b00650}{Sipes et al. (2017): An Intuitive Approach for Predicting Potential Human Health Risk with the Tox21 10k Library} | ^ checkRd: (-1) httk-package.Rd:30: Lost braces 30 | \doi{10.1093/toxsci/kfy020}{Wambaugh et al. (2018): Evaluating In Vitro-In Vivo Extrapolation of Toxicokinetics} | ^ checkRd: (-1) httk-package.Rd:32: Lost braces 32 | \doi{10.1371/journal.pone.0217564}{Honda et al. (2019): Using the concordance of in vitro and in vivo data to evaluate extrapolation assumptions} | ^ checkRd: (-1) httk-package.Rd:34: Lost braces 34 | \doi{10.1093/toxsci/kfz205}{Wambaugh et al. (2019): Assessing Toxicokinetic Uncertainty and Variability in Risk Prioritization} | ^ checkRd: (-1) httk-package.Rd:36: Lost braces 36 | \doi{10.1038/s41370-020-0238-y}{Linakis et al. (2020): Development and evaluation of a high-throughput inhalation model for organic chemicals} | ^ * 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 ... [29s/29s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [60s/60s] OK Running ‘1comp_test.R’ [4s/4s] Comparing ‘1comp_test.Rout’ to ‘1comp_test.Rout.save’ ... OK Running ‘3comp_test.R’ [4s/4s] Comparing ‘3comp_test.Rout’ to ‘3comp_test.Rout.save’ ...318a319 > hematocrit : 0.44 319a321 > kgutabs : 2.18 322a325 > liver.density : 1.05 323a327 > million.cells.per.gliver : 110 324a329,330 > pKa_Accept : 8.09 > pKa_Donor : 2.81 334,339d339 < hematocrit : 0.44 < kgutabs : 2.18 < liver.density : 1.05 < million.cells.per.gliver : 110 < pKa_Accept : 8.09 < pKa_Donor : 2.81 Running ‘3compss_test.R’ [2s/2s] Comparing ‘3compss_test.Rout’ to ‘3compss_test.Rout.save’ ... OK Running ‘adddata_test.R’ [3s/3s] Comparing ‘adddata_test.Rout’ to ‘adddata_test.Rout.save’ ... OK Running ‘caco2_test.R’ [4s/4s] 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’ [3s/3s] Comparing ‘fetal_pbtk_testing.Rout’ to ‘fetal_pbtk_testing.Rout.save’ ... OK Running ‘ivive_test.R’ [7s/7s] Comparing ‘ivive_test.Rout’ to ‘ivive_test.Rout.save’ ... OK Running ‘montecarlo_tests.R’ [8s/8s] Comparing ‘montecarlo_tests.Rout’ to ‘montecarlo_tests.Rout.save’ ... OK Running ‘other_tests.R’ [13s/13s] Comparing ‘other_tests.Rout’ to ‘other_tests.Rout.save’ ... OK Running ‘pbtk_test.R’ [3s/3s] Comparing ‘pbtk_test.Rout’ to ‘pbtk_test.Rout.save’ ...219a220 > hematocrit : 0.44 220a222 > kgutabs : 2.18 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 : 2.18 < liver.density : 1.05 < million.cells.per.gliver : 110 < pKa_Accept : 8.09 < pKa_Donor : 2.81 Running ‘solve_gas_test.R’ [3s/3s] Comparing ‘solve_gas_test.Rout’ to ‘solve_gas_test.Rout.save’ ... OK Running ‘unit_test.R’ [2s/2s] Comparing ‘unit_test.Rout’ to ‘unit_test.Rout.save’ ... OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking re-building of vignette outputs ... [91s/91s] OK * checking PDF version of manual ... [9s/9s] 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: 3 NOTEs