* using log directory ‘/data/localhost/ripley/R/packages/tests-donttest/graphPAF.Rcheck’ * using R Under development (unstable) (2026-08-24 r90445) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (GCC) 16.1.1 20260515 (Red Hat 16.1.1-2) GNU Fortran (GCC) 16.1.1 20260515 (Red Hat 16.1.1-2) * running under: Fedora Linux 44 (Server Edition) * using session charset: UTF-8 * current time: 2026-08-25 09:14:51 UTC * checking for file ‘graphPAF/DESCRIPTION’ ... OK * this is package ‘graphPAF’ version ‘2.0.1’ * 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 ‘graphPAF’ can be installed ... [8s/15s] OK * 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 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 ... [14s/22s] 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 sizes of PDF files under ‘inst/doc’ ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [32s/44s] OK * checking examples with --run-donttest ... [15s/511s] ERROR Running examples in ‘graphPAF-Ex.R’ failed The error most likely occurred in: > ### Name: PAF_calc_continuous > ### Title: Calculation of attributable fractions with a continuous exposure > ### Aliases: PAF_calc_continuous > > ### ** Examples > > library(splines) > library(survival) > library(parallel) > options(boot.parallel="snow") > options(boot.ncpus=2) > # The above could be set to the number of available cores on the machine > # Example with logistic regression. PAF_q (as in Ferguson, 2020) > # estimated at q=0.01, 0.1, 0.3, 0.5, 0.7. 0.9. PAF_0.01 is roughly > # analogous to 'eliminating' a discrete risk factor, but its estimation > # may be unstable for some exposures, and the corresponding intervention > # may be impractical. Comparing PAF_q for q >= 0.1 over different risk factors > # may lead to more sensible comparisons of disease burden. > # Either method (direct, D, or Bruzzi ) > # reduce dataset to improve run time (not recommended on real data!) > stroke_small <- stroke_reduced[sample(1:nrow(stroke_reduced),1000),] > model_continuous <- glm(formula = case ~ region * ns(age, df = 5) + + sex * ns(age, df = 5) + education +exercise + ns(diet, df = 3) + + alcohol + stress + ns(lipids,df = 3) + ns(waist_hip_ratio, df = 3) + + high_blood_pressure, family = "binomial", data = stroke_small) > out <- PAF_calc_continuous(model_continuous,riskfactor_vec= + c("diet","lipids","waist_hip_ratio"),q_vec=c(0.1,0.5,0.9), + ci=FALSE,calculation_method="D",data=stroke_small, prev=0.0035) > print(out) riskfactor q paf_q 1 diet 0.1 0.353000 2 diet 0.5 0.148000 3 diet 0.9 0.018400 4 lipids 0.1 0.400000 5 lipids 0.5 0.110000 6 lipids 0.9 0.000853 7 waist_hip_ratio 0.1 0.164000 8 waist_hip_ratio 0.5 0.100000 9 waist_hip_ratio 0.9 0.017700 > plot(out) Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0. ℹ Please use `linewidth` instead. ℹ The deprecated feature was likely used in the graphPAF package. Please report the issue at . Warning in ggplot2::geom_line(ggplot2::aes(group = riskfactor, width = 1), : Ignoring unknown aesthetics: width > ## No test: > # with confidence intervals (via bootstrap) on full dataset. Slower. > model_continuous_clogit <- clogit(formula = case ~ region * ns(age, df = 5) + + sex * ns(age, df = 5) + education +exercise + ns(diet, df = 3) + + alcohol + stress + ns(lipids,df = 3) + ns(waist_hip_ratio, df = 3) + + high_blood_pressure + strata(strata), data = stroke_reduced) > out <- PAF_calc_continuous(model_continuous_clogit,riskfactor_vec=c("diet", + "lipids","waist_hip_ratio"),q_vec=c(0.01, 0.1,0.3,0.5,0.7,0.9), + ci=TRUE,calculation_method="B",data=stroke_reduced, prev=0.01) Error in if (const(t, min(1e-08, mean(t, na.rm = TRUE)/1e+06))) { : missing value where TRUE/FALSE needed Calls: PAF_calc_continuous -> structure -> extract_ci -> Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [6s/21s] OK * checking PDF version of manual ... [5s/15s] OK * checking HTML version of manual ... OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * checking for new files in some other directories ... OK * DONE Status: 1 ERROR See ‘/data/localhost/ripley/R/packages/tests-donttest/graphPAF.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 13:22.50, 123.81 + 29.62