* using log directory ‘/srv/hornik/tmp/CRAN_pretest/jskm.Rcheck’
* using R Under development (unstable) (2025-11-27 r89071)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 21.1.5 (1)
    Debian flang version 21.1.5 (1)
* running under: Debian GNU/Linux forky/sid
* using session charset: UTF-8
* checking for file ‘jskm/DESCRIPTION’ ... OK
* this is package ‘jskm’ version ‘0.5.22’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [5s/6s] OK
* 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 ‘jskm’ can be installed ... [7s/7s] OK
* 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 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 ... [11s/11s] OK
* checking Rd files ... [0s/0s] 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 ... WARNING
Codoc mismatches from Rd file 'jskm.Rd':
jskm
  Code: function(sfit, table = FALSE, table.censor = FALSE, xlabs =
                 "Time-to-event", ylabs = NULL, xlims = c(0,
                 max(sfit$time)), ylims = c(0, 1), surv.scale =
                 c("default", "percent"), ystratalabs = NULL,
                 ystrataname = "Strata", timeby =
                 signif(max(sfit$time)/7, 1), main = "", pval = FALSE,
                 pval.size = 5, pval.coord = c(NULL, NULL),
                 pval.testname = T, marks = TRUE, shape = 3, med =
                 FALSE, med.decimal = 2, legend = TRUE, legendposition
                 = c(0.85, 0.8), ci = FALSE, subs = NULL, label.nrisk =
                 "Numbers at risk", left.nrisk = FALSE,
                 size.label.nrisk = 10, linecols = "Set1", dashed =
                 FALSE, cumhaz = F, cluster.option = "None",
                 cluster.var = NULL, data = NULL, cut.landmark = NULL,
                 showpercent = F, status.cmprsk = NULL, linewidth =
                 0.75, theme = NULL, nejm.infigure.ratiow = 0.6,
                 nejm.infigure.ratioh = 0.5, nejm.infigure.xlim = NULL,
                 nejm.infigure.ylim = c(0, 1), surv.by = NULL,
                 nejm.surv.by = NULL, hr = FALSE, hr.size = 5, hr.coord
                 = c(NULL, NULL), hr.testname = F, ...)
  Docs: function(sfit, table = FALSE, table.censor = FALSE, xlabs =
                 "Time-to-event", ylabs = NULL, xlims = c(0,
                 max(sfit$time)), ylims = c(0, 1), surv.scale =
                 c("default", "percent"), ystratalabs = NULL,
                 ystrataname = "Strata", timeby =
                 signif(max(sfit$time)/7, 1), main = "", pval = FALSE,
                 pval.size = 5, pval.coord = c(NULL, NULL),
                 pval.testname = T, marks = TRUE, shape = 3, med =
                 FALSE, legend = TRUE, legendposition = c(0.85, 0.8),
                 ci = FALSE, subs = NULL, label.nrisk = "Numbers at
                 risk", left.nrisk = FALSE, size.label.nrisk = 10,
                 linecols = "Set1", dashed = FALSE, cumhaz = F,
                 cluster.option = "None", cluster.var = NULL, data =
                 NULL, cut.landmark = NULL, showpercent = F,
                 status.cmprsk = NULL, linewidth = 0.75, theme = NULL,
                 nejm.infigure.ratiow = 0.6, nejm.infigure.ratioh =
                 0.5, nejm.infigure.xlim = NULL, nejm.infigure.ylim =
                 c(0, 1), surv.by = NULL, nejm.surv.by = NULL, hr =
                 FALSE, hr.size = 5, hr.coord = c(NULL, NULL),
                 hr.testname = F, ...)
  Argument names in code not in docs:
    med.decimal
  Mismatches in argument names (first 3):
    Position: 20 Code: med.decimal Docs: legend
    Position: 21 Code: legend Docs: legendposition
    Position: 22 Code: legendposition Docs: ci

Codoc mismatches from Rd file 'svyjskm.Rd':
svyjskm
  Code: function(sfit, theme = NULL, xlabs = "Time-to-event", ylabs =
                 "Survival probability", xlims = NULL, ylims = c(0, 1),
                 ystratalabs = NULL, ystrataname = NULL, surv.scale =
                 c("default", "percent"), timeby = NULL, main = "",
                 pval = FALSE, pval.size = 4, pval.coord = c(NULL,
                 NULL), pval.testname = F, marks = FALSE, hr = FALSE,
                 hr.size = 2, hr.coord = c(NULL, NULL), med = FALSE,
                 med.decimal = 2, legend = TRUE, legendposition =
                 c(0.85, 0.8), ci = NULL, linecols = "Set1", dashed =
                 FALSE, cumhaz = F, design = NULL, subs = NULL, table =
                 F, table.censor = F, label.nrisk = "Numbers at risk",
                 left.nrisk = FALSE, size.label.nrisk = 10,
                 cut.landmark = NULL, showpercent = F, linewidth =
                 0.75, nejm.infigure.ratiow = 0.6, nejm.infigure.ratioh
                 = 0.5, nejm.infigure.xlim = NULL, nejm.infigure.ylim =
                 c(0, 1), surv.by = NULL, nejm.surv.by = NULL, ...)
  Docs: function(sfit, theme = NULL, xlabs = "Time-to-event", ylabs =
                 "Survival probability", xlims = NULL, ylims = c(0, 1),
                 ystratalabs = NULL, ystrataname = NULL, surv.scale =
                 c("default", "percent"), timeby = NULL, main = "",
                 pval = FALSE, pval.size = 4, pval.coord = c(NULL,
                 NULL), pval.testname = F, marks = FALSE, hr = FALSE,
                 hr.size = 2, hr.coord = c(NULL, NULL), med = FALSE,
                 legend = TRUE, legendposition = c(0.85, 0.8), ci =
                 NULL, linecols = "Set1", dashed = FALSE, cumhaz = F,
                 design = NULL, subs = NULL, table = F, table.censor =
                 F, label.nrisk = "Numbers at risk", left.nrisk =
                 FALSE, size.label.nrisk = 10, cut.landmark = NULL,
                 showpercent = F, linewidth = 0.75,
                 nejm.infigure.ratiow = 0.6, nejm.infigure.ratioh =
                 0.5, nejm.infigure.xlim = NULL, nejm.infigure.ylim =
                 c(0, 1), surv.by = NULL, nejm.surv.by = NULL, ...)
  Argument names in code not in docs:
    med.decimal
  Mismatches in argument names (first 3):
    Position: 21 Code: med.decimal Docs: legend
    Position: 22 Code: legend Docs: legendposition
    Position: 23 Code: legendposition Docs: ci

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [3s/3s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [7s/7s] OK
  Running ‘testthat.R’ [6s/6s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [13s/13s] OK
* checking PDF version of manual ... [3s/3s] OK
* checking HTML version of manual ... [0s/0s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 WARNING