Check results for 'survminer'

using R version 4.5.2 (2025-10-31)
using platform: x86_64-pc-linux-gnu
R was compiled by gcc-14 (Debian 14.3.0-10) 14.3.0 GNU Fortran (Debian 14.3.0-10) 14.3.0
running under: Debian GNU/Linux forky/sid
using session charset: UTF-8
checking for file ‘survminer/DESCRIPTION’ ... OK
checking extension type ... Package
this is package ‘survminer’ version ‘0.5.1’
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 serialization versions ... OK
checking whether package ‘survminer’ can be installed ... OK See the install log for details.
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 ... [4s/5s] OK
checking whether the package can be loaded with stated dependencies ... [3s/4s] OK
checking whether the package can be unloaded cleanly ... [3s/5s] OK
checking whether the namespace can be loaded with stated dependencies ... [3s/5s] OK
checking whether the namespace can be unloaded cleanly ... [4s/5s] OK
checking loading without being on the library search path ... [4s/5s] 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 ... [26s/34s] OK
checking Rd files ... [1s/1s] 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/1s] OK
checking LazyData ... OK
checking data for ASCII and uncompressed saves ... OK
checking installed files from ‘inst/doc’ ... OK
checking files in ‘vignettes’ ... OK
checking examples ... [76s/107s] ERROR Running examples in ‘survminer-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: surv_fit > ### Title: Create Survival Curves > ### Aliases: surv_fit > > ### ** Examples > > > library("survival") Attaching package: ‘survival’ The following object is masked from ‘package:survminer’: myeloma > library("magrittr") > > # Case 1: One formula and One data set > #::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > fit <- surv_fit(Surv(time, status) ~ sex, + data = colon) > surv_pvalue(fit) variable pval method pval.txt 1 sex 0.6107936 Log-rank p = 0.61 > > > # Case 2: List of formulas and One data set. > # - Different formulas are applied to the same data set > # - Returns a (named) list of survfit objects > #::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > # Create a named list of formulas > formulas <- list( + sex = Surv(time, status) ~ sex, + rx = Surv(time, status) ~ rx + ) > > # Fit survival curves for each formula > fit <- surv_fit(formulas, data = colon) > surv_pvalue(fit) $`colon::sex` variable pval method pval.txt 1 sex 0.6107936 Log-rank p = 0.61 $`colon::rx` variable pval method pval.txt 1 rx 4.990735e-08 Log-rank p < 0.0001 > > # Case 3: One formula and List of data sets > #::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > fit <- surv_fit(Surv(time, status) ~ sex, + data = list(colon, lung)) > surv_pvalue(fit) $`colon::sex` variable pval method pval.txt 1 sex 0.6107936 Log-rank p = 0.61 $`lung::sex` variable pval method pval.txt 1 sex 0.001311165 Log-rank p = 0.0013 > > > # Case 4: List of formulas and List of data sets > # - Each formula is applied to each of the data in the data list > # - argument: match.fd = FALSE > #::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > > # Create two data sets > set.seed(123) > colon1 <- dplyr::sample_frac(colon, 1/2) > set.seed(1234) > colon2 <- dplyr::sample_frac(colon, 1/2) > > # Create a named list of formulas > formula.list <- list( + sex = Surv(time, status) ~ sex, + adhere = Surv(time, status) ~ adhere, + rx = Surv(time, status) ~ rx + ) > > # Fit survival curves > fit <- surv_fit(formula.list, data = list(colon1, colon2), + match.fd = FALSE) Error: ! `combine()` was deprecated in dplyr 1.0.0 and is now defunct. ℹ Please use `vctrs::vec_c()` instead. Backtrace: ▆ 1. ├─survminer::surv_fit(...) 2. │ └─purrr::map(formula, .map_each, data) %>% dplyr::combine() 3. └─dplyr::combine(.) 4. └─lifecycle::deprecate_stop("1.0.0", "combine()", "vctrs::vec_c()") 5. └─lifecycle:::deprecate_stop0(msg) 6. └─rlang::cnd_signal(...) Execution halted Examples with CPU (user + system) or elapsed time > 5s user system elapsed ggsurvplot_group_by 6.936 0.042 8.692 ggsurvplot 6.532 0.075 8.785 ggsurvplot_add_all 5.002 0.032 8.176 ggsurvplot_facet 4.791 0.000 6.669 ggcoxdiagnostics 4.373 0.043 5.743 ggsurvevents 4.095 0.020 6.271 ggcoxfunctional 3.897 0.027 5.673 ggsurvplot_df 3.727 0.001 6.511 ggsurvtheme 3.482 0.023 5.043
checking for unstated dependencies in ‘tests’ ... OK
checking tests ... [10s/13s] OK Running ‘testthat.R’ [10s/13s]
checking for unstated dependencies in vignettes ... OK
checking package vignettes ... OK
checking re-building of vignette outputs ... [55s/74s] OK
checking PDF version of manual ... [8s/10s] OK
checking HTML version of manual ... [2s/3s] OK
checking for non-standard things in the check directory ... OK
DONE

Status: 1 ERROR