* using log directory 'd:/Rcompile/CRANpkg/local/4.5/vpc.Rcheck' * using R version 4.5.2 (2025-10-31 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 14.3.0 GNU Fortran (GCC) 14.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * checking for file 'vpc/DESCRIPTION' ... OK * this is package 'vpc' version '1.2.2' * 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 hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'vpc' can be installed ... OK * checking installed package size ... OK * checking package 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] OK * checking whether the package can be loaded with stated dependencies ... [1s] OK * checking whether the package can be unloaded cleanly ... [1s] OK * checking whether the namespace can be loaded with stated dependencies ... [1s] OK * checking whether the namespace can be unloaded cleanly ... [1s] OK * checking loading without being on the library search path ... [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 ... [7s] OK * checking Rd files ... [1s] NOTE checkRd: (-1) new_vpc_theme.Rd:21: Lost braces; missing escapes or markup? 21 | \item{obs_color}: {color for observations points} | ^ checkRd: (-1) new_vpc_theme.Rd:22: Lost braces; missing escapes or markup? 22 | \item{obs_size}: {size for observation points} | ^ checkRd: (-1) new_vpc_theme.Rd:23: Lost braces; missing escapes or markup? 23 | \item{obs_median_color}: {color for median observation line} | ^ checkRd: (-1) new_vpc_theme.Rd:24: Lost braces; missing escapes or markup? 24 | \item{obs_median_linetype}: {linetype for median observation line} | ^ checkRd: (-1) new_vpc_theme.Rd:25: Lost braces; missing escapes or markup? 25 | \item{obs_median_size}: {size for median observation line} | ^ checkRd: (-1) new_vpc_theme.Rd:26: Lost braces; missing escapes or markup? 26 | \item{obs_ci_fill}: {color for observation CI fill} | ^ checkRd: (-1) new_vpc_theme.Rd:27: Lost braces; missing escapes or markup? 27 | \item{obs_ci_color}: {color for observation CI lines} | ^ checkRd: (-1) new_vpc_theme.Rd:28: Lost braces; missing escapes or markup? 28 | \item{obs_ci_linetype}: {linetype for observation CI lines} | ^ checkRd: (-1) new_vpc_theme.Rd:29: Lost braces; missing escapes or markup? 29 | \item{obs_ci_size}: {size for observations CI lines} | ^ checkRd: (-1) new_vpc_theme.Rd:30: Lost braces; missing escapes or markup? 30 | \item{sim_pi_fill}: {fill color for simulated prediction interval areas} | ^ checkRd: (-1) new_vpc_theme.Rd:31: Lost braces; missing escapes or markup? 31 | \item{sim_pi_alpha}: {transparency for simulated prediction interval areas} | ^ checkRd: (-1) new_vpc_theme.Rd:32: Lost braces; missing escapes or markup? 32 | \item{sim_pi_color}: {color for simulated prediction interval lines} | ^ checkRd: (-1) new_vpc_theme.Rd:33: Lost braces; missing escapes or markup? 33 | \item{sim_pi_linetype}: {linetype for simulated prediction interval lines} | ^ checkRd: (-1) new_vpc_theme.Rd:34: Lost braces; missing escapes or markup? 34 | \item{sim_pi_size}: {size for simulated prediction interval lines} | ^ checkRd: (-1) new_vpc_theme.Rd:35: Lost braces; missing escapes or markup? 35 | \item{sim_median_fill}: {fill color for simulated median area} | ^ checkRd: (-1) new_vpc_theme.Rd:36: Lost braces; missing escapes or markup? 36 | \item{sim_median_alpha}: {transparency for simulated median area} | ^ checkRd: (-1) new_vpc_theme.Rd:37: Lost braces; missing escapes or markup? 37 | \item{sim_median_color}: {color for simulated median line} | ^ checkRd: (-1) new_vpc_theme.Rd:38: Lost braces; missing escapes or markup? 38 | \item{sim_median_linetype}: {linetype for simulated median line} | ^ checkRd: (-1) new_vpc_theme.Rd:39: Lost braces; missing escapes or markup? 39 | \item{sim_median_size}: {size for simulated median line} | ^ checkRd: (-1) new_vpc_theme.Rd:40: Lost braces; missing escapes or markup? 40 | \item{bin_separators_color}: {color for bin separator lines, NA for don't plot} | ^ checkRd: (-1) new_vpc_theme.Rd:41: Lost braces; missing escapes or markup? 41 | \item{bin_separators_location}: {where to plot bin separators ("t" for top, "b" for bottom)} | ^ checkRd: (-1) new_vpc_theme.Rd:42: Lost braces; missing escapes or markup? 42 | \item{loq_color}: {color of line showing limit of quantification} | ^ * checking Rd metadata ... 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] OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking examples ... [21s] ERROR Running examples in 'vpc-Ex.R' failed The error most likely occurred in: > ### Name: vpc_tte > ### Title: VPC function for time-to-event (survival) data > ### Aliases: vpc_tte > > ### ** Examples > > ## See vpc-docs.ronkeizer.com for more documentation and examples. > > ## Example for repeated) time-to-event data > ## with NONMEM-like data (e.g. simulated using a dense grid) > > data(rtte_obs_nm) > data(rtte_sim_nm) > > # treat RTTE as TTE, no stratification > vpc_tte(sim = rtte_sim_nm[rtte_sim_nm$sim <= 20,], + obs = rtte_obs_nm, + rtte = FALSE, + sim_cols=list(dv = "dv", idv = "t"), obs_cols=list(idv = "t")) Initializing. Error: ! `group_by_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `group_by()` instead. ℹ See vignette('programming') for more help Backtrace: ▆ 1. ├─vpc::vpc_tte(...) 2. │ └─... %>% dplyr::filter(!duplicated(id)) 3. ├─dplyr::filter(., !duplicated(id)) 4. ├─dplyr::filter(., dv == 1 | last_obs == 1) 5. ├─dplyr::mutate(...) 6. └─dplyr::group_by_(., "id") 7. └─dplyr:::lazy_defunct("group_by") 8. └─lifecycle::deprecate_stop(...) 9. └─lifecycle:::deprecate_stop0(msg) 10. └─rlang::cnd_signal(...) Execution halted * checking for unstated dependencies in 'tests' ... OK * checking tests ... [36s] ERROR Running 'test-add_sim_index_number.R' [9s] Running 'test-filter_dv.R' [1s] Running 'test-labeller.R' [5s] Running 'test-scales.R' [5s] Running 'test-softwaretype.R' [1s] Running 'test-strat-col-detection.R' [1s] Running 'test-vpc.R' [5s] Running 'test-vpc_cat.R' [3s] Running 'test-vpc_cens.R' [5s] Running 'test-vpc_tte.R' [2s] Running the tests in 'tests/test-add_sim_index_number.R' failed. Complete output: > library(dplyr) Attaching package: 'dplyr' The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union > library(vpc) > library(testit) > Sys.setenv("R_TESTS" = "") > > ## Load the theophylline PK dataset > obs <- Theoph > colnames(obs) <- c("id", "wt", "dose", "time", "dv") > obs <- obs %>% + dplyr::group_by(id) %>% + mutate(sex = round(runif(1))) # randomly assign a "sex" covariate > sim <- sim_data(obs, # the design of the dataset + model = function(x) { # the model + vpc:::pk_oral_1cmt (t = x$time, dose=x$dose * x$wt, ka = x$ka, ke = x$ke, cl = x$cl * x$wt) + }, + error = list(additive = 0.1), + theta = c(2.774, 0.0718, .0361), # parameter values + omega_mat = c(0.08854, # specified as lower triangle by default; + 0.02421, 0.02241, # note: assumed that every theta has iiv, set to 0 if no iiv. + 0.008069, 0.008639, 0.02862), + par_names = c("ka", "ke", "cl"), # link the parameters in the model to the thetas/omegas + n = 500) Error: ! `arrange_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `arrange()` instead. ℹ See vignette('programming') for more help Backtrace: ▆ 1. ├─vpc::sim_data(...) 2. │ └─tmp %>% dplyr::arrange_("sim", "id", "time") 3. └─dplyr::arrange_(., "sim", "id", "time") 4. └─dplyr:::lazy_defunct("arrange") 5. └─lifecycle::deprecate_stop(...) 6. └─lifecycle:::deprecate_stop0(msg) 7. └─rlang::cnd_signal(...) Execution halted Running the tests in 'tests/test-vpc_tte.R' failed. Complete output: > library(vpc) > library(testit) > Sys.setenv("R_TESTS" = "") > > ## Test for bug AR 20171025 column name simulation dataset > test <- vpc::rtte_sim_nm[1:200000,] > test$bla <- test$t > test$t <- NULL > obj <- vpc_tte(sim = test, # stratified for covariate and study arm + obs = vpc::rtte_obs_nm, + rtte = FALSE, + sim_cols = list(dv = "dv", idv = "bla"), + obs_cols = list(idv = "t"), + labeller = ggplot2::label_both) Initializing. Error: ! `group_by_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `group_by()` instead. ℹ See vignette('programming') for more help Backtrace: ▆ 1. ├─vpc::vpc_tte(...) 2. │ └─... %>% dplyr::filter(!duplicated(id)) 3. ├─dplyr::filter(., !duplicated(id)) 4. ├─dplyr::filter(., dv == 1 | last_obs == 1) 5. ├─dplyr::mutate(...) 6. └─dplyr::group_by_(., "id") 7. └─dplyr:::lazy_defunct("group_by") 8. └─lifecycle::deprecate_stop(...) 9. └─lifecycle:::deprecate_stop0(msg) 10. └─rlang::cnd_signal(...) Execution halted * checking PDF version of manual ... [20s] OK * checking HTML version of manual ... [5s] OK * DONE Status: 2 ERRORs, 1 NOTE