• using R version 4.4.3 (2025-02-28 ucrt)
• using platform: x86_64-w64-mingw32
• R was compiled by     gcc.exe (GCC) 13.3.0     GNU Fortran (GCC) 13.3.0
• 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 See the install log for details.
• 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
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• checking whether the package can be unloaded cleanly ... [1s] OK
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• checking loading without being on the library search path ... [1s] OK
• checking use of S3 registration ... OK
• checking dependencies in R code ... OK
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• checking foreign function calls ... OK
• checking R code for possible problems ... [11s] 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
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• 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 ... [29s] 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$sim <= 20,], + obs = rtte_obs_nm, + rtte = FALSE, + sim_cols=list(dv = "dv", idv = "t"), obs_cols=list(idv = "t")) Initializing. Error: ! `group_by_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `group_by()` instead. ℹ See vignette('programming') for more help Backtrace:      ▆   1. ├─vpc::vpc_tte(...)   2. │ └─... %>% dplyr::filter(!duplicated(id))   3. ├─dplyr::filter(., !duplicated(id))   4. ├─dplyr::filter(., dv == 1 | last_obs == 1)   5. ├─dplyr::mutate(...)   6. └─dplyr::group_by_(., "id")   7. └─dplyr:::lazy_defunct("group_by")   8. └─lifecycle::deprecate_stop(...)   9. └─lifecycle:::deprecate_stop0(msg)  10. └─rlang::cnd_signal(...) Execution halted
• checking for unstated dependencies in 'tests' ... OK
• checking tests ... [52s] ERROR   Running 'test-add_sim_index_number.R' [13s]   Running 'test-filter_dv.R' [1s]   Running 'test-labeller.R' [7s]   Running 'test-scales.R' [7s]   Running 'test-softwaretype.R' [1s]   Running 'test-strat-col-detection.R' [1s]   Running 'test-vpc.R' [7s]   Running 'test-vpc_cat.R' [4s]   Running 'test-vpc_cens.R' [6s]   Running 'test-vpc_tte.R' [3s] Running the tests in 'tests/test-add_sim_index_number.R' failed. Complete output:   > library(dplyr)      Attaching package: 'dplyr'      The following objects are masked from 'package:stats':          filter, lag      The following objects are masked from 'package:base':          intersect, setdiff, setequal, union      > library(vpc)   > library(testit)   > Sys.setenv("R_TESTS" = "")   >   > ## Load the theophylline PK dataset   > obs <- Theoph   > colnames(obs) <- c("id", "wt", "dose", "time", "dv")   > obs <- obs %>%   + dplyr::group_by(id) %>%   + mutate(sex = round(runif(1))) # randomly assign a "sex" covariate   > sim <- sim_data(obs, # the design of the dataset   + model = function(x) { # the model   + vpc:::pk_oral_1cmt (t = x$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 ... [18s] OK
• checking HTML version of manual ... [6s] OK
• DONE

Status: 2 ERRORs, 1 NOTE