- using R Under development (unstable) (2026-02-10 r89394)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
gcc-15 (Debian 15.2.0-12) 15.2.0
GNU Fortran (Debian 15.2.0-12) 15.2.0
- running under: Debian GNU/Linux forky/sid
- using session charset: UTF-8
* current time: 2026-02-11 18:33:39 UTC
- checking for file ‘vpc/DESCRIPTION’ ... OK
- this is package ‘vpc’ version ‘1.2.2’
- checking CRAN incoming feasibility ... [1s/1s] NOTE
Maintainer: ‘Ron Keizer <ronkeizer@gmail.com>’
No Authors@R field in DESCRIPTION.
Please add one, modifying
Authors@R: person(given = "Ron",
family = "Keizer",
role = c("aut", "cre"),
email = "ronkeizer@gmail.com")
as necessary.
- 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 ‘vpc’ can be installed ... OK
See the install log for details.
- checking package directory ... OK
- checking for future file timestamps ... 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/1s] OK
- checking whether the package can be loaded with stated dependencies ... [0s/1s] OK
- checking whether the package can be unloaded cleanly ... [1s/1s] OK
- checking whether the namespace can be loaded with stated dependencies ... [0s/1s] OK
- checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
- checking loading without being on the library search path ... [1s/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 ... [9s/13s] OK
- checking Rd files ... [0s/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 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/1s] OK
- checking LazyData ... OK
- checking data for ASCII and uncompressed saves ... OK
- checking examples ... [15s/19s] ERROR
Running examples in ‘vpc-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### 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$sim <= 20,],
+ obs = rtte_obs_nm,
+ rtte = FALSE,
+ sim_cols=list(dv = "dv", idv = "t"), obs_cols=list(idv = "t"))
Initializing.
Error:
! `group_by_()` was deprecated in dplyr 0.7.0 and is now defunct.
ℹ Please use `group_by()` instead.
ℹ See vignette('programming') for more help
Backtrace:
▆
1. ├─vpc::vpc_tte(...)
2. │ └─... %>% dplyr::filter(!duplicated(id))
3. ├─dplyr::filter(., !duplicated(id))
4. ├─dplyr::filter(., dv == 1 | last_obs == 1)
5. ├─dplyr::mutate(...)
6. └─dplyr::group_by_(., "id")
7. └─dplyr:::lazy_defunct("group_by")
8. └─lifecycle::deprecate_stop(...)
9. └─lifecycle:::deprecate_stop0(msg)
10. └─rlang::cnd_signal(...)
Execution halted
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [27s/34s] ERROR
Running ‘test-add_sim_index_number.R’ [7s/9s]
Running ‘test-filter_dv.R’ [1s/1s]
Running ‘test-labeller.R’ [4s/4s]
Running ‘test-scales.R’ [4s/4s]
Running ‘test-softwaretype.R’ [1s/1s]
Running ‘test-strat-col-detection.R’ [1s/1s]
Running ‘test-vpc.R’ [4s/5s]
Running ‘test-vpc_cat.R’ [2s/3s]
Running ‘test-vpc_cens.R’ [3s/4s]
Running ‘test-vpc_tte.R’ [2s/2s]
Running the tests in ‘tests/test-add_sim_index_number.R’ failed.
Complete output:
> library(dplyr)
Attaching package: 'dplyr'
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
> library(vpc)
> library(testit)
> Sys.setenv("R_TESTS" = "")
>
> ## Load the theophylline PK dataset
> obs <- Theoph
> colnames(obs) <- c("id", "wt", "dose", "time", "dv")
> obs <- obs %>%
+ dplyr::group_by(id) %>%
+ mutate(sex = round(runif(1))) # randomly assign a "sex" covariate
> sim <- sim_data(obs, # the design of the dataset
+ model = function(x) { # the model
+ vpc:::pk_oral_1cmt (t = x$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 ... [4s/6s] OK
- checking HTML version of manual ... [1s/2s] OK
- checking for non-standard things in the check directory ... OK
- DONE
Status: 2 ERRORs, 2 NOTEs