Running ‘test-add_sim_index_number.R’ [11s/15s]
  Running ‘test-filter_dv.R’ [1s/1s]
  Running ‘test-labeller.R’ [6s/8s]
  Running ‘test-scales.R’ [6s/8s]
  Running ‘test-softwaretype.R’ [1s/2s]
  Running ‘test-strat-col-detection.R’ [1s/1s]
  Running ‘test-vpc.R’ [5s/8s]
  Running ‘test-vpc_cat.R’ [3s/4s]
  Running ‘test-vpc_cens.R’ [6s/7s]
  Running ‘test-vpc_tte.R’ [2s/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