* using log directory 'd:/RCompile/CRANincoming/R-devel/BCEA.Rcheck'
* using R Under development (unstable) (2023-11-20 r85569 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 12.3.0
    GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'BCEA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BCEA' version '2.4.5'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [26s] Note_to_CRAN_maintainers
Maintainer: 'Gianluca Baio <g.baio@ucl.ac.uk>'
* 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 'BCEA' can be installed ... OK
* checking installed package size ... OK
* 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... 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 ... [23s] OK
* checking Rd files ... 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 ... NOTE
Documented arguments not in \usage in Rd file 'contour_ggplot_params.Rd':
  'pos_legend'

Documented arguments not in \usage in Rd file 'geom_quad_txt.Rd':
  'graph'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... [36s] ERROR
Running examples in 'BCEA-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: evppi
> ### Title: Expected Value of Perfect Partial Information (EVPPI) for
> ###   Selected Parameters
> ### Aliases: evppi evppi.default evppi.bcea
> 
> ### ** Examples
> 
> # See Baio G., Dawid A.P. (2011) for a detailed description of the 
> # Bayesian model and economic problem
> 
> ## Not run: 
> ##D # Load the post-processed results of the MCMC simulation model
> ##D # original JAGS output is can be downloaded from here
> ##D # https://gianluca.statistica.it/book/bcea/code/vaccine.RData
> ##D 
> ##D data(Vaccine, package = "BCEA")
> ##D treats <- c("Status quo", "Vaccination")
> ##D 
> ##D # Run the health economic evaluation using BCEA
> ##D m <- bcea(e.pts, c.pts, ref = 2, interventions = treats)
> ##D 
> ##D # Compute the EVPPI for a bunch of parameters
> ##D inp <- createInputs(vaccine_mat)
> ##D 
> ##D EVPPI <- evppi(m, c("beta.1." , "beta.2."), inp$mat)
> ##D 
> ##D plot(EVPPI)
> ##D 
> ##D # deprecated (single parameter) methods
> ##D EVPPI.so <- evppi(m, c("beta.1.", "beta.2."), inp$mat, method = "so", n.blocks = 50)
> ##D EVPPI.sad <- evppi(m, c("beta.1.", "beta.2."), inp$mat, method = "sad", n.seps = 1)
> ##D 
> ##D plot(EVPPI.so)
> ##D plot(EVPPI.sad)
> ##D  
> ##D # Compute the EVPPI using INLA/SPDE
> ##D if (require("INLA"))
> ##D   x_inla <- evppi(he = m, 39:40, input = inp$mat)
> ##D 
> ##D # using GAM regression
> ##D x_gam <- evppi(he = m, 39:40, input = inp$mat, method = "GAM")
> ##D 
> ##D # using Strong et al GP regression
> ##D x_gp <- evppi(he = m, 39:40, input = inp$mat, method = "GP")
> ##D 
> ##D # plot results
> ##D if (require("INLA")) plot(x_inla)
> ##D points(x_inla$k, x_inla$evppi, type = "l", lwd = 2, lty = 2)
> ##D points(x_gam$k, x_gam$evppi, type = "l", col = "red")
> ##D points(x_gp$k, x_gp$evppi, type = "l", col = "blue")
> ##D 
> ##D if (require("INLA")) {
> ##D   plot(x_inla$k, x_inla$evppi, type = "l", lwd = 2, lty = 2)
> ##D   points(x_gam$k, x_gam$evppi, type = "l", col = "red")
> ##D   points(x_gp$k, x_gp$evppi, type = "l", col = "blue")
> ##D }
> ##D 
> ##D data(Smoking)
> ##D treats <- c("No intervention", "Self-help",
> ##D "Individual counselling", "Group counselling")
> ##D m <- bcea(eff, cost, ref = 4, interventions = treats, Kmax = 500)
> ##D inp <- createInputs(smoking_output)
> ##D EVPPI <- evppi(m, c(2,3), inp$mat, h.value = 0.0000005)
> ##D plot(EVPPI)
> ## End(Not run)
> 
> data(Vaccine, package = "BCEA")
> treats <- c("Status quo", "Vaccination")
> bcea_vacc <- bcea(e.pts, c.pts, ref = 2, interventions = treats)
> inp <- createInputs(vaccine_mat)
 [1] "14 \nLinear dependence: removing column pi.2.2."
 [2] "15 \nLinear dependence: removing column pi.2.2."
 [3] "16 \nLinear dependence: removing column pi.2.2."
 [4] "17 \nLinear dependence: removing column pi.2.2."
 [5] "18 \nLinear dependence: removing column pi.2.2."
 [6] "19 \nLinear dependence: removing column pi.2.2."
 [7] "20 \nLinear dependence: removing column pi.2.2."
 [8] "21 \nLinear dependence: removing column pi.2.2."
 [9] "22 \nLinear dependence: removing column pi.2.2."
[10] "29 \nLinear dependence: removing column pi.2.2."
[11] "44 \nLinear dependence: removing column pi.2.2."
[12] "45 \nLinear dependence: removing column pi.2.2."
[13] "46 \nLinear dependence: removing column pi.2.2."
[14] "47 \nLinear dependence: removing column pi.2.2."
 [1] "14 \nLinear dependence: removing column pi.2.1."
 [2] "15 \nLinear dependence: removing column pi.2.1."
 [3] "16 \nLinear dependence: removing column pi.2.1."
 [4] "17 \nLinear dependence: removing column pi.2.1."
 [5] "18 \nLinear dependence: removing column pi.2.1."
 [6] "19 \nLinear dependence: removing column pi.2.1."
 [7] "20 \nLinear dependence: removing column pi.2.1."
 [8] "21 \nLinear dependence: removing column pi.2.1."
 [9] "22 \nLinear dependence: removing column pi.2.1."
[10] "29 \nLinear dependence: removing column pi.2.1."
[11] "44 \nLinear dependence: removing column pi.2.1."
[12] "45 \nLinear dependence: removing column pi.2.1."
 [1] "14 \nLinear dependence: removing column pi.1.1."
 [2] "15 \nLinear dependence: removing column pi.1.1."
 [3] "16 \nLinear dependence: removing column pi.1.1."
 [4] "17 \nLinear dependence: removing column pi.1.1."
 [5] "18 \nLinear dependence: removing column pi.1.1."
 [6] "19 \nLinear dependence: removing column pi.1.1."
 [7] "20 \nLinear dependence: removing column pi.1.1."
 [8] "21 \nLinear dependence: removing column pi.1.1."
 [9] "22 \nLinear dependence: removing column pi.1.1."
[10] "29 \nLinear dependence: removing column pi.1.1."
[11] "44 \nLinear dependence: removing column pi.1.1."
[1] "14 \nLinear dependence: removing column Repeat.GP.2.2."
[2] "15 \nLinear dependence: removing column Repeat.GP.2.2."
[3] "16 \nLinear dependence: removing column Repeat.GP.2.2."
[4] "17 \nLinear dependence: removing column Repeat.GP.2.2."
[5] "18 \nLinear dependence: removing column Repeat.GP.2.2."
[6] "19 \nLinear dependence: removing column Repeat.GP.2.2."
[7] "20 \nLinear dependence: removing column Repeat.GP.2.2."
[8] "21 \nLinear dependence: removing column Repeat.GP.2.2."
[9] "22 \nLinear dependence: removing column Repeat.GP.2.2."
[1] "14 \nLinear dependence: removing column Repeat.GP.2.1."
[2] "15 \nLinear dependence: removing column Repeat.GP.2.1."
[3] "17 \nLinear dependence: removing column Repeat.GP.2.1."
[4] "18 \nLinear dependence: removing column Repeat.GP.2.1."
[5] "20 \nLinear dependence: removing column Repeat.GP.2.1."
[6] "21 \nLinear dependence: removing column Repeat.GP.2.1."
[1] "14 \nLinear dependence: removing column Repeat.GP.1.1."
[2] "17 \nLinear dependence: removing column Repeat.GP.1.1."
[3] "20 \nLinear dependence: removing column Repeat.GP.1.1."
> evppi(bcea_vacc, c("beta.1.", "beta.2."), inp$mat)
Error in names(attr(res, "models")) <- res$pars : 
  'names' attribute [501] must be the same length as the vector [1]
Calls: evppi -> evppi.bcea -> <Anonymous>
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [58s] ERROR
  Running 'testthat.R' [57s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(BCEA)
  Registered S3 method overwritten by 'BCEA':
    method     from
    plot.evppi voi 
  The BCEA version loaded is: 2.4.5
  
  Attaching package: 'BCEA'
  
  The following object is masked from 'package:graphics':
  
      contour
  
  > 
  > test_check("BCEA")
  [ FAIL 7 | WARN 1 | SKIP 6 | PASS 98 ]
  
  ══ Skipped tests (6) ═══════════════════════════════════════════════════════════
  • INLA cannot be loaded (1): 'test-evppi.R:181:3'
  • empty test (3): 'test-ceac_plot_ggplot.R:5:1', 'test-compute_U.R:7:1',
    'test-eib_plot_ggplot.R:9:1'
  • more than two interventions to be revisited after {voi} update (1):
    'test-evppi.R:518:3'
  • plot = TRUE mesh plot to be snapshot (1): 'test-evppi.R:255:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-evppi.R:29:3'): GAM regression (default) with vaccine data ─────
  Error in `names(attr(res, "models")) <- res$pars`: 'names' attribute [501] must be the same length as the vector [1]
  Backtrace:
      ▆
   1. ├─BCEA::evppi(bcea_vacc, c("beta.1.", "beta.2."), inp$mat) at test-evppi.R:29:3
   2. └─BCEA:::evppi.bcea(bcea_vacc, c("beta.1.", "beta.2."), inp$mat)
   3.   └─voi::evppi(...)
  ── Error ('test-evppi.R:77:3'): Strong & Oakley with vaccine data ──────────────
  Error in `names(attr(res, "models")) <- res$pars`: 'names' attribute [501] must be the same length as the vector [1]
  Backtrace:
      ▆
   1. ├─BCEA::evppi(bcea_vacc, "beta.1.", inp$mat, method = "so", n.blocks = 50) at test-evppi.R:77:3
   2. └─BCEA:::evppi.bcea(...)
   3.   └─voi::evppi(...)
  ── Error ('test-evppi.R:123:3'): Sadatsafavi et al with vaccine data ───────────
  Error in `names(attr(res, "models")) <- res$pars`: 'names' attribute [501] must be the same length as the vector [1]
  Backtrace:
      ▆
   1. ├─BCEA::evppi(bcea_vacc, "beta.2.", inp$mat, method = "sad", n.seps = 1) at test-evppi.R:123:3
   2. └─BCEA:::evppi.bcea(...)
   3.   └─voi::evppi(...)
  ── Error ('test-evppi.R:161:3'): Select parameters by position with vaccine data ──
  Error in `names(attr(res, "models")) <- res$pars`: 'names' attribute [501] must be the same length as the vector [1]
  Backtrace:
      ▆
   1. ├─BCEA::evppi(he = bcea_vacc, param_idx = 39:40, input = inp$mat) at test-evppi.R:161:3
   2. └─BCEA:::evppi.bcea(he = bcea_vacc, param_idx = 39:40, input = inp$mat)
   3.   └─voi::evppi(...)
  ── Error ('test-evppi.R:216:3'): Different argument formats with vaccine data ──
  Error in `names(attr(res, "models")) <- res$pars`: 'names' attribute [501] must be the same length as the vector [1]
  Backtrace:
      ▆
   1. ├─BCEA::evppi(he = bcea_vacc, 39:40, input = inp$mat, method = "gam") at test-evppi.R:216:3
   2. └─BCEA:::evppi.bcea(he = bcea_vacc, 39:40, input = inp$mat, method = "gam")
   3.   └─voi::evppi(...)
  ── Error ('test-evppi.R:299:3'): Fitted values with vaccine data two parameters ──
  Error in `names(attr(res, "models")) <- res$pars`: 'names' attribute [501] must be the same length as the vector [1]
  Backtrace:
      ▆
   1. ├─BCEA::evppi(...) at test-evppi.R:299:3
   2. └─BCEA:::evppi.bcea(...)
   3.   └─voi::evppi(...)
  ── Error ('test-evppi.R:431:3'): Fitted values with vaccine data three parameters ──
  Error in `names(attr(res, "models")) <- res$pars`: 'names' attribute [501] must be the same length as the vector [1]
  Backtrace:
      ▆
   1. ├─BCEA::evppi(...) at test-evppi.R:431:3
   2. └─BCEA:::evppi.bcea(...)
   3.   └─voi::evppi(...)
  
  [ FAIL 7 | WARN 1 | SKIP 6 | PASS 98 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking re-building of vignette outputs ... [109s] OK
* checking PDF version of manual ... [15s] OK
* checking HTML version of manual ... [14s] OK
* DONE
Status: 2 ERRORs, 1 NOTE