* using log directory ‘/srv/hornik/tmp/CRAN_pretest/TimeDepFrail.Rcheck’
* using R Under development (unstable) (2024-10-22 r87265)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 19.1.1 (1)
    Debian flang-new version 19.1.1 (1)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘TimeDepFrail/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TimeDepFrail’ version ‘0.0.0.9’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [3s/4s] NOTE
Maintainer: ‘Alessandra Ragni <alessandra.ragni@polimi.it>’

New submission

Possibly misspelled words in DESCRIPTION:
  Houwelingen (11:294)
  Paik (11:85)
  Wintrebert (11:242)
  Zwinderman (11:270)
  al (11:93)
  et (11:90)
* 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 whether package ‘TimeDepFrail’ can be installed ... [2s/2s] OK
* 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 ... [0s/0s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the package can be unloaded cleanly ... [0s/0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
* checking loading without being on the library search path ... [0s/0s] 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 ... [4s/4s] OK
* checking Rd files ... [0s/0s] 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 ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [0s/0s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... [30m/30m] ERROR
Running examples in ‘TimeDepFrail-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_bas_hazard
> ### Title: lot the Baseline Hazard Step-Function
> ### Aliases: plot_bas_hazard
> 
> ### ** Examples
> 
> # Import data
> data(data_dropout)
> 
> # Define the variables needed for the model execution
> eps_paik <- 1e-10
> categories_range_min <- c(-8, -2, eps_paik, eps_paik, eps_paik)
> categories_range_max <- c(-eps_paik, 0.4, 1 - eps_paik, 1, 10)
> time_axis <- c(1.0, 1.4, 1.8, 2.3, 3.1, 3.8, 4.3, 5.0, 5.5, 5.8, 6.0)
> formula <- time_to_event ~ Gender + CFUP + cluster(group)
> 
> # Call the main model function
> result <- AdPaikModel(formula, data_dropout, time_axis, categories_range_min, categories_range_max)
Adapted Paik et al.'s Model:
Warning in terms.formula(formula, special, data) :
  setting 'abb' in terms.formula() is deprecated
Start log-likelihood optimization ... 
Run  1
Global log-likelihood:  -2285.3096135621
Run  2
Global log-likelihood:  -2285.3096135621
Global log-likelihood:  -2189.83940697392
Run  3
Global log-likelihood:  -2285.3096135621
Global log-likelihood:  -2189.83940697392
Global log-likelihood:  -2176.59966695168
Run  4
Global log-likelihood:  -2189.83940697392
Global log-likelihood:  -2176.59966695168
Global log-likelihood:  -2175.98040354791
Run  5
Global log-likelihood:  -2176.59966695168
Global log-likelihood:  -2175.98040354791
Global log-likelihood:  -2175.68748887479
Run  6
Global log-likelihood:  -2175.98040354791
Global log-likelihood:  -2175.68748887479
Global log-likelihood:  -2175.47673577463
Run  7
Global log-likelihood:  -2175.68748887479
Global log-likelihood:  -2175.47673577463
Global log-likelihood:  -2175.34796168102
Run  8
Global log-likelihood:  -2175.47673577463
Global log-likelihood:  -2175.34796168102
Global log-likelihood:  -2175.26500491396
Run  9
Global log-likelihood:  -2175.34796168102
Global log-likelihood:  -2175.26500491396
Global log-likelihood:  -2175.21380933185
Run  10
Global log-likelihood:  -2175.26500491396
Global log-likelihood:  -2175.21380933185
Global log-likelihood:  -2175.18220719155
Run  11
Global log-likelihood:  -2175.21380933185
Global log-likelihood:  -2175.18220719155
Global log-likelihood:  -2175.16316243157
Run  12
Global log-likelihood:  -2175.18220719155
Global log-likelihood:  -2175.16316243157
Global log-likelihood:  -2175.15083269749
Run  13
Global log-likelihood:  -2175.16316243157
Global log-likelihood:  -2175.15083269749
Global log-likelihood:  -2175.14543609089
Run  14
Global log-likelihood:  -2175.15083269749
Global log-likelihood:  -2175.14543609089
Global log-likelihood:  -2175.14172564305
Run  15
Global log-likelihood:  -2175.14543609089
Global log-likelihood:  -2175.14172564305
Global log-likelihood:  -2175.1392074048
Run  16
Global log-likelihood:  -2175.14172564305
Global log-likelihood:  -2175.1392074048
Global log-likelihood:  -2175.13757444061
Run  17
Global log-likelihood:  -2175.1392074048
Global log-likelihood:  -2175.13757444061
Global log-likelihood:  -2175.13654875682
Run  18
Global log-likelihood:  -2175.13757444061
Global log-likelihood:  -2175.13654875682
Global log-likelihood:  -2175.13591818865
Run  19
Global log-likelihood:  -2175.13654875682
Global log-likelihood:  -2175.13591818865
Global log-likelihood:  -2175.1355353199
Run  20
Global log-likelihood:  -2175.13591818865
Global log-likelihood:  -2175.1355353199
Global log-likelihood:  -2175.13530567022
Run  21
Global log-likelihood:  -2175.1355353199
Global log-likelihood:  -2175.13530567022
Global log-likelihood:  -2175.13516981761
Run  22
Global log-likelihood:  -2175.13530567022
Global log-likelihood:  -2175.13516981761
Global log-likelihood:  -2175.13508863543
Run  23
Global log-likelihood:  -2175.13516981761
Global log-likelihood:  -2175.13508863543
Global log-likelihood:  -2175.13504078539
Run  24
Global log-likelihood:  -2175.13508863543
Global log-likelihood:  -2175.13504078539
Global log-likelihood:  -2175.13501257627
Run  25
Global log-likelihood:  -2175.13504078539
Global log-likelihood:  -2175.13501257627
Global log-likelihood:  -2175.13499509907
Run  26
Global log-likelihood:  -2175.13501257627
Global log-likelihood:  -2175.13499509907
Global log-likelihood:  -2175.13498603713
Run  27

Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
AdPaikModel       371.143  0.003 371.256
frailty_sd.AdPaik 368.167  0.000 368.293
frailty_sd        368.012  0.000 368.208
* checking PDF version of manual ... [4s/4s] WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<recently read> \Z 
                   
l.190 ...= \alpha_j + \epsilon{jk}, \forall j,k}{}
                                                  . Matrix of dimension (N, L).
! Undefined control sequence.
<recently read> \Z 
                   
l.201 ...= \alpha_j + \epsilon{jk}, \forall j,k}{}
                                                  . Matrix of dimension (N, L).
! Undefined control sequence.
<recently read> \Z 
                   
l.837 ...= \alpha_j + \epsilon{jk}, \forall j,k}{}
                                                  . Matrix of dimension (N, L).
! Undefined control sequence.
<recently read> \Z 
                   
l.848 ...= \alpha_j + \epsilon{jk}, \forall j,k}{}
                                                  . Matrix of dimension (N, L).
! Undefined control sequence.
<recently read> \Z 
                   
l.945 ...= \alpha_j + \epsilon{jk}, \forall j,k}{}
                                                  . It is a matrix of dimens...
! Undefined control sequence.
<recently read> \Z 
                   
l.978 ...= \alpha_j + \epsilon{jk}, \forall j,k}{}
                                                  . It is a matrix of dimens...
* checking PDF version of manual without index ... ERROR
* checking HTML version of manual ... [1s/1s] OK
* checking for non-standard things in the check directory ... NOTE
Found the following files/directories:
  ‘TimeDepFrail-manual.tex’
* checking for detritus in the temp directory ... OK
* DONE
Status: 2 ERRORs, 1 WARNING, 2 NOTEs