* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/vacalibration.Rcheck’
* using R Under development (unstable) (2025-11-19 r89039)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
    GNU Fortran (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
* running under: Fedora Linux 40 (Workstation Edition)
* using session charset: UTF-8
* checking for file ‘vacalibration/DESCRIPTION’ ... OK
* this is package ‘vacalibration’ version ‘2.0’
* package encoding: UTF-8
* 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 ‘vacalibration’ can be installed ... [12s/11s] OK
* checking package directory ... 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 code 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 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 ... [19s/17s] 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 ... OK
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking examples with --run-donttest ... ERROR
Running examples in ‘vacalibration-Ex.R’ failed
The error most likely occurred in:

> ### Name: Mmat_champs
> ### Title: Misclassification Estimates Based on CHAMPS Data
> ### Aliases: Mmat_champs
> ### Keywords: datasets
> 
> ### ** Examples
> 
> 
> ## No test: 
> 
> ## misclassification estimates
> data(Mmat_champs)
> 
> # misclassification estimates for "neonate" age group and "insilicova" algorithm in Mozambique
> ## posterior summaries of the sensitivity of "pneumonia"
> Mmat_champs$neonate$insilicova$postsumm$Mozambique[,"pneumonia","pneumonia"]
       mean         min        2.5%         25%         50%         75% 
0.241610943 0.006325332 0.065263562 0.166323235 0.233196078 0.307354730 
      97.5%         max 
0.465015871 0.676044172 
> 
> ## posterior summaries of the false negative rates
> ## CHAMPS cause "pneumonia" and VA cause "ipre"
> Mmat_champs$neonate$insilicova$postsumm$Mozambique[,"pneumonia","ipre"]
      mean        min       2.5%        25%        50%        75%      97.5% 
0.30976737 0.02828608 0.12620219 0.23510081 0.30094222 0.37843057 0.53692348 
       max 
0.79483740 
> 
> # COMSA-Mozambique: Example (Publicly Available Version)
> # Individual-Level Specific (High-Resolution) Cause of Death Data
> data(comsamoz_public_openVAout)
> head(comsamoz_public_openVAout$data)  # head of the data
     ID                              cause
1 10004 Other and unspecified neonatal CoD
2 10006                     Birth asphyxia
3 10008                    Neonatal sepsis
4 10036                     Birth asphyxia
5 10046                     Birth asphyxia
6 10051                    Neonatal sepsis
> 
> ## VA-calibration for the "neonate" age group and "insilicova" algorithm
> calib_out1 = vacalibration(va_data =
+                                      setNames(list(comsamoz_public_openVAout$data),
+                                               list(comsamoz_public_openVAout$va_algo)),
+                            age_group = comsamoz_public_openVAout$age_group,
+                            country = "Mozambique")
Using cause as value column: use value.var to override.
Calibrating ...
Error in prep_call_sampler(object) : 
  the compiled object from C++ code for this model is invalid, possible reasons:
  - compiled with save_dso=FALSE;
  - compiled on a different platform;
  - does not exist (created from reading csv files).
Calls: vacalibration ... <Anonymous> -> .local -> <Anonymous> -> prep_call_sampler
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* checking for new files in some other directories ... OK
* DONE

Status: 1 ERROR
See
  ‘/data/blackswan/ripley/R/packages/tests-devel/vacalibration.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 1:56.55, 105.47 + 20.72