Installation issue (caused by Stan deprecating some functions)

[athowes]

(Duplication of issue from Zulip. Thought it would be useful others with same issue, and to have a record of debugging here.)

Currently unable to install this package. Suggestion from Swapnil on Zulip that some of the functions used in the package have since been deprecating by Stan, so may need to change these to be compatible with later versions of rstan and cmdstanr.

Calling devtools::install_github("ImperialCollegeLondon/epidemia") gives me:

   ../inst/include/csr_matrix_times_vector2.hpp:5:1: note: candidate template ignored: could not match 'Matrix' against 'Map'
   csr_matrix_times_vector2(const int& m,
   ^
   152 warnings and 17 errors generated.
   make: *** [stanExports_epidemia_base.o] Error 1
   ERROR: compilation failed for package ‘epidemia’
─  removing ‘/private/var/folders/4r/hkp4v9fn3wx044_hk8qnsjxw0000gn/T/Rtmp7NL5hR/Rinstd8a4e2bb689/epidemia’
         -----------------------------------
   ERROR: package installation failed

And for install.packages("epidemia") I get:

Warning in install.packages :
  package ‘epidemia’ is not available for this version of R

Here is my session information. Most relevant part is that I have cmdstanr_0.7.1 and rstan_2.32.5:

> sessionInfo()
R version 4.3.2 (2023-10-31)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Sonoma 14.2.1

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: Europe/London
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] cmdstanr_0.7.1     rstan_2.32.5       StanHeaders_2.32.5

loaded via a namespace (and not attached):
 [1] tensorA_0.36.2.1     gtable_0.3.4         xfun_0.42            ggplot2_3.5.0       
 [5] QuickJSR_1.1.3       htmlwidgets_1.6.4    devtools_2.4.5       remotes_2.4.2.1     
 [9] processx_3.8.3       inline_0.3.19        callr_3.7.5          vctrs_0.6.5         
[13] tools_4.3.2          ps_1.7.6             generics_0.1.3       stats4_4.3.2        
[17] curl_5.2.0           parallel_4.3.2       tibble_3.2.1         fansi_1.0.6         
[21] pkgconfig_2.0.3      checkmate_2.3.1      desc_1.4.3           distributional_0.4.0
[25] RcppParallel_5.1.7   lifecycle_1.0.4      compiler_4.3.2       stringr_1.5.1       
[29] munsell_0.5.0        codetools_0.2-19     httpuv_1.6.14        htmltools_0.5.7     
[33] usethis_2.2.2        later_1.3.2          pillar_1.9.0         urlchecker_1.0.1    
[37] ellipsis_0.3.2       cachem_1.0.8         sessioninfo_1.2.2    abind_1.4-5         
[41] mime_0.12            posterior_1.5.0      tidyselect_1.2.0     digest_0.6.34       
[45] stringi_1.8.3        dplyr_1.1.4          purrr_1.0.2          fastmap_1.1.1       
[49] grid_4.3.2           colorspace_2.1-0     cli_3.6.2            magrittr_2.0.3      
[53] loo_2.7.0            pkgbuild_1.4.3       utf8_1.2.4           backports_1.4.1     
[57] scales_1.3.0         promises_1.2.1       matrixStats_1.2.0    gridExtra_2.3       
[61] memoise_2.0.1        shiny_1.8.0          knitr_1.45           V8_4.4.2            
[65] miniUI_0.1.1.1       profvis_0.3.8        rlang_1.1.3          Rcpp_1.0.12         
[69] xtable_1.8-4         glue_1.7.0           pkgload_1.3.4        rstudioapi_0.15.0   
[73] jsonlite_1.8.8       R6_2.5.1             fs_1.6.3