trouble with installation

[mfisher5]

I'm excited to try the new release with some data that are grouped by site habitat, but I keep getting a non-zero exit status warning when I use devtools to install zoid from github. It looks like there might be an error in the code for model_dirichregmod? Or maybe I need to try updating another package / R permissions on my desktop first? I'm in R version 4.1.3 (2022-03-10). Thanks for the help!

> devtools::install_github("noaa-nwfsc/zoid")

The downloaded source packages are in
	‘C:\Users\mfisher5\AppData\Local\Temp\RtmpOErnoU\downloaded_packages’
-- R CMD build ------------------------------------------------------------------------------------------------------------------------
v  checking for file 'C:\Users\mfisher5\AppData\Local\Temp\RtmpOErnoU\remotes2ae820826225\noaa-nwfsc-zoid-c82b045/DESCRIPTION' ...
-  preparing 'zoid': (714ms)
v  checking DESCRIPTION meta-information ... 
-  cleaning src
-  checking for LF line-endings in source and make files and shell scripts
-  checking for empty or unneeded directories
-  building 'zoid_1.3.1.tar.gz'
   Warning: file 'zoid/configure' did not have execute permissions: corrected
   
* installing *source* package 'zoid' ...
** using staged installation
SYNTAX ERROR, MESSAGE(S) FROM PARSER:
 error in 'model_dirichregmod' at line 7, column 2
  -------------------------------------------------
     5:   int N_covar; // number of covariates in design matrix X
     6:   matrix[N_samples, N_covar] design_X;
     7:   array[N_bins,N_bins-1] int prod_idx;
         ^
     8:   int overdisp; // whether or not to include overdispersion term
  -------------------------------------------------

PARSER EXPECTED: <one of the following:
  a variable declaration, beginning with type,
      (int, real, vector, row_vector, matrix, unit_vector,
       simplex, ordered, positive_ordered,
       corr_matrix, cov_matrix,
       cholesky_corr, cholesky_cov
  or '}' to close variable declarations>
Error in rstan::stanc(file_name, allow_undefined = TRUE, obfuscate_model_name = FALSE,  : 
  failed to parse Stan model 'dirichregmod' due to the above error.
Calls: <Anonymous> -> sapply -> lapply -> FUN -> <Anonymous>
Execution halted
ERROR: configuration failed for package 'zoid'
* removing 'C:/Users/mfisher5/Documents/R/R-4.1.3/library/zoid'
* restoring previous 'C:/Users/mfisher5/Documents/R/R-4.1.3/library/zoid'
Warning message:
In i.p(...) :
  installation of package ‘C:/Users/mfisher5/AppData/Local/Temp/RtmpOErnoU/file2ae8f3c3fa4/zoid_1.3.1.tar.gz’ had non-zero exit status

[ericward-noaa]

I think this may be a package update issue? I just tried a new installation on a Mac and it seems to work fine.

R version 4.3.1 (2023-06-16)
Platform: x86_64-apple-darwin20 (64-bit)
Running under: macOS Monterey 12.6.7

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-x86_64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

My version of R is slightly newer, so that may be also worth trying. For packages, I'd update everything -- but Stan/StanHeaders seem like the obvious ones that could be causing issues.

Related, I also started working this up in TMB -- which may be a good solution for some of the giant datasets you're working with. This is still very much in development, but available here: https://github.com/noaa-nwfsc/zoidtmb