AFSC pollock case study does not render on remote repo

[Bai-Li-NOAA]

The AFSC pollock case study renders successfully locally but it does not render on remote repo.

The warning from the FIMS installation process:

Warning in checkMatrixPackageVersion(getOption("TMB.check.Matrix", TRUE)) :
  Package version inconsistency detected.
TMB was built with Matrix version 1.6.4
Current Matrix version is 1.6.1.1
Please re-install 'TMB' from source using install.packages('TMB', type = 'source') or ask CRAN for a binary version of 'TMB' matching CRAN's 'Matrix' package

The error after running [run-FIMS] section of code:

*** caught segfault ***
address 0x0, cause 'memory not mapped'

The pollock case study needs to use the FIMS isNA branch, but I am not sure if GHA is installing the correct version of FIMS for this case study. When I tried to use the latest version of FIMS locally for this case study, I encountered the following error:

Quitting from lines 94-190 [run-FIMS] (AFSC-GOA-pollock.qmd)
Error in `nlminb()`:
! NA/NaN gradient evaluation
Backtrace:
 1. TMBhelper::fit_tmb(obj, getsd = FALSE, newtonsteps = 0, control = list(trace = 100))
 2. stats::nlminb(...)                                                                                                      
Execution halted

Potential solutions to try:

• Force installing FIMS isNA branch in the case study
• Re-install 'TMB' from source using install.packages('TMB', type = 'source') in the case study

[Bai-Li-NOAA]

The case study is using FIMS isNA branch. This has been tested through commit 436f605.

[Cole-Monnahan-NOAA]

Just an FYI it will fail on the main branch b/c I'm inputting negative observations for both the indices and age compositions (-999) so those will be logged and thus NaN so the likelihood calculations break downstream. That's expected.