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James-Thorson-NOAA / VAST

Spatio-temporal analysis of univariate or multivariate data, e.g., standardizing data for multiple species or stages
http://www.FishStats.org
GNU General Public License v3.0
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Compilation failed while running fit_model() using R 4.0.2 #391

Closed johannafaure closed 3 months ago

johannafaure commented 3 months ago

Hello !

I am trying to run fit_model() using R version 4.0.2 so I can run within Microsoft R Open 4.0.

I installed VAST as follow : devtools::install_github("James-Thorson-NOAA/VAST", ref="main") and I set VAST_v14_0_1 in settings.

When running the following code, I obtain a compilation error with TMB object :

fit <- fit_model( settings = settings, Lat_i = Lat_i, Lon_i = Lon_i, t_i = as.numeric( as.character( spp_data[, "Year"] ) ), c_i = rep( 0, nrow( spp_data ) ), b_i = as.numeric( as.character( spp_data[, "CPUE_mean"] ) ), a_i = rep( 1, nrow( spp_data ) ), v_i = v_i - 1, Use_REML = FALSE, input_grid = input_grid, newtonsteps = 3 )

Making TMB object

Error in TMB::compile(file = paste0(Version_framework, ".cpp"), framework = framework, : Compilation failed

I tried to uninstall VAST and TMB packages, re-install Rtools 4.0 and then VAST, but I still get the same error when running fit-model().

Could you please tell me how to solve this issue? I have TMB version 1.9.12

Thanks a lot

agruss2 commented 3 months ago

Hi Johanna,

Regarding your compiling error – Could you please try something else? (1) Uninstall VAST and TMB packages and then re-install Rtools 4.0 (2) Make sure that Rtools 4.0 is in your PATH by doing the following: (i) Type “env” in the search box. (ii) Select “Edit the system environment variables”. (iii) Click on “Environment variables…” (iv) In “use variables” double-click on “Path”. (v) If rtools40 does not appear in your Path add it. (3) Only after that re-install VAST.

Hopefully that solves your issue. Sorry that I did not think about this earlier.

@James-Thorson-NOAA and VAST users - Please let us know if you have other ideas in case mine is not going to solve the problem that Johanna is facing.

Cheers, Arnaud

agruss2 commented 3 months ago

Issue solved :)