Models with smooth terms no longer run - "object of type 'symbol' is not subsettable"

[seananderson]

Discussed in https://github.com/pbs-assess/sdmTMB/discussions/260

^{Originally posted by **nilescbn** October 10, 2023} ### The Error I'm a very new user of sdmTMB but have successfully run a number of models on fisheries data. In going back to some models I was running successfully last week. I'm getting this error and have traced it to the inclusion of smooth terms: > Error in x[[3]] : object of type 'symbol' is not subsettable I came back to the models because I was having convergence problems. I saw the note about the nlminb_loops. Increasing the number of loops to 2 worked on models without smooth terms. I tried installing the development version of sdmTMB but that didn't solve it. I tried running the same model with smooth terms using gam() from mgcv and it runs. Same for brm() from brms. ### Simulated Example In terms of reproducible example, using this simulated data I get the same errror. `sim_data <- data.frame(X = runif(1000, 164.5, 415), Y = runif(1000, 4560, 5366), depth = runif(1000, 100, 300), haul_hours = runif(1000, 0.5, 5), catch = rnorm(1000, mean = 50, sd = 24) ) ` `sim_mesh <- make_mesh(sim_data, xy_cols = c("X", "Y"), cutoff = 10)` This runs: ` m1 <- sdmTMB(catch ~ depth + haul_hours, data = sim_data, mesh = sim_mesh, anisotropy = FALSE, spatial = "on") ` This produces the error: `m1s <- sdmTMB(catch ~ s(depth) + s(haul_hours), data = sim_data, mesh = sim_mesh, anisotropy = FALSE, spatial = "on")` ### Traceback This is from RStudio's Traceback feature. 7. deparse(x, 500L) 6. paste(deparse(x, 500L), collapse = collapse) 5. safe_deparse(x[[3]]) 4. FUN(X[[i]], ...) 3. vapply(bars, function(x) safe_deparse(x[[3]]), "") 2. barnames(split_formula[[ii]]$reTrmFormulas) 1. sdmTMB(catch ~ s(depth) + s(haul_hours), data = sim_data, mesh = sim_mesh, anisotropy = FALSE, spatial = "on") ### Package Updates I updated a number of R packages since running the models successfully before, I wasn't paying close attention to which ones updated. I was getting a warning about a mismatch in versions of the Matrix package, but that was back when the models ran fine. ### Session Info Here is the session info from running the model on the simple, simulate data. > R version 4.2.3 (2023-03-15 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19044) Matrix products: default locale: [1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8 [3] LC_MONETARY=English_United States.utf8 LC_NUMERIC=C [5] LC_TIME=English_United States.utf8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] sdmTMB_0.3.1.9000 loaded via a namespace (and not attached): [1] Rcpp_1.0.11 INLA_23.04.24 nloptr_2.0.3 TMB_1.9.6 [5] glmmTMB_1.1.8 compiler_4.2.3 pillar_1.9.0 class_7.3-21 [9] tools_4.2.3 boot_1.3-28.1 lme4_1.1-34 tibble_3.2.1 [13] lifecycle_1.0.3 nlme_3.1-162 lattice_0.20-45 mgcv_1.8-42 [17] pkgconfig_2.0.3 rlang_1.1.1 Matrix_1.6-1.1 DBI_1.1.3 [21] cli_3.6.1 rstudioapi_0.15.0 parallel_4.2.3 mvtnorm_1.2-3 [25] xfun_0.40 e1071_1.7-13 coda_0.19-4 fmesher_0.1.2 [29] dplyr_1.1.3 knitr_1.44 generics_0.1.3 vctrs_0.6.3 [33] tidyselect_1.2.0 classInt_0.4-10 grid_4.2.3 glue_1.6.2 [37] sf_1.0-14 R6_2.5.1 fansi_1.0.5 sp_2.1-0 [41] minqa_1.2.6 magrittr_2.0.3 MASS_7.3-58.2 emmeans_1.8.8 [45] splines_4.2.3 units_0.8-4 assertthat_0.2.1 xtable_1.8-4 [49] numDeriv_2016.8-1.1 KernSmooth_2.23-20 utf8_1.2.3 estimability_1.4.1 [53] proxy_0.4-27

[seananderson]

I have fixed this temporarily, but it involved copying over a bunch of glmmTMB code from reformulas.R in version 1.1.7. I'm not sure we need all that complexity or want to deal with all the license issues.

[seananderson]

This has been resolved here and on CRAN.