This :
> foo <- brm(bf(mvbind(DeltaPoids, DeltaPouls, DeltaTAS, DeltaTAD)~DeltaDate,
family=gaussian)+set_rescor(TRUE),
data=nData, sample_prior="yes", save_pars=save_pars("all"),
backend="rstan", future=TRUE, cores=4)
runs, but this :
> bar <- brm(bf(mvbind(DeltaPoids, DeltaPouls, DeltaTAS, DeltaTAD)~DeltaDate,
family=gaussian)+set_rescor(TRUE),
data=nData, sample_prior="yes", save_pars=save_pars("all"),
backend="cmdstanr", future=TRUE, cores=4)
fails wit the following message :
bin/stanc: unknown option '--canonicalize=deprecations,braces,parentheses'.
Usage: stanc [option] ... <model_file.stan>
--debug-lex For debugging purposes: print the lexer actions
--debug-parse For debugging purposes: print the parser actions
--debug-ast For debugging purposes: print the undecorated AST, before semantic checking
--debug-decorated-ast For debugging purposes: print the decorated AST, after semantic checking
--debug-generate-data For debugging purposes: generate a mock dataset to run the model on
--debug-mir For debugging purposes: print the MIR as an S-expression.
--debug-mir-pretty For debugging purposes: pretty-print the MIR.
--debug-optimized-mir For debugging purposes: print the MIR after it's been optimized. Only has an effect when optimizations are turned on.
--debug-optimized-mir-pretty For debugging purposes: pretty print the MIR after it's been optimized. Only has an effect when optimizations are turned on.
--debug-transformed-mir For debugging purposes: print the MIR after the backend has transformed it.
--debug-transformed-mir-pretty For debugging purposes: pretty print the MIR after the backend has transformed it.
--dump-stan-math-signatures Dump out the list of supported type signatures for Stan Math backend.
--warn-uninitialized Emit warnings about uninitialized variables to stderr. Currently an experimental feature.
--warn-pedantic Emit warnings about common mistakes in Stan programs.
--auto-format Pretty prints the program to the console
--print-canonical Prints the canonicalized program to the console
--version Display stanc version number
--name Take a string to set the model name (default = "$model_filename_model")
--O Allow the
compiler to apply all optimizations to the Stan code.
--o Take the path to an output file for generated C++ code (default = "$name.hpp")
--print-cpp If set, output the generated C++ Stan model class to stdout.
--allow-undefined Do not fail if a function is declared but not defined
--allow_undefined Deprecated. Same as --allow-undefined.
--include-paths Takes a comma-separated list of directories that may contain a file in an #include directive (default = "")
--include_paths Deprecated. Same as --include-paths.
--use-opencl If set, try to use matrix_cl signatures.
--standalone-functions If set, the generated C++ will be the standalone functions C++ code.
--filename-in-msg Sets the filename used in compiler errors. Uses actual filename by default.
--info If set, print information about the model.
-help Display this list of options
--help Display this list of options
Error in `processx::run(command = stanc_cmd, args = c(stan_file, stanc_flags), …`:
! System command 'stanc' failed
---
Exit status: 2
Stderr (last 10 lines, see `$stderr` for more):
--allow-undefined Do not fail if a function is declared but not defined
--allow_undefined Deprecated. Same as --allow-undefined.
--include-paths Takes a comma-separated list of directories that may contain a file in an #include directive (default = "")
--include_paths Deprecated. Same as --include-paths.
--use-opencl If set, try to use matrix_cl signatures.
--standalone-functions If set, the generated C++ will be the standalone functions C++ code.
--filename-in-msg Sets the filename used in compiler errors. Uses actual filename by default.
--info If set, print information about the model.
-help Display this list of options
--help Display this list of options
---
Type .Last.error to see the more details.
> .Last.error
<system_command_status_error/rlib_error_3_0/rlib_error/error>
Error in `processx::run(command = stanc_cmd, args = c(stan_file, stanc_flags), …`:
! System command 'stanc' failed
---
Exit status: 2
Stderr (last 10 lines, see `$stderr` for more):
--allow-undefined Do not fail if a function is declared but not defined
--allow_undefined Deprecated. Same as --allow-undefined.
--include-paths Takes a comma-separated list of directories that may contain a file in an #include directive (default = "")
--include_paths Deprecated. Same as --include-paths.
--use-opencl If set, try to use matrix_cl signatures.
--standalone-functions If set, the generated C++ will be the standalone functions C++ code.
--filename-in-msg Sets the filename used in compiler errors. Uses actual filename by default.
--info If set, print information about the model.
-help Display this list of options
--help Display this list of options
---
Backtrace:
1. brms::brm(bf(mvbind(DeltaPoids, DeltaPouls, DeltaTAS, DeltaTAD) ~ DeltaDate, …
2. brms:::.make_stancode(bterms, data = data, prior = prior, stanvars = stanvars, …
3. brms:::.canonicalize_stan_model(tmp_file, overwrite_file = FALSE)
4. processx::run(command = stanc_cmd, args = c(stan_file, stanc_flags), …
5. processx:::throw(new_process_error(res, call = sys.call(), echo = echo, …
>
which could as well be in Akkadian…
FWIW :
OS : Linux (Debian testing)
> sessionInfo()
R version 4.2.1 (2022-06-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux bookworm/sid
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so
locale:
[1] LC_CTYPE=fr_FR.UTF-8 LC_NUMERIC=C
[3] LC_TIME=fr_FR.UTF-8 LC_COLLATE=fr_FR.UTF-8
[5] LC_MONETARY=fr_FR.UTF-8 LC_MESSAGES=fr_FR.UTF-8
[7] LC_PAPER=fr_FR.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] tools stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] rstan_2.21.5 StanHeaders_2.21.0-7 brms_2.17.0
[4] Rcpp_1.0.9 cmdstanr_0.5.2 ggplot2_3.3.6
[7] mgcv_1.8-40 nlme_3.1-158 digest_0.6.29
[10] DBI_1.1.3
loaded via a namespace (and not attached):
[1] TH.data_1.1-1 minqa_1.2.4 colorspace_2.0-3
[4] ellipsis_0.3.2 ggridges_0.5.3 estimability_1.4
[7] markdown_1.1 base64enc_0.1-3 listenv_0.8.0
[10] farver_2.1.1 DT_0.23 bit64_4.0.5
[13] fansi_1.0.3 mvtnorm_1.1-3 bridgesampling_1.1-2
[16] codetools_0.2-18 splines_4.2.1 cachem_1.0.6
[19] knitr_1.39 shinythemes_1.2.0 bayesplot_1.9.0
[22] projpred_2.1.2 jsonlite_1.8.0 nloptr_2.0.3
[25] shiny_1.7.1 compiler_4.2.1 emmeans_1.7.5
[28] backports_1.4.1 assertthat_0.2.1 Matrix_1.4-1
[31] fastmap_1.1.0 cli_3.3.0 later_1.3.0
[34] htmltools_0.5.2 prettyunits_1.1.1 igraph_1.3.2
[37] coda_0.19-4 gtable_0.3.0 glue_1.6.2
[40] reshape2_1.4.4 dplyr_1.0.9 posterior_1.2.2
[43] vctrs_0.4.1 crosstalk_1.2.0 tensorA_0.36.2
[46] xfun_0.31 stringr_1.4.0 globals_0.15.1
[49] ps_1.7.1 lme4_1.1-30 mime_0.12
[52] miniUI_0.1.1.1 lifecycle_1.0.1 gtools_3.9.3
[55] future_1.26.1 MASS_7.3-57 zoo_1.8-10
[58] scales_1.2.0 colourpicker_1.1.1 promises_1.2.0.1
[61] Brobdingnag_1.2-7 parallel_4.2.1 sandwich_3.0-2
[64] inline_0.3.19 shinystan_2.6.0 gamm4_0.2-6
[67] memoise_2.0.1 gridExtra_2.3 loo_2.5.1
[70] stringi_1.7.8 RSQLite_2.2.14 dygraphs_1.1.1.6
[73] checkmate_2.1.0 boot_1.3-28 pkgbuild_1.3.1
[76] rlang_1.0.4 pkgconfig_2.0.3 matrixStats_0.62.0
[79] distributional_0.3.0 lattice_0.20-45 purrr_0.3.4
[82] rstantools_2.2.0 htmlwidgets_1.5.4 labeling_0.4.2
[85] bit_4.0.4 processx_3.7.0 tidyselect_1.1.2
[88] parallelly_1.32.0 plyr_1.8.7 magrittr_2.0.3
[91] R6_2.5.1 generics_0.1.3 multcomp_1.4-19
[94] pillar_1.7.0 withr_2.5.0 xts_0.12.1
[97] survival_3.3-1 abind_1.4-5 tibble_3.1.7
[100] crayon_1.5.1 utf8_1.2.2 grid_4.2.1
[103] blob_1.2.3 callr_3.7.0 threejs_0.3.3
[106] xtable_1.8-4 httpuv_1.6.5 RcppParallel_5.1.5
[109] stats4_4.2.1 munsell_0.5.0 shinyjs_2.1.0
> system("/usr/local/cmdstan/bin/stanc --version")
stanc3 766bbf10 (Unix)
>
This might be a subtle misfeature introduced by my cmdstan version (hand-compiled from the github tree).
I just checked that cmdstanr is at 0.5.2, i. e. the latest available…
Advice ?