Has anyone had an error when trying to run {brms} functions in R4.2? It requires Rtools42 which I have installed. [rethinking] functions calling cmdstan seem to work fine.
here is the model, which is taken from McElreath's Rethinking Statistics course:
b5.2 <-
brm(data = d,
family = gaussian,
d ~ 1 + m,
prior = c(prior(normal(0, 0.2), class = Intercept),
prior(normal(0, 0.5), class = b),
prior(exponential(1), class = sigma)),
iter = 2000, warmup = 1000, chains = 4, cores = 4,
seed = 5,
file = "[mypath]/b05.02")
throws this error:
Error in compileCode(f, code, language = language, verbose = verbose) :
C:\rtools42\x86_64-w64-mingw32.static.posix\bin/ld.exe: file2e8825ef5ea5.o:file2e8825ef5ea5.cpp:(.text$_ZN3tbb8internal26task_scheduler_observer_v3D0Ev[_ZN3tbb8internal26task_scheduler_observer_v3D0Ev]+0x1d): undefined reference to `tbb::internal::task_scheduler_observer_v3::observe(bool)'C:\rtools42\x86_64-w64-mingw32.static.posix\bin/ld.exe: file2e8825ef5ea5.o:file2e8825ef5ea5.cpp:(.text$_ZN3tbb10interface623task_scheduler_observerD1Ev[_ZN3tbb10interface623task_scheduler_observerD1Ev]+0x1d): undefined reference to `tbb::internal::task_scheduler_observer_v3::observe(bool)'C:\rtools42\x86_64-w64-mingw32.static.posix\bin/ld.exe: file2e8825ef5ea5.o:file2e8825ef5ea5.cpp:(.text$_ZN3tbb10interface623task_scheduler_observerD1Ev[_ZN3tbb10interface623task_scheduler_observerD1Ev]+0x3a): undefined reference to `tbb::internal::task_scheduler_observer_v3::observe(bool)'C:\rtools42\x86_64-w64-mingw32.static.posix\bin/ld.exe: file2e8825ef5ea5.o:file2e8825ef5ea5.cpp:(.text$_ZN3tbb10interface
Error in sink(type = "output") : invalid connection
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Hi @John_Belmont I am getting exactly the same error messages when running brm_multiple function.
Mine was working smoothly until I updated R and RStudio and Rtools, I am now running into these issues. Did you have any luck finding a solution?
Instead of trying to solve the issue I just reverted to an older version of R and Rtools4
R version 4.1.3 (2022-03-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19043)
Matrix products: default
locale:
[1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252 LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C LC_TIME=English_United Kingdom.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] geosphere_1.5-14 GGally_2.1.2 brms_2.17.0 Rcpp_1.0.7 RColorBrewer_1.1-3 corrplot_0.92 forcats_0.5.1
[8] stringr_1.4.0 dplyr_1.0.9 purrr_0.3.4 readr_2.1.2 tidyr_1.2.0 tibble_3.1.2 ggplot2_3.3.5
[15] tidyverse_1.3.1 mice_3.14.0
loaded via a namespace (and not attached):
[1] colorspace_2.0-3 ellipsis_0.3.2 ggridges_0.5.3 markdown_1.1 base64enc_0.1-3 fs_1.5.2
[7] rstudioapi_0.13 listenv_0.8.0 farver_2.1.0 rstan_2.21.5 DT_0.22 fansi_1.0.3
[13] mvtnorm_1.1-3 lubridate_1.8.0 ranger_0.13.1 xml2_1.3.3 codetools_0.2-18 bridgesampling_1.1-2
[19] knitr_1.39 shinythemes_1.2.0 bayesplot_1.9.0 jsonlite_1.8.0 broom_0.8.0 dbplyr_2.1.1
[25] shiny_1.7.1 compiler_4.1.3 httr_1.4.3 backports_1.4.1 assertthat_0.2.1 Matrix_1.4-0
[31] fastmap_1.1.0 cli_3.0.1 later_1.3.0 htmltools_0.5.2 prettyunits_1.1.1 tools_4.1.3
[37] igraph_1.3.1 coda_0.19-4 gtable_0.3.0 glue_1.6.2 reshape2_1.4.4 posterior_1.2.1
[43] cellranger_1.1.0 vctrs_0.4.1 nlme_3.1-155 crosstalk_1.2.0 tensorA_0.36.2 xfun_0.30
[49] globals_0.14.0 ps_1.6.0 rvest_1.0.2 mime_0.12 miniUI_0.1.1.1 lifecycle_1.0.1
[55] gtools_3.9.2 future_1.25.0 zoo_1.8-10 scales_1.2.0 colourpicker_1.1.1 hms_1.1.1
[61] promises_1.2.0.1 Brobdingnag_1.2-7 parallel_4.1.3 inline_0.3.19 shinystan_2.6.0 yaml_2.3.5
[67] gridExtra_2.3 StanHeaders_2.21.0-7 loo_2.5.1 reshape_0.8.9 stringi_1.7.6 dygraphs_1.1.1.6
[73] checkmate_2.1.0 pkgbuild_1.3.1 rlang_1.0.2 pkgconfig_2.0.3 matrixStats_0.62.0 distributional_0.3.0
[79] evaluate_0.15 lattice_0.20-45 rstantools_2.2.0 htmlwidgets_1.5.4 tidyselect_1.1.2 processx_3.5.2
[85] parallelly_1.31.1 plyr_1.8.7 magrittr_2.0.3 R6_2.5.1 generics_0.1.2 DBI_1.1.2
[91] pillar_1.7.0 haven_2.5.0 withr_2.5.0 xts_0.12.1 sp_1.4-7 abind_1.4-5
[97] modelr_0.1.8 crayon_1.5.1 utf8_1.2.2 rmarkdown_2.14 tzdb_0.3.0 grid_4.1.3
[103] readxl_1.4.0 callr_3.7.0 threejs_0.3.3 reprex_2.0.1 digest_0.6.29 xtable_1.8-4
[109] httpuv_1.6.5 RcppParallel_5.1.4 stats4_4.1.3 munsell_0.5.0 shinyjs_2.1.0
I was not able to use R4.2, so I also reverted to the previous version. I reverted everything back to R4.1.x since I don’t want to keep track of two different versions of R. Maybe a Windows-specific issue, but I like the convenience of running Rstudio in Windows.
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There are some known issues (and a few known workarounds) with R4.2 on Windows and Stan packages. See: Stan & R 4.2 on Windows – The Stan Blog
For some reason, R(tools) 4.2 ignores LOCAL_LIBS environment variables on Windows only. See Stan & R 4.2 on Windows - #8 by hsbadr