Hello! I am running into a perplexing issue with fitting brms models on my PC. I say that this is a “machine specific” problem because it only occurs on a specific PC, and does not happen on any of my other computers (my work laptop and desktop).
Specifically, whenever I attempt to fit any model using brms (even the tutorial), I receive something like the following warning:
library(brms)
prior1 <- prior(normal(0,10), class = b) +
prior(cauchy(0,2), class = sd)
fit1 <- brm(count ~ zAge + zBase * Trt + (1|patient),
data = epilepsy, family = poisson(), prior = prior1,
backend = "cmdstanr")
…
Chain 3 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue:
Chain 3 Exception: poisson_log_glm_lpmf: Intercept[1] is inf, but must be finite! (in 'C:/Users/rydbe/AppData/Local/Temp/RtmpC4ekvt/model-11dc8002898.stan', line 51, column 4 to column 50)
Chain 3 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine,
Chain 3 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified.
In this case, the model does fit, but for more complex models sampling never occurs. The warnings are specific to the likelihood specified in the model. For instance, a more complex item response model with a bernoulli likelihood produces a similar warning, but never actually samples.
I am able to fit models using rstanarm just fine. I was able to run the example stan model from the cmdstanr tutorial just fine as well. I am really over my head when it comes to diagnosing why this is occuring on this specific machine and not my other computers. I’ll note that I have already tried reinstalling both brms and cmdstan.
> sessionInfo()
R version 4.3.1 (2023-06-16 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 11 x64 (build 22621)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8 LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C LC_TIME=English_United States.utf8
time zone: America/New_York
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] brms_2.20.1 Rcpp_1.0.11
loaded via a namespace (and not attached):
[1] gridExtra_2.3 inline_0.3.19 rlang_1.1.1 magrittr_2.0.3 matrixStats_1.0.0 compiler_4.3.1
[7] loo_2.6.0 callr_3.7.3 vctrs_0.6.3 reshape2_1.4.4 stringr_1.5.0 crayon_1.5.2
[13] pkgconfig_2.0.3 fastmap_1.1.1 backports_1.4.1 ellipsis_0.3.2 utf8_1.2.3 cmdstanr_0.6.0
[19] threejs_0.3.3 promises_1.2.1 markdown_1.7 ps_1.7.5 nloptr_2.0.3 purrr_1.0.2
[25] xfun_0.40 jsonlite_1.8.7 later_1.3.1 sjmisc_2.8.9 ggeffects_1.2.3 prettyunits_1.1.1
[31] broom_1.0.5 parallel_4.3.1 R6_2.5.1 dygraphs_1.1.1.6 StanHeaders_2.26.27 stringi_1.7.12
[37] boot_1.3-28.1 estimability_1.4.1 rstan_2.21.8 knitr_1.43 modelr_0.1.11 zoo_1.8-12
[43] base64enc_0.1-3 bayesplot_1.10.0 httpuv_1.6.11 Matrix_1.6-0 splines_4.3.1 igraph_1.5.1
[49] tidyselect_1.2.0 rstudioapi_0.15.0 abind_1.4-5 codetools_0.2-19 miniUI_0.1.1.1 sjlabelled_1.2.0
[55] processx_3.8.2 pkgbuild_1.4.2 lattice_0.21-8 tibble_3.2.1 plyr_1.8.8 withr_2.5.0
[61] shiny_1.7.4.1 robustHD_0.7.4 bridgesampling_1.1-2 bayestestR_0.13.1 posterior_1.4.1 coda_0.19-4
[67] RcppParallel_5.1.7 xts_0.13.1 pillar_1.9.0 tensorA_0.36.2 checkmate_2.2.0 DT_0.28
[73] stats4_4.3.1 insight_0.19.3 shinyjs_2.1.0 distributional_0.3.2 generics_0.1.3 ggplot2_3.4.2
[79] rstantools_2.3.1.1 munsell_0.5.0 scales_1.2.1 minqa_1.2.5 gtools_3.9.4 xtable_1.8-4
[85] glue_1.6.2 sjPlot_2.8.14 emmeans_1.8.7 tools_4.3.1 shinystan_2.6.0 data.table_1.14.8
[91] robustbase_0.99-0 lme4_1.1-34 colourpicker_1.2.0 mvtnorm_1.2-2 grid_4.3.1 tidyr_1.3.0
[97] crosstalk_1.2.0 colorspace_2.1-0 nlme_3.1-162 performance_0.10.4 cli_3.6.1 perry_0.3.1
[103] fansi_1.0.4 Brobdingnag_1.2-9 sjstats_0.18.2 dplyr_1.1.2 gtable_0.3.3 DEoptimR_1.1-1
[109] digest_0.6.33 htmlwidgets_1.6.2 farver_2.1.1 htmltools_0.5.5 lifecycle_1.0.3 mime_0.12
[115] shinythemes_1.2.0 MASS_7.3-60
For my machine specs…
OS Name Microsoft Windows 11 Home
Version 10.0.22621 Build 22621
Other OS Description Not Available
OS Manufacturer Microsoft Corporation
System Name JASON-ENVY-DESK
System Manufacturer HP
System Model HP ENVY Desktop TE02-0xxx
System Type x64-based PC
System SKU 319M1AA#ABA
Processor 12th Gen Intel(R) Core(TM) i7-12700, 2100 Mhz, 12 Core(s), 20 Logical Processor(s)
BIOS Version/Date AMI F.30, 3/17/2023
SMBIOS Version 3.4
Embedded Controller Version 90.28
BIOS Mode UEFI
BaseBoard Manufacturer HP
BaseBoard Product 894B
BaseBoard Version 10
Platform Role Desktop
Secure Boot State On
PCR7 Configuration Elevation Required to View
Windows Directory C:\windows
System Directory C:\windows\system32
Boot Device \Device\HarddiskVolume1
Locale United States
Hardware Abstraction Layer Version = "10.0.22621.1413"
User Name Jason-Envy-Desk\rydbe
Time Zone Eastern Daylight Time
Installed Physical Memory (RAM) 32.0 GB
Total Physical Memory 31.7 GB
Available Physical Memory 17.1 GB
Total Virtual Memory 36.4 GB
Available Virtual Memory 17.2 GB
Page File Space 4.75 GB
Page File C:\pagefile.sys
Kernel DMA Protection On
Virtualization-based security Running
Virtualization-based security Required Security Properties
Virtualization-based security Available Security Properties Base Virtualization Support, Secure Boot, DMA Protection, UEFI Code Readonly, SMM Security Mitigations 1.0, Mode Based Execution Control, APIC Virtualization
Virtualization-based security Services Configured Hypervisor enforced Code Integrity
Virtualization-based security Services Running Hypervisor enforced Code Integrity
Windows Defender Application Control policy Enforced
Windows Defender Application Control user mode policy Off
Device Encryption Support Elevation Required to View
A hypervisor has been detected. Features required for Hyper-V will not be displayed.