Brms Causing R Session Aborted (R Encountered Fatal Error) Only With Control Parameters Included

Interfaces brms
,
1

I have been attempting to run a zero-inflated poisson model with the attached data and following code:

Example.csv (21.5 KB)

example<-read.csv(“Example.csv”,header=T)
as.factor(example$ID)->example$ID
as.factor(example$Sex)->example$Sex
as.factor(example$Level)->example$Level
as.factor(example$LesionType)->example$LesionType

formula<-bf(LesionNumber ~ Level + LesionType + Level:LesionType + Sex + AgeDeath + DD + PMI + (1 | ID), zi ~ Level + LesionType + Level:LesionType + Sex + AgeDeath + DD + PMI + (1 | ID))

model<-brm(formula=formula, data=example, family=“zero_inflated_poisson”,warmup=2000,iter=4000,seed=34)

I then received errors about treedepth, Rhat, bulk ESS, and tail ESS. Therefore, I tried to adjust the code with the following:

model.updated<-brm(formula=formula, data=lesion_number_total_staged, family=“zero_inflated_poisson”,warmup=4000,iter=8000,seed=34,control=list(max_treedepth=15))

However, I then get an R Session Aborted error. I’ve never encountered this with recent models and have narrowed down that it only happens when inputting control parameters. Any insight on why this is happening? I’ve tried uninstalling brms, rstan, and rstantools and reinstalling but that didn’t seem to help.

I’m using a MacBook Pro with 16GB memory on Mojave Version 10.14.6 and RStudio version Version 1.4.1717.

1 Like
2

I ran into a similar issue the other week with adapt_delta (see here). After a lot of fooling around, the quick fix was to install the developmental version of brms from GitHub.

remotes::install_github("paul-buerkner/brms")
2 Likes
3

Sorry, did not work for me. Same problem when including the adapt_delta control. Any more thoughts?

4

That’s frustrating. Sadly, that’s all I’ve got on this one.

5

Thanks anyway, Solomon! Much appreciated. I try rstanarm now, however, I liked the possibility for multivariate responses in brms. All the best from Norway, Ulrich

1 Like
6

I just updated to R 4.1.2 on an Intel Mac with Big Sur 11.6 and experienced the same issue. Specifying a model with adapt_delta caused R Studio to crash. I tried uninstalling rstan and brms to no avail but Solomon’s solution appears to have worked.

1 Like
7

Other users have reported that upgrading to the preview of the next RStan version has solved this problem for them:

remove.packages(c("StanHeaders", "rstan"))
install.packages("StanHeaders", repos = c("https://mc-stan.org/r-packages/", getOption("repos")))
install.packages("rstan", repos = c("https://mc-stan.org/r-packages/", getOption("repos")))
2 Likes
8

Unfortunately @Solomon’s package re-installation didn’t work for me. The R session doesn’t abort but a segfault is created. Using control = list(adapt_delta = 0.95). Last chain completes (this happened to be chain 3 this time) and then segfaults reported for all 4 chains. Strangely the brmsfit object saves correctly (phew!), which may indicate at what point the segfault occurs.

Chain 3: Iteration: 100000 / 100000 [100%]  (Sampling)
Chain 3: 
Chain 3:  Elapsed Time: 753.436 seconds (Warm-up)
Chain 3:                10048.5 seconds (Sampling)
Chain 3:                10801.9 seconds (Total)
Chain 3: 

 *** caught segfault ***
address 0x18, cause 'memory not mapped'
An irrecoverable exception occurred. R is aborting now ...

 *** caught segfault ***
address 0x18, cause 'memory not mapped'
An irrecoverable exception occurred. R is aborting now ...

 *** caught segfault ***
address 0x18, cause 'memory not mapped'
An irrecoverable exception occurred. R is aborting now ...

 *** caught segfault ***
address 0x18, cause 'memory not mapped'
An irrecoverable exception occurred. R is aborting now ...
Warning messages:
1: There were 379858 divergent transitions after warmup. See
https://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
to find out why this is a problem and how to eliminate them. 
2: Examine the pairs() plot to diagnose sampling problems

R version 4.2.1
Linux Mint 20.3

9

I have a similar problem, with none of the suggested solutions helping. When I run the following code, it causes the R session to abort.
library(brms)
mod ← brm(number_plants ~ mixture * seed date, data=dat, family=negbinomial)
grafik

What could be the cause? I am working with rtools42 and R version 4.3.1

10

Does it work if you install this preview version of RStan?

install.packages(c("StanHeaders", "rstan"), repos = c("https://mc-stan.org/r-packages/", getOption("repos")))
11

I had the same issue. I updated to rtools 4.3 and installed brms and rstan from github with the code provided by jonah above. I also got a popup about windows firewall access this last time. After I allowed access, it all started working.

2 Likes
12

Glad it’s working for you!

1 Like
13

No, it doesn’t work.

14

the solution was rtools43. I still had rtools42 installed. Sorry!

1 Like
15

No problem, glad it’s working