Problem with running brms Mac OS X with R 4.0

Interfaces brms
1

I upgraded to R 4.0, and this has apparently broken my entire Stan-related workflow.

I posted earlier about my problems with rstan, but these are partially resolved, as discussed in this thread:

I am now trying to install and run brms. I simply did

install.packages(“brms”)

.R/Makevars and .Renviron were removed a few hrs ago as advised by Stephen Martin’s post on R 4.0.

brms seemed to install. Then I tested it:

> bprior1 <- prior(student_t(5,0,10), class = b) +
+        prior(cauchy(0,2), class = sd)
>      fit1 <- brm(count ~ zAge + zBase * Trt + (1|patient),
+                  data = epilepsy, family = poisson(), prior = bprior1)
Compiling the C++ model
Fehler in compileCode(f, code, language = language, verbose = verbose) : 
  Compilation ERROR, function(s)/method(s) not created! In file included from <built-in>:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Dense:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Core:82:
In file included from /Users/shravanvasishth/miniconda3/bin/../include/c++/v1/new:89:
In file included from /Users/shravanvasishth/miniconda3/bin/../include/c++/v1/exception:82:
In file included from /Users/shravanvasishth/miniconda3/bin/../include/c++/v1/cstdlib:86:
/Users/shravanvasishth/miniconda3/bin/../include/c++/v1/stdlib.h:94:15: fatal error: 'stdlib.h' file not found
#include_next <stdlib.h>
              ^~~~~~~~~~
1 error generated.
make: *** [file15b8405e4419.o] Error 1
Zusätzlich: Warnmeldung:
In system(cmd, intern = !verbose) :
  Ausführung von Kommando '/Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB file15b8405e4419.cpp 2> file15b8405e4419.cpp.err.txt' ergab Status 1
Fehler in sink(type = "output") : ungültige Verbindung
>

Any advice on fixing this is appreciated.

  • Operating System

OS: Mac, 10.14.6 Mojave

  • RStan Version

2.19.3

R version 4.0.0 (2020-04-24) – “Arbor Day”

devtools::session_info(“brms”)
─ Session info ───────────────────────────────────────────────────────────────
setting value
version R version 4.0.0 (2020-04-24)
os macOS Mojave 10.14.6
system x86_64, darwin17.0
ui X11
language (EN)
collate C
ctype UTF-8
tz Europe/Berlin
date 2020-05-05

─ Packages ───────────────────────────────────────────────────────────────────
package * version date lib source
abind 1.4-5 2016-07-21 [1] CRAN (R 4.0.0)
askpass 1.1 2019-01-13 [1] CRAN (R 4.0.0)
assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.0.0)
backports 1.1.6 2020-04-05 [1] CRAN (R 4.0.0)
base64enc 0.1-3 2015-07-28 [1] CRAN (R 4.0.0)
bayesplot 1.7.1 2019-12-01 [1] CRAN (R 4.0.0)
BH 1.72.0-3 2020-01-08 [1] CRAN (R 4.0.0)
bridgesampling 1.0-0 2020-02-26 [1] CRAN (R 4.0.0)
brms * 2.12.0 2020-02-23 [1] CRAN (R 4.0.0)
Brobdingnag 1.2-6 2018-08-13 [1] CRAN (R 4.0.0)
callr 3.4.3 2020-03-28 [1] CRAN (R 4.0.0)
checkmate 2.0.0 2020-02-06 [1] CRAN (R 4.0.0)
cli 2.0.2 2020-02-28 [1] CRAN (R 4.0.0)
coda 0.19-3 2019-07-05 [1] CRAN (R 4.0.0)
codetools 0.2-16 2018-12-24 [1] CRAN (R 4.0.0)
colorspace 1.4-1 2019-03-18 [1] CRAN (R 4.0.0)
colourpicker 1.0 2017-09-27 [1] CRAN (R 4.0.0)
crayon 1.3.4 2017-09-16 [1] CRAN (R 4.0.0)
crosstalk 1.1.0.1 2020-03-13 [1] CRAN (R 4.0.0)
curl 4.3 2019-12-02 [1] CRAN (R 4.0.0)
desc 1.2.0 2018-05-01 [1] CRAN (R 4.0.0)
digest 0.6.25 2020-02-23 [1] CRAN (R 4.0.0)
dplyr 0.8.5 2020-03-07 [1] CRAN (R 4.0.0)
DT 0.13 2020-03-23 [1] CRAN (R 4.0.0)
dygraphs 1.1.1.6 2018-07-11 [1] CRAN (R 4.0.0)
ellipsis 0.3.0 2019-09-20 [1] CRAN (R 4.0.0)
evaluate 0.14 2019-05-28 [1] CRAN (R 4.0.0)
fansi 0.4.1 2020-01-08 [1] CRAN (R 4.0.0)
farver 2.0.3 2020-01-16 [1] CRAN (R 4.0.0)
fastmap 1.0.1 2019-10-08 [1] CRAN (R 4.0.0)
future 1.17.0 2020-04-18 [1] CRAN (R 4.0.0)
ggplot2 3.3.0 2020-03-05 [1] CRAN (R 4.0.0)
ggridges 0.5.2 2020-01-12 [1] CRAN (R 4.0.0)
globals 0.12.5 2019-12-07 [1] CRAN (R 4.0.0)
glue 1.4.0 2020-04-03 [1] CRAN (R 4.0.0)
gridExtra 2.3 2017-09-09 [1] CRAN (R 4.0.0)
gtable 0.3.0 2019-03-25 [1] CRAN (R 4.0.0)
gtools 3.8.2 2020-03-31 [1] CRAN (R 4.0.0)
htmltools 0.4.0 2019-10-04 [1] CRAN (R 4.0.0)
htmlwidgets 1.5.1 2019-10-08 [1] CRAN (R 4.0.0)
httpuv 1.5.2 2019-09-11 [1] CRAN (R 4.0.0)
igraph 1.2.5 2020-03-19 [1] CRAN (R 4.0.0)
inline 0.3.15 2018-05-18 [1] CRAN (R 4.0.0)
isoband 0.2.1 2020-04-12 [1] CRAN (R 4.0.0)
jsonlite 1.6.1 2020-02-02 [1] CRAN (R 4.0.0)
labeling 0.3 2014-08-23 [1] CRAN (R 4.0.0)
later 1.0.0 2019-10-04 [1] CRAN (R 4.0.0)
lattice 0.20-41 2020-04-02 [1] CRAN (R 4.0.0)
lazyeval 0.2.2 2019-03-15 [1] CRAN (R 4.0.0)
lifecycle 0.2.0 2020-03-06 [1] CRAN (R 4.0.0)
listenv 0.8.0 2019-12-05 [1] CRAN (R 4.0.0)
loo 2.2.0 2019-12-19 [1] CRAN (R 4.0.0)
magrittr 1.5 2014-11-22 [1] CRAN (R 4.0.0)
markdown 1.1 2019-08-07 [1] CRAN (R 4.0.0)
MASS 7.3-51.5 2019-12-20 [1] CRAN (R 4.0.0)
Matrix 1.2-18 2019-11-27 [1] CRAN (R 4.0.0)
matrixStats 0.56.0 2020-03-13 [1] CRAN (R 4.0.0)
mgcv 1.8-31 2019-11-09 [1] CRAN (R 4.0.0)
mime 0.9 2020-02-04 [1] CRAN (R 4.0.0)
miniUI 0.1.1.1 2018-05-18 [1] CRAN (R 4.0.0)
munsell 0.5.0 2018-06-12 [1] CRAN (R 4.0.0)
mvtnorm 1.1-0 2020-02-24 [1] CRAN (R 4.0.0)
nleqslv 3.3.2 2018-05-17 [1] CRAN (R 4.0.0)
nlme 3.1-147 2020-04-13 [1] CRAN (R 4.0.0)
openssl 1.4.1 2019-07-18 [1] CRAN (R 4.0.0)
packrat 0.5.0 2018-11-14 [1] CRAN (R 4.0.0)
pillar 1.4.4 2020-05-05 [1] CRAN (R 4.0.0)
pkgbuild 1.0.7 2020-04-25 [1] CRAN (R 4.0.0)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.0.0)
pkgload 1.0.2 2018-10-29 [1] CRAN (R 4.0.0)
plogr 0.2.0 2018-03-25 [1] CRAN (R 4.0.0)
plyr 1.8.6 2020-03-03 [1] CRAN (R 4.0.0)
praise 1.0.0 2015-08-11 [1] CRAN (R 4.0.0)
prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.0.0)
processx 3.4.2 2020-02-09 [1] CRAN (R 4.0.0)
promises 1.1.0 2019-10-04 [1] CRAN (R 4.0.0)
ps 1.3.2 2020-02-13 [1] CRAN (R 4.0.0)
purrr 0.3.4 2020-04-17 [1] CRAN (R 4.0.0)
R6 2.4.1 2019-11-12 [1] CRAN (R 4.0.0)
RColorBrewer 1.1-2 2014-12-07 [1] CRAN (R 4.0.0)
Rcpp * 1.0.4.6 2020-04-09 [1] CRAN (R 4.0.0)
RcppEigen 0.3.3.7.0 2019-11-16 [1] CRAN (R 4.0.0)
reshape2 1.4.4 2020-04-09 [1] CRAN (R 4.0.0)
rlang 0.4.5 2020-03-01 [1] CRAN (R 4.0.0)
rprojroot 1.3-2 2018-01-03 [1] CRAN (R 4.0.0)
rsconnect 0.8.16 2019-12-13 [1] CRAN (R 4.0.0)
rstan 2.19.3 2020-02-11 [1] CRAN (R 4.0.0)
rstantools 2.0.0 2019-09-15 [1] CRAN (R 4.0.0)
rstudioapi 0.11 2020-02-07 [1] CRAN (R 4.0.0)
scales 1.1.0 2019-11-18 [1] CRAN (R 4.0.0)
shiny 1.4.0.2 2020-03-13 [1] CRAN (R 4.0.0)
shinyjs 1.1 2020-01-13 [1] CRAN (R 4.0.0)
shinystan 2.5.0 2018-05-01 [1] CRAN (R 4.0.0)
shinythemes 1.1.2 2018-11-06 [1] CRAN (R 4.0.0)
sourcetools 0.1.7 2018-04-25 [1] CRAN (R 4.0.0)
StanHeaders 2.19.2 2020-02-11 [1] CRAN (R 4.0.0)
stringi 1.4.6 2020-02-17 [1] CRAN (R 4.0.0)
stringr 1.4.0 2019-02-10 [1] CRAN (R 4.0.0)
sys 3.3 2019-08-21 [1] CRAN (R 4.0.0)
testthat 2.3.2 2020-03-02 [1] CRAN (R 4.0.0)
threejs 0.3.3 2020-01-21 [1] CRAN (R 4.0.0)
tibble 3.0.1 2020-04-20 [1] CRAN (R 4.0.0)
tidyselect 1.0.0 2020-01-27 [1] CRAN (R 4.0.0)
utf8 1.1.4 2018-05-24 [1] CRAN (R 4.0.0)
vctrs 0.2.4 2020-03-10 [1] CRAN (R 4.0.0)
viridisLite 0.3.0 2018-02-01 [1] CRAN (R 4.0.0)
withr 2.2.0 2020-04-20 [1] CRAN (R 4.0.0)
xfun 0.13 2020-04-13 [1] CRAN (R 4.0.0)
xtable 1.8-4 2019-04-21 [1] CRAN (R 4.0.0)
xts 0.12-0 2020-01-19 [1] CRAN (R 4.0.0)
yaml 2.2.1 2020-02-01 [1] CRAN (R 4.0.0)
zoo 1.8-7 2020-01-10 [1] CRAN (R 4.0.0)

[1] /Library/Frameworks/R.framework/Versions/4.0/Resources/library

1 Like
2

Move, rename, or delete ~/.Renviron and ~/.R/Makevars and try again.
More specifically, those files should not define the paths anymore; you can still include CXX flags for optimizations.

My guess is you have macos-rtools installed and configured, but R is now configured to use Xcode. I received the same error before I modified those to exclude any paths. R4.0 should work fine on OSX with only Xcode installed, and no configuration in ~/.Renviron and ~/.R/Makevars

3

Thanks for the reply. I have the exact problem. But I could not change the path “~/.Renviron and ~/.R/Makevars”. Will you give some insight on how to do it? Thank you so much.

4

I’m getting these problems after deleting .Renviron and Makevars, as you had suggested in an earlier thread. So that doesn’t solve the problem.

1 Like
5

Have you all checked this thread?

6

Yes, I have read and worked through this thread. The parallel workaround did not work for me (Mojave). I am thinking of upgrading to Catalina and trying again.

7

Ah, right, I’m on Catalina… :)

8

Ah sorry; that’s what I get for skimming.

This sounds trivial, and I apologize - But 1) Did you restart R after changing those files and 2) What have you used miniconda for? It seems to be looking for the C++ standard library headers in /Users//miniconda/include

Contrary to my previous advice, you may need to set up a ~/.Renviron that specifies a path that searches for the Xcode c++ headers first. My guess is that miniconda changed some path variables to search for miniconda’s c++ headers first, rather than Xcode’s. Although I tested on OSX, I am primarily a linux user, so I am unsure how to change the R session’s path, or your system path, to prioritize Xcode. (I literally only ran OSX for a 10-20 hours in a VM to verify the installation procedure from a clean installation; likewise with windows 10).

Is there an OSX user here that can give either the system-method or an R session variable/expression that forces R to look for headers in the correct path?

9

I solved the brms problem as follows:

  1. Installed Catalina (and reset bash as my default shell)
  2. Reinstalled R and RStudio, and rstan and brms
  3. Discovered that miniconda had edited my .bash_profile file and added the offending path which was causing all the confusion. Removed it from .bash_profile.
  4. I added back an .Renviron file with the path to the C++ toolchain from Xcode:

PATH=/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1:${PATH}

Restarted R in RStudio. brms works fine now. However, I could not get 4 chains to run in rstan, despite adding this line:

cl <- parallel::makeCluster(2, setup_strategy = “sequential”)

When I run the following code, I still get an error:

library(rstan)
options(mc.cores = parallel::detectCores())
rstan_options(auto_write = TRUE)

cl <- parallel::makeCluster(2, setup_strategy = "sequential") 

schools_dat <- list(J = 8, 
                    y = c(28,  8, -3,  7, -1,  1, 18, 12),
                    sigma = c(15, 10, 16, 11,  9, 11, 10, 18))

fit <- stan(file = 'schools.stan', data = schools_dat)

Errors:

starting worker pid=3053 on localhost:11664 at 17:02:57.875
starting worker pid=3052 on localhost:11664 at 17:02:57.880
starting worker pid=3051 on localhost:11664 at 17:02:57.883
starting worker pid=3050 on localhost:11664 at 17:02:57.884
Error in unserialize(node$con) : error reading from connection
Calls: <Anonymous> -> slaveLoop -> makeSOCKmaster
Execution halted
Error in unserialize(node$con) : error reading from connection
Calls: <Anonymous> -> slaveLoop -> makeSOCKmaster
Error in unserialize(node$con) : error reading from connection
Calls: <Anonymous> -> slaveLoop -> makeSOCKmaster
Execution halted
Error in unserialize(node$con) : error reading from connection
Calls: <Anonymous> -> slaveLoop -> makeSOCKmaster
Execution halted
Execution halted
Error in makePSOCKcluster(names = spec, ...) : 
  Cluster setup failed. 4 of 4 workers failed to connect.
In addition: Warning message:
In readLines(file, warn = TRUE) :
  incomplete final line found on '/Users/shravanvasishth/Downloads/schools.stan'

I hope that RStudio will fix this soon, because right now I am in the middle of teaching a course in Bayesian data analysis, and stuck in hospital already for two weeks (i.e., away from my backup machines which actually run rstan etc.). It’s going to be embarrassing if I have to tell my students that, sorry, I can’t run my own rstan code right now (well, I can run it from the command line). :)

10

If you cant find a fix for running the cores in parallel, you could try adding cores = 1 as an argument to brm().

11

I can’t do that because I am working collaboratively with someone else on a book, and I can’t customize the code so it works for me alone. I would rather by-pass RStudio,

Right now I am trying to compile the bookdown book from the command line, and am getting weird pop-ups in my browser, with weird messages like:

“Click the Refresh button to see progress of the chains”

"Click the Refresh button to see progress of the chains
starting worker pid=4270 on localhost:11926 at 17:31:58.747
starting worker pid=4273 on localhost:11926 at 17:31:58.751
starting worker pid=4272 on localhost:11926 at 17:31:58.751
starting worker pid=4271 on localhost:11926 at 17:31:58.753
"
Somehow, running the book after starting R on the command line and then rendering the book is leading to this novel behavior.

12

Hi @vasishth

https://github.com/rstudio/rstudio/issues/6692#issuecomment-619645114

13

thanks,tried it, didn’t work.