C Stack Trace Errors

bacalfa · November 9, 2020, 4:35pm

What could cause the following behavior? Unfortunately, I can’t share the code. But all of a sudden, I’m unable to successfully run brms on the same examples I used to be able to.

I have:

R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

And below is the run log. I try to fit a model twice, and they seem to run fine. The problem seems to occur afterward.

Loading required package: StanHeaders
Loading required package: ggplot2
rstan (Version 2.21.2, GitRev: 2e1f913d3ca3)
For execution on a local, multicore CPU with excess RAM we recommend calling
options(mc.cores = parallel::detectCores()).
To avoid recompilation of unchanged Stan programs, we recommend calling
rstan_options(auto_write = TRUE)
Do not specify '-march=native' in 'LOCAL_CPPFLAGS' or a Makevars file
Loading required package: Rcpp
Loading 'brms' package (version 2.14.4). Useful instructions
can be found by typing help('brms'). A more detailed introduction
to the package is available through vignette('brms_overview').

Attaching package: 'brms'

The following object is masked from 'package:rstan':

    loo

The following object is masked from 'package:stats':

    ar

Loading required package: usethis
Compiling Stan program...
Warning message:
In system(paste(cmd, "-n")) : 'make' not found
Start sampling
starting worker pid=11432 on localhost:11102 at 11:23:20.635
starting worker pid=9212 on localhost:11102 at 11:23:21.047
starting worker pid=14828 on localhost:11102 at 11:23:21.500
starting worker pid=13952 on localhost:11102 at 11:23:21.955

SAMPLING FOR MODEL '27306ff5df2e1c257221e6aa1f6284d4' NOW (CHAIN 1).
Chain 1: 
Chain 1: Gradient evaluation took 0 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1: 
Chain 1: 
Chain 1: Iteration:    1 / 4000 [  0%]  (Warmup)
Chain 1: Iteration:  400 / 4000 [ 10%]  (Warmup)
Chain 1: Iteration:  800 / 4000 [ 20%]  (Warmup)
Chain 1: Iteration: 1200 / 4000 [ 30%]  (Warmup)
Chain 1: Iteration: 1600 / 4000 [ 40%]  (Warmup)
Chain 1: Iteration: 2000 / 4000 [ 50%]  (Warmup)
Chain 1: Iteration: 2001 / 4000 [ 50%]  (Sampling)
Chain 1: Iteration: 2400 / 4000 [ 60%]  (Sampling)
Chain 1: Iteration: 2800 / 4000 [ 70%]  (Sampling)

SAMPLING FOR MODEL '27306ff5df2e1c257221e6aa1f6284d4' NOW (CHAIN 2).
Chain 2: 
Chain 2: Gradient evaluation took 0 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2: 
Chain 2: 
Chain 1: Iteration: 3200 / 4000 [ 80%]  (Sampling)
Chain 2: Iteration:    1 / 4000 [  0%]  (Warmup)
Chain 1: Iteration: 3600 / 4000 [ 90%]  (Sampling)
Chain 2: Iteration:  400 / 4000 [ 10%]  (Warmup)
Chain 1: Iteration: 4000 / 4000 [100%]  (Sampling)
Chain 1: 
Chain 1:  Elapsed Time: 0.172 seconds (Warm-up)
Chain 1:                0.151 seconds (Sampling)
Chain 1:                0.323 seconds (Total)
Chain 1: 
Chain 2: Iteration:  800 / 4000 [ 20%]  (Warmup)
Chain 2: Iteration: 1200 / 4000 [ 30%]  (Warmup)
Chain 2: Iteration: 1600 / 4000 [ 40%]  (Warmup)
Chain 2: Iteration: 2000 / 4000 [ 50%]  (Warmup)
Chain 2: Iteration: 2001 / 4000 [ 50%]  (Sampling)
Chain 2: Iteration: 2400 / 4000 [ 60%]  (Sampling)
Chain 2: Iteration: 2800 / 4000 [ 70%]  (Sampling)
Chain 2: Iteration: 3200 / 4000 [ 80%]  (Sampling)
Chain 2: Iteration: 3600 / 4000 [ 90%]  (Sampling)
Chain 2: Iteration: 4000 / 4000 [100%]  (Sampling)
Chain 2: 
Chain 2:  Elapsed Time: 0.184 seconds (Warm-up)
Chain 2:                0.164 seconds (Sampling)
Chain 2:                0.348 seconds (Total)
Chain 2: 

SAMPLING FOR MODEL '27306ff5df2e1c257221e6aa1f6284d4' NOW (CHAIN 3).
Chain 3: 
Chain 3: Gradient evaluation took 0 seconds
Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0 seconds.
Chain 3: Adjust your expectations accordingly!
Chain 3: 
Chain 3: 
Chain 3: Iteration:    1 / 4000 [  0%]  (Warmup)
Chain 3: Iteration:  400 / 4000 [ 10%]  (Warmup)
Chain 3: Iteration:  800 / 4000 [ 20%]  (Warmup)
Chain 3: Iteration: 1200 / 4000 [ 30%]  (Warmup)
Chain 3: Iteration: 1600 / 4000 [ 40%]  (Warmup)
Chain 3: Iteration: 2000 / 4000 [ 50%]  (Warmup)
Chain 3: Iteration: 2001 / 4000 [ 50%]  (Sampling)
Chain 3: Iteration: 2400 / 4000 [ 60%]  (Sampling)
Chain 3: Iteration: 2800 / 4000 [ 70%]  (Sampling)
Chain 3: Iteration: 3200 / 4000 [ 80%]  (Sampling)
Chain 3: Iteration: 3600 / 4000 [ 90%]  (Sampling)
Chain 3: Iteration: 4000 / 4000 [100%]  (Sampling)
Chain 3: 
Chain 3:  Elapsed Time: 0.157 seconds (Warm-up)
Chain 3:                0.144 seconds (Sampling)
Chain 3:                0.301 seconds (Total)
Chain 3: 

SAMPLING FOR MODEL '27306ff5df2e1c257221e6aa1f6284d4' NOW (CHAIN 4).
Chain 4: 
Chain 4: Gradient evaluation took 0 seconds
Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0 seconds.
Chain 4: Adjust your expectations accordingly!
Chain 4: 
Chain 4: 
Chain 4: Iteration:    1 / 4000 [  0%]  (Warmup)
Chain 4: Iteration:  400 / 4000 [ 10%]  (Warmup)
Chain 4: Iteration:  800 / 4000 [ 20%]  (Warmup)
Chain 4: Iteration: 1200 / 4000 [ 30%]  (Warmup)
Chain 4: Iteration: 1600 / 4000 [ 40%]  (Warmup)
Chain 4: Iteration: 2000 / 4000 [ 50%]  (Warmup)
Chain 4: Iteration: 2001 / 4000 [ 50%]  (Sampling)
Chain 4: Iteration: 2400 / 4000 [ 60%]  (Sampling)
Chain 4: Iteration: 2800 / 4000 [ 70%]  (Sampling)
Chain 4: Iteration: 3200 / 4000 [ 80%]  (Sampling)
Chain 4: Iteration: 3600 / 4000 [ 90%]  (Sampling)
Chain 4: Iteration: 4000 / 4000 [100%]  (Sampling)
Chain 4: 
Chain 4:  Elapsed Time: 0.157 seconds (Warm-up)
Chain 4:                0.156 seconds (Sampling)
Chain 4:                0.313 seconds (Total)
Chain 4: 
Compiling Stan program...
Warning message:
In system(paste(cmd, "-n")) : 'make' not found
Start sampling
starting worker pid=1656 on localhost:11102 at 11:24:06.261
starting worker pid=10868 on localhost:11102 at 11:24:06.685
starting worker pid=15252 on localhost:11102 at 11:24:07.062
starting worker pid=15980 on localhost:11102 at 11:24:07.468

SAMPLING FOR MODEL '5705fb2064205c5f40a89a50756107f7' NOW (CHAIN 1).
Chain 1: 
Chain 1: Gradient evaluation took 0 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1: 
Chain 1: 
Chain 1: Iteration:    1 / 4000 [  0%]  (Warmup)
Chain 1: Iteration:  400 / 4000 [ 10%]  (Warmup)
Chain 1: Iteration:  800 / 4000 [ 20%]  (Warmup)
Chain 1: Iteration: 1200 / 4000 [ 30%]  (Warmup)
Chain 1: Iteration: 1600 / 4000 [ 40%]  (Warmup)
Chain 1: Iteration: 2000 / 4000 [ 50%]  (Warmup)
Chain 1: Iteration: 2001 / 4000 [ 50%]  (Sampling)
Chain 1: Iteration: 2400 / 4000 [ 60%]  (Sampling)
Chain 1: Iteration: 2800 / 4000 [ 70%]  (Sampling)
Chain 1: Iteration: 3200 / 4000 [ 80%]  (Sampling)
Chain 1: Iteration: 3600 / 4000 [ 90%]  (Sampling)

SAMPLING FOR MODEL '5705fb2064205c5f40a89a50756107f7' NOW (CHAIN 2).
Chain 2: 
Chain 2: Gradient evaluation took 0 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2: 
Chain 2: 
Chain 2: Iteration:    1 / 4000 [  0%]  (Warmup)
Chain 1: Iteration: 4000 / 4000 [100%]  (Sampling)
Chain 1: 
Chain 1:  Elapsed Time: 0.157 seconds (Warm-up)
Chain 1:                0.14 seconds (Sampling)
Chain 1:                0.297 seconds (Total)
Chain 1: 
Chain 2: Iteration:  400 / 4000 [ 10%]  (Warmup)
Chain 2: Iteration:  800 / 4000 [ 20%]  (Warmup)
Chain 2: Iteration: 1200 / 4000 [ 30%]  (Warmup)
Chain 2: Iteration: 1600 / 4000 [ 40%]  (Warmup)
Chain 2: Iteration: 2000 / 4000 [ 50%]  (Warmup)
Chain 2: Iteration: 2001 / 4000 [ 50%]  (Sampling)
Chain 2: Iteration: 2400 / 4000 [ 60%]  (Sampling)
Chain 2: Iteration: 2800 / 4000 [ 70%]  (Sampling)
Chain 2: Iteration: 3200 / 4000 [ 80%]  (Sampling)
Chain 2: Iteration: 3600 / 4000 [ 90%]  (Sampling)
Chain 2: Iteration: 4000 / 4000 [100%]  (Sampling)
Chain 2: 
Chain 2:  Elapsed Time: 0.17 seconds (Warm-up)
Chain 2:                0.156 seconds (Sampling)
Chain 2:                0.326 seconds (Total)
Chain 2: 

SAMPLING FOR MODEL '5705fb2064205c5f40a89a50756107f7' NOW (CHAIN 3).
Chain 3: 
Chain 3: Gradient evaluation took 0 seconds
Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0 seconds.
Chain 3: Adjust your expectations accordingly!
Chain 3: 
Chain 3: 
Chain 3: Iteration:    1 / 4000 [  0%]  (Warmup)
Chain 3: Iteration:  400 / 4000 [ 10%]  (Warmup)
Chain 3: Iteration:  800 / 4000 [ 20%]  (Warmup)
Chain 3: Iteration: 1200 / 4000 [ 30%]  (Warmup)
Chain 3: Iteration: 1600 / 4000 [ 40%]  (Warmup)
Chain 3: Iteration: 2000 / 4000 [ 50%]  (Warmup)
Chain 3: Iteration: 2001 / 4000 [ 50%]  (Sampling)
Chain 3: Iteration: 2400 / 4000 [ 60%]  (Sampling)
Chain 3: Iteration: 2800 / 4000 [ 70%]  (Sampling)
Chain 3: Iteration: 3200 / 4000 [ 80%]  (Sampling)
Chain 3: Iteration: 3600 / 4000 [ 90%]  (Sampling)
Chain 3: Iteration: 4000 / 4000 [100%]  (Sampling)
Chain 3: 
Chain 3:  Elapsed Time: 0.143 seconds (Warm-up)
Chain 3:                0.15 seconds (Sampling)
Chain 3:                0.293 seconds (Total)
Chain 3: 

SAMPLING FOR MODEL '5705fb2064205c5f40a89a50756107f7' NOW (CHAIN 4).
Chain 4: 
Chain 4: Gradient evaluation took 0 seconds
Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0 seconds.
Chain 4: Adjust your expectations accordingly!
Chain 4: 
Chain 4: 
Chain 4: Iteration:    1 / 4000 [  0%]  (Warmup)
Chain 4: Iteration:  400 / 4000 [ 10%]  (Warmup)
Chain 4: Iteration:  800 / 4000 [ 20%]  (Warmup)
Chain 4: Iteration: 1200 / 4000 [ 30%]  (Warmup)
Chain 4: Iteration: 1600 / 4000 [ 40%]  (Warmup)
Chain 4: Iteration: 2000 / 4000 [ 50%]  (Warmup)
Chain 4: Iteration: 2001 / 4000 [ 50%]  (Sampling)
Chain 4: Iteration: 2400 / 4000 [ 60%]  (Sampling)
Chain 4: Iteration: 2800 / 4000 [ 70%]  (Sampling)
Chain 4: Iteration: 3200 / 4000 [ 80%]  (Sampling)
Chain 4: Iteration: 3600 / 4000 [ 90%]  (Sampling)
Chain 4: Iteration: 4000 / 4000 [100%]  (Sampling)
Chain 4: 
Chain 4:  Elapsed Time: 0.196 seconds (Warm-up)
Chain 4:                0.165 seconds (Sampling)
Chain 4:                0.361 seconds (Total)
Chain 4: 
Loading required package: survival

Attaching package: 'survival'

The following object is masked from 'package:brms':

    kidney


==== C stack trace ===============================

	(No symbol) [0x0x472f730]
	R_RunWeakRefFinalizer [0x0xc7f326f+383]
	R_RunWeakRefFinalizer [0x0xc7f3507+1047]
	R_initAssignSymbols [0x0xc7b67a9+72761]
	Rf_eval [0x0xc7bb841+369]
	R_cmpfun1 [0x0xc7bd547+1191]
	Rf_applyClosure [0x0xc7be7aa+442]
	R_has_methods_attached [0x0xc7fa088+920]
	R_has_methods_attached [0x0xc7fa5d4+2276]
	R_initAssignSymbols [0x0xc7a504f+1247]
	R_initAssignSymbols [0x0xc7b2cee+57726]
	Rf_eval [0x0xc7bb841+369]
	R_cmpfun1 [0x0xc7bd547+1191]
	Rf_applyClosure [0x0xc7be7aa+442]
	R_initAssignSymbols [0x0xc7b2994+56868]
	R_forceAndCall [0x0xc7c3896+10726]
	R_forceAndCall [0x0xc7c3eb6+12294]
	Rf_eval [0x0xc7bbc25+1365]
	Rf_ReplIteration [0x0xc7e4c61+673]
	Rf_ReplIteration [0x0xc7e4fc1+1537]
	run_Rmainloop [0x0xc7e505d+77]
	(No symbol) [0x0x4016da]
	(No symbol) [0x0x4038bf]
	(No symbol) [0x0x4013c5]
	(No symbol) [0x0x40152b]
	BaseThreadInitThunk [0x0x7ffa1b327974+20]
	RtlUserThreadStart [0x0x7ffa1c9fa271+33]

hhau · November 9, 2020, 6:32pm

The messages just before that error suggest it is coming from another R package, or from some function inside R. I would suggest

reinstalling all of your R packages.
figuring out what is giving you the make not found error, which may be illuminating.

bacalfa · November 9, 2020, 8:18pm

Thanks. I’m running the following command:

install.packages(pkgs=unname(installed.packages()[, "Package"]))

As to missing make, for Rtools35, I noticed that C:\Rtools\mingw_32\bin and C:\Rtools\mingw_64\bin have no make.exe. It’s in C:\Rtools\bin. For Rtools40, it’s in C:\rtools40\usr\bin. Maybe this has something to do with how BINPREF is set. Will investigate.

bacalfa · November 9, 2020, 9:23pm

rstan is giving me problems. It requires CXX14 to be defined. I had renamed Makevars.win to Makevars.win.bak following another thread’s suggestion.

> install.packages(pkgs="rstan")

  There is a binary version available but the source version is later:
      binary source needs_compilation
rstan 2.19.3 2.21.2              TRUE

Do you want to install from sources the package which needs compilation? (Yes/no/cancel) Yes
installing the source package 'rstan'

trying URL 'https://cran.case.edu/src/contrib/rstan_2.21.2.tar.gz'
Content type 'application/x-gzip' length 1152008 bytes (1.1 MB)
downloaded 1.1 MB

In R CMD INSTALL
* installing *source* package 'rstan' ...
** package 'rstan' successfully unpacked and MD5 sums checked
** libs

*** arch - i386
Error in .shlib_internal(args) :
  C++14 standard requested but CXX14 is not defined
* removing 'C:/Users/abreucbr/Documents/R/R-3.5.0/library/rstan'
* restoring previous 'C:/Users/abreucbr/Documents/R/R-3.5.0/library/rstan'

The downloaded source packages are in
        'C:\Users\abreucbr\AppData\Local\Temp\RtmpAVbpDP\downloaded_packages'
Warning message:
In install.packages(pkgs = "rstan") :
  installation of package 'rstan' had non-zero exit status

So I renamed it back and it contains the following:

CXX14FLAGS=-O3
CXX14 = g++ -m$(WIN) -std=c++14
CXX11FLAGS=-O3

After renaming it back, I get the following error:

> install.packages(pkgs="rstan")

  There is a binary version available but the source version is later:
      binary source needs_compilation
rstan 2.19.3 2.21.2              TRUE

Do you want to install from sources the package which needs compilation? (Yes/no/cancel) Yes
installing the source package 'rstan'

trying URL 'https://cran.case.edu/src/contrib/rstan_2.21.2.tar.gz'
Content type 'application/x-gzip' length 1152008 bytes (1.1 MB)
downloaded 1.1 MB

In R CMD INSTALL
* installing *source* package 'rstan' ...
** package 'rstan' successfully unpacked and MD5 sums checked
** libs

*** arch - i386
g++ -m32 -std=c++14  -I"C:/Users/abreucbr/DOCUME~1/R/R-35~1.0/include" -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"." -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -DSTAN_THREADS  -DRCPP_PARALLEL_USE_TBB=1 -I"C:/Users/abreucbr/Documents/R/R-3.5.0/library/Rcpp/include" -I"C:/Users/abreucbr/Documents/R/R-3.5.0/library/RcppEigen/include" -I"C:/Users/abreucbr/Documents/R/R-3.5.0/library/BH/include" -I"C:/Users/abreucbr/Documents/R/R-3.5.0/library/StanHeaders/include" -I"C:/Users/abreucbr/Documents/R/R-3.5.0/library/RcppParallel/include"     -DRCPP_PARALLEL_USE_TBB=1   -O3 -c sparse_extractors.cpp -o sparse_extractors.o
In file included from C:/Users/abreucbr/Miniconda3/Library/mingw-w64/include/c++/5.3.0/random:49:0,
                 from C:/Users/abreucbr/Miniconda3/Library/mingw-w64/include/c++/5.3.0/bits/stl_algo.h:66,
                 from C:/Users/abreucbr/Miniconda3/Library/mingw-w64/include/c++/5.3.0/algorithm:62,
                 from C:/Users/abreucbr/Documents/R/R-3.5.0/library/RcppEigen/include/Eigen/Core:288,
                 from C:/Users/abreucbr/Documents/R/R-3.5.0/library/RcppEigen/include/Eigen/Dense:1,
                 from C:/Users/abreucbr/Documents/R/R-3.5.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13,
                 from C:/Users/abreucbr/Documents/R/R-3.5.0/library/StanHeaders/include/stan/math/prim/mat/meta/append_return_type.hpp:4,
                 from C:/Users/abreucbr/Documents/R/R-3.5.0/library/StanHeaders/include/stan/math/prim/meta.hpp:9,
                 from C:/Users/abreucbr/Documents/R/R-3.5.0/library/StanHeaders/include/stan/math/prim/mat/fun/csr_extract_u.hpp:4,
                 from sparse_extractors.cpp:2:
C:/Users/abreucbr/Miniconda3/Library/mingw-w64/include/c++/5.3.0/bits/random.h:106:26: error: expected unqualified-id before '__int128'
       { typedef unsigned __int128 type; };
                          ^
make: *** [C:/Users/abreucbr/DOCUME~1/R/R-35~1.0/etc/i386/Makeconf:215: sparse_extractors.o] Error 1
ERROR: compilation failed for package 'rstan'
* removing 'C:/Users/abreucbr/Documents/R/R-3.5.0/library/rstan'
* restoring previous 'C:/Users/abreucbr/Documents/R/R-3.5.0/library/rstan'

Why is it looking for headers in C:/Users/abreucbr/Miniconda3/Library/mingw-w64/include?

bgoodri · November 9, 2020, 9:49pm

The miniconda installation messed with the configuration files. However, you should be able to install binary rstan packages for Windows from

Although my guess is that you will have miniconda-related problems later.

bacalfa · November 9, 2020, 9:52pm

What a nightmare…!

How about install.packages("rstan", type = "win.binary", dependencies = TRUE)?

bacalfa · November 9, 2020, 10:30pm

That seems to have worked.

install.packages(pkgs=unname(installed.packages()[, "Package"]), type = "win.binary", dependencies = TRUE)

My example isn’t crashing again.

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C Stack Trace Errors

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