Compilation ERROR - brms and stan model

armando · October 20, 2018, 1:05am

C:\Program Files\R\R-3.5.1\bin\x64
C:\Rtools\bin
C:\Rtools\mingw_32\bin
C:\Rtools\mingw_64\bin
C:\Windows\system32
C:\Windows
C:\Windows\System32\Wbem
C:\Windows\System32\WindowsPowerShell\v1.0
C:\Program Files\MiKTeX 2.9\miktex\bin\x64
C:\Program Files (x86)\Sennheiser\SoftphoneSDK\

bgoodri · October 20, 2018, 1:17am

OK, according to @paul.buerkner , the problem is the presence of C:\Rtools\mingw_32\bin in your PATH. To delete this, click something like

left-click on Start
right-click on Computer
left-click on Properties
left-click on Advanced System Settings
left-click on Environmental variables
scroll down in the bottom window to Path and left-click it
left-click Edit
move the cursor all the way to the left then delete the part that says C:\Rtools\mingw_32\bin; (be sure to delete exactly one semi-colon)
left-click three Ok buttons

For me, it looks like

Then restart R, and try

fx <- inline::cxxfunction( signature(x = "integer", y = "numeric" ) , '
	return ScalarReal( INTEGER(x)[0] * REAL(y)[0] ) ;
' )
fx( 2L, 5 ) # should be 10

without and then with first specifying Sys.setenv(USE_CXX14 = 1). Then rstan should work.

jrydberg · October 21, 2018, 4:56am

I am unfortunately getting a similar error here now. This happened suddenly - brms was working one day, and now it does not. Here is the error I receive.

> bprior1 <- prior(student_t(5,0,10), class = b) +

prior(cauchy(0,2), class = sd)

fit1 ← brm(count ~ log_Age_c + log_Base4_c * Trt + (1|patient),

        data = epilepsy, family = poisson(), prior = bprior1)

Compiling the C++ model
Error in compileCode(f, code, language = language, verbose = verbose) :
Compilation ERROR, function(s)/method(s) not created! Error in .shlib_internal(commandArgs(TRUE)) :
C++14 standard requested but CXX14 is not defined
Calls: → .shlib_internal
Execution halted
In addition: Warning message:
In system(cmd, intern = !verbose) :
running command ‘C:/PROGRA~1/R/R-35~1.1/bin/x64/R CMD SHLIB file28b039dd1f8f.cpp 2> file28b039dd1f8f.cpp.err.txt’ had status 1

I have tried many of the suggestions here. I’ll just report a few of the results.

fx <- inline::cxxfunction( signature(x = "integer", y = "numeric" ) , '
return ScalarReal( INTEGER(x)[0] * REAL(y)[0] ) ;
                       ' )
fx( 2L, 5 ) # should be 10

Returns 10.

So, based on the last comment I have tried playing with the system path a bit, and this is what it looks like…

 > cat(strsplit(Sys.getenv("PATH"), ";")[[1]], sep = "\n")

C:\Program Files\R\R-3.5.1\bin\x64
C:\Program Files\R\R-3.5.1\bin\x64
C:\Rtools\bin
C:\Rtools\mingw_64\bin
C:\Program Files\ImageMagick-6.9.2-Q16
C:\ProgramData\Oracle\Java\javapath
C:\Program Files (x86)\Intel\iCLS Client
C:\Program Files\Intel\iCLS Client
C:\windows\system32
C:\windows
C:\windows\System32\Wbem
C:\windows\System32\WindowsPowerShell\v1.0
C:\ProgramData\Lenovo\ReadyApps
C:\Program Files (x86)\Lenovo\Password Manager
C:\Program Files\MiKTeX 2.9\miktex\bin\x64
C:\WINDOWS\system32
C:\WINDOWS
C:\WINDOWS\System32\Wbem
C:\WINDOWS\System32\WindowsPowerShell\v1.0
C:\Program Files\Intel\Intel(R) Management Engine Components\DAL
C:\Program Files\Intel\Intel(R) Management Engine Components\IPT
C:\Program Files\IBM\SPSS\Statistics\24\JRE\bin
C:\Program Files\Microsoft SQL Server\120\Tools\Binn
C:\WINDOWS\System32\OpenSSH
C:\Users\Jason\AppData\Local\Microsoft\WindowsApps

I’ll also note that I do not seem to have a ~/.R/Makevars file.

> normalizePath("~/.R/Makevars")

[1] “C:\Users\Jason\Documents\.R\Makevars”
Warning message:
In normalizePath(path.expand(path), winslash, mustWork) :
path[1]=“C:/Users/Jason/Documents/.R/Makevars”: The system cannot find the path specified

When I search for one, I have two that are associated with the Rcpp and RcppArmadillo packages. Needless to say, I am fairly lost here. Any advice would be welcome.

bgoodri · October 21, 2018, 4:58am

jrydberg · October 21, 2018, 11:47pm

Thanks - I focused my search there and found script to create a makevars file. That solved my problem. For any other laypersons out there who run into this same issue, the following resolved it for me.

dotR <- file.path(Sys.getenv("HOME"), ".R")
if (!file.exists(dotR)) 
  dir.create(dotR)
M <- file.path(dotR, "Makevars")
if (!file.exists(M)) 
  file.create(M)
cat("\nCXX14FLAGS=-O3 -Wno-unused-variable -Wno-unused-function",
    "CXX14 = $(BINPREF)g++ -m$(WIN) -std=c++1y",
    "CXX11FLAGS=-O3 -Wno-unused-variable -Wno-unused-function",
    file = M, sep = "\n", append = TRUE)

https://github.com/stan-dev/rstan/wiki/Installing-RStan-on-Windows

bgoodri · October 22, 2018, 12:36am

Those instructions are also applicable if you are the Pope.

armando · October 22, 2018, 11:06pm

I have amended the path per instructions. I get the fx function to return 10 both with and without setting USE_CXX14. When I load rstan and try to run 8schools, I get the following:

Restarting R session…

fx ← inline::cxxfunction( signature(x = “integer”, y = “numeric” ) , ’

        return ScalarReal( INTEGER(x)[0] * REAL(y)[0] ) ;

’ )

fx( 2L, 5 ) # should be 10
[1] 10
Sys.setenv(USE_CXX14=1)
fx ← inline::cxxfunction( signature(x = “integer”, y = “numeric” ) , ’

        return ScalarReal( INTEGER(x)[0] * REAL(y)[0] ) ;

’ )

fx( 2L, 5 ) # should be 10
[1] 10

library(rstan)
Loading required package: ggplot2
Loading required package: StanHeaders
rstan (Version 2.18.1, 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)
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 = ‘./code/8schools.stan’, data = schools_dat,

```
        iter = 1000, chains = 4)
```

Error in if (grepl(pattern, makefile_txt[i])) { :
argument is of length zero

Here is the path for reference:
C:\Program Files\R\R-3.5.1\bin\x64
C:\Rtools\bin
C:\Rtools\mingw_64\bin
C:\Windows\System32
C:\Windows
C:\Windows\System32\wbem
C:\Windows\System32\WindowsPowerShell\v1.0
C:\Program Files\MiKTeX 2.9\miktex\bin\x64
C:\Program Files (x86)\Sennheiser\SoftphoneSDK\

bgoodri · October 22, 2018, 11:18pm

You seem to have the same problem as

which I currently do not understand fully. Can you go through the posts on that thread and how much of it applies to your situation?

armando · October 23, 2018, 12:17am

That’s my situation too.

bgoodri · October 23, 2018, 12:20am

Right. What does system2(file.path(Sys.getenv("R_HOME"), "bin", "R"), args = "CMD SHLIB --dry-run", stdout = TRUE) say?

armando · October 23, 2018, 12:22am

[1] “’\\sffile01\Projects2\5838_EV_Acceleration\Analysis\Statistical Models’”
[2] “CMD.EXE was started with the above path as the current directory.”
[3] “UNC paths are not supported. Defaulting to Windows directory.”
[4] “make cmd is”
[5] " make -f “C:/PROGRA~1/R/R-35~1.1/etc/x64/Makeconf” -f “C:/PROGRA~1/R/R-35~1.1/share/make/winshlib.mk” -f “C:/Users/armando levy/Documents/.R/Makevars” SHLIB="" WIN=64 TCLBIN=64 OBJECTS="""
[6] “”
[7] “make would use”
[8] “make: Nothing to be done for ‘all’.”

bgoodri · October 23, 2018, 12:25am

It looks like I am going to have to generalize the function in rstan that deals with this because I did not take into account the possibility of this “UNC paths are not supported” business. It might be a few days. In the meantime, you can use Stan via https://rstudio.cloud/project/56157 .

bgoodri · October 23, 2018, 6:58am

Can you try installing rstan from GitHub to see if it gets past that error:

devtools::install_github("stan-dev/rstan", ref = "develop", subdir = "rstan/rstan")

armando · October 23, 2018, 7:23pm

devtools::install_github(“stan-dev/rstan”, ref = “develop”, subdir = “rstan/rstan”)
Downloading GitHub repo stan-dev/rstan@develop
/Rtools/bin/tar: stan-dev-rstan-d96845d/StanHeaders/inst/include/libsundials: Cannot create symlink to ‘mathlib/lib/sundials_3.1.0/’: No such file or directory
/Rtools/bin/tar: stan-dev-rstan-d96845d/StanHeaders/inst/include/src: Cannot create symlink to ‘upstream/src/’: No such file or directory
/Rtools/bin/tar: stan-dev-rstan-d96845d/StanHeaders/inst/include/stan: Cannot create symlink to ‘mathlib/stan/’: No such file or directory
/Rtools/bin/tar: Exiting with failure status due to previous errors
External tar failed with --force-local, trying without
/Rtools/bin/tar: stan-dev-rstan-d96845d/StanHeaders/inst/include/libsundials: Cannot create symlink to ‘mathlib/lib/sundials_3.1.0/’: No such file or directory
/Rtools/bin/tar: stan-dev-rstan-d96845d/StanHeaders/inst/include/src: Cannot create symlink to ‘upstream/src/’: No such file or directory
/Rtools/bin/tar: stan-dev-rstan-d96845d/StanHeaders/inst/include/stan: Cannot create symlink to ‘mathlib/stan/’: No such file or directory
/Rtools/bin/tar: Exiting with failure status due to previous errors
These packages have more recent versions available.
Which would you like to update?

1: rlang (0.2.2 → 0.3.0) [CRAN]

Enter one or more numbers separated by spaces, or an empty line to cancel
1:
√ checking for file ‘C:\Users\armando levy\AppData\Local\Temp\RtmpGgVORU\remotes26c06a222286\stan-dev-rstan-d96845d\rstan\rstan/DESCRIPTION’ …

preparing ‘rstan’: (2s)
√ checking DESCRIPTION meta-information …
cleaning src
checking for LF line-endings in source and make files and shell scripts (746ms)
checking for empty or unneeded directories
looking to see if a ‘data/datalist’ file should be added
building ‘rstan_2.18.2.tar.gz’

‘\sffile01\Projects2\5838_EV_Acceleration\Analysis\Statistical Models\code’
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported. Defaulting to Windows directory.

installing source package ‘rstan’ …
** libs

*** arch - i386
g++ -m32 -std=c++1y -I"C:/PROGRA~1/R/R-35~1.1/include" -DNDEBUG -I"…/inst/include" -I""C:/PROGRA~1/R/R-35~1.1/bin/i386/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"" -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -I"C:/Program Files/R/R-3.5.1/library/Rcpp/include" -I"C:/Program Files/R/R-3.5.1/library/RcppEigen/include" -I"C:/Program Files/R/R-3.5.1/library/BH/include" -I"C:/Program Files/R/R-3.5.1/library/StanHeaders/include" -O3 -Wno-unused-variable -Wno-unused-function -c chains.cpp -o chains.o
In file included from C:/Rtools/mingw_64/x86_64-w64-mingw32/include/c++/random:49:0,
from C:/Rtools/mingw_64/x86_64-w64-mingw32/include/c++/bits/stl_algo.h:66,
from C:/Rtools/mingw_64/x86_64-w64-mingw32/include/c++/algorithm:62,
from C:/Program Files/R/R-3.5.1/library/RcppEigen/include/Eigen/Core:285,
from C:/Program Files/R/R-3.5.1/library/RcppEigen/include/Eigen/Dense:1,
from C:/Program Files/R/R-3.5.1/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4,
from C:/Program Files/R/R-3.5.1/library/StanHeaders/include/stan/math/prim/mat/fun/mean.hpp:5,
from chains.cpp:19:
C:/Rtools/mingw_64/x86_64-w64-mingw32/include/c++/bits/random.h:106:26: error: expected unqualified-id before ‘__int128’
{ typedef unsigned __int128 type; };
^
make: *** [C:/PROGRA~1/R/R-35~1.1/etc/i386/Makeconf:215: chains.o] Error 1
ERROR: compilation failed for package ‘rstan’

removing ‘C:/Program Files/R/R-3.5.1/library/rstan’
restoring previous ‘C:/Program Files/R/R-3.5.1/library/rstan’
In R CMD INSTALL
Error in i.p(…) :
(converted from warning) installation of package ‘C:/Users/ARMAND~1/AppData/Local/Temp/RtmpGgVORU/file26c0bb3383d/rstan_2.18.2.tar.gz’ had non-zero exit status
In addition: Warning message:
In utils::untar(tarfile, …) :
‘tar.exe -zxf “C:\Users\ARMAND~1\AppData\Local\Temp\RtmpGgVORU\file26c034342d2f.tar.gz” -C “C:/Users/ARMAND~1/AppData/Local/Temp/RtmpGgVORU/remotes26c06a222286”’ returned error code 2

bgoodri · October 23, 2018, 7:28pm

OK. First, you should install the StanHeaders binary via

install.packages("StanHeaders")

before trying

devtools::install_github("stan-dev/rstan", ref = "develop", subdir = "rstan/rstan")

but the error that says

C:/Rtools/mingw_64/x86_64-w64-mingw32/include/c++/bits/random.h:106:26: error: expected unqualified-id before ‘__int128’

indicates that your toolchain is not configured correctly. Since Rtools is in C:/Rtools, you should not need a ~/.Rprofile file that sets the BINPREF environment variable but your ~/.R/Makevars file should look exactly like what is produced by

dotR <- file.path(Sys.getenv("HOME"), ".R")
if (!file.exists(dotR)) 
  dir.create(dotR)
M <- file.path(dotR, "Makevars.win")
if (!file.exists(M)) 
  file.create(M)
cat("\nCXX14FLAGS=-O3 -Wno-unused-variable -Wno-unused-function",
    "CXX14 = $(BINPREF)g++ -m$(WIN) -std=c++1y",
    "CXX11FLAGS=-O3 -Wno-unused-variable -Wno-unused-function",
    file = M, sep = "\n", append = TRUE)

Also, make sure your PATH does not include any directories that have mingw_32 or mingw_64 in them when you install Rtools35.

armando · October 23, 2018, 9:11pm

OK, configured Makevars as above, cleaned up the system Path in Windows and reinstalled Rtools. When I did that C:\Rtools\mingw_64\bin got added to the Path:

cat(strsplit(Sys.getenv(“PATH”), “;”)[[1]], sep = “\n”)
C:\Program Files\R\R-3.5.1\bin\x64
C:\Rtools\bin
C:\Rtools\mingw_64\bin
C:\Windows\system32
C:\Windows
C:\Windows\System32\Wbem
C:\Windows\System32\WindowsPowerShell\v1.0
C:\Program Files\MiKTeX 2.9\miktex\bin\x64
C:\Program Files (x86)\Sennheiser\SoftphoneSDK\

When I look up Path in Windows the “mingw_64” is not there.

Edit: I should add that the mingw_64 was not in the Path window during the Rtools install.

–a

bgoodri · October 23, 2018, 9:38pm

And you still get the same error when you try to install rstan from GitHub?

armando · October 23, 2018, 10:08pm

Here’s the output below.

devtools::install_github(“stan-dev/rstan”, ref = “develop”, subdir = “rstan/rstan”)
Downloading GitHub repo stan-dev/rstan@develop
/Rtools/bin/tar: stan-dev-rstan-d96845d/StanHeaders/inst/include/libsundials: Cannot create symlink to ‘mathlib/lib/sundials_3.1.0/’: No such file or directory
/Rtools/bin/tar: stan-dev-rstan-d96845d/StanHeaders/inst/include/src: Cannot create symlink to ‘upstream/src/’: No such file or directory
/Rtools/bin/tar: stan-dev-rstan-d96845d/StanHeaders/inst/include/stan: Cannot create symlink to ‘mathlib/stan/’: No such file or directory
/Rtools/bin/tar: Exiting with failure status due to previous errors
External tar failed with --force-local, trying without
/Rtools/bin/tar: stan-dev-rstan-d96845d/StanHeaders/inst/include/libsundials: Cannot create symlink to ‘mathlib/lib/sundials_3.1.0/’: No such file or directory
/Rtools/bin/tar: stan-dev-rstan-d96845d/StanHeaders/inst/include/src: Cannot create symlink to ‘upstream/src/’: No such file or directory
/Rtools/bin/tar: stan-dev-rstan-d96845d/StanHeaders/inst/include/stan: Cannot create symlink to ‘mathlib/stan/’: No such file or directory
/Rtools/bin/tar: Exiting with failure status due to previous errors
These packages have more recent versions available.
Which would you like to update?

1: rlang (0.2.2 → 0.3.0) [CRAN]

Enter one or more numbers separated by spaces, or an empty line to cancel
1:
√ checking for file ‘C:\Users\armando levy\AppData\Local\Temp\RtmpqQEarM\remotes104449fe556c\stan-dev-rstan-d96845d\rstan\rstan/DESCRIPTION’ …

preparing ‘rstan’: (1.8s)
√ checking DESCRIPTION meta-information …
cleaning src
checking for LF line-endings in source and make files and shell scripts (725ms)
checking for empty or unneeded directories
looking to see if a ‘data/datalist’ file should be added
building ‘rstan_2.18.2.tar.gz’

‘\sffile01\Projects2\5838_EV_Acceleration\Analysis\Statistical Models\code’
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported. Defaulting to Windows directory.

installing source package ‘rstan’ …
** libs

*** arch - i386
C:/Rtools/mingw_64/bin/g++ -m32 -std=c++1y -I"C:/PROGRA~1/R/R-35~1.1/include" -DNDEBUG -I"…/inst/include" -I""C:/PROGRA~1/R/R-35~1.1/bin/i386/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"" -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -I"C:/Program Files/R/R-3.5.1/library/Rcpp/include" -I"C:/Program Files/R/R-3.5.1/library/RcppEigen/include" -I"C:/Program Files/R/R-3.5.1/library/BH/include" -I"C:/Program Files/R/R-3.5.1/library/StanHeaders/include" -O3 -Wno-unused-variable -Wno-unused-function -c chains.cpp -o chains.o
In file included from C:/Rtools/mingw_64/x86_64-w64-mingw32/include/c++/random:49:0,
from C:/Rtools/mingw_64/x86_64-w64-mingw32/include/c++/bits/stl_algo.h:66,
from C:/Rtools/mingw_64/x86_64-w64-mingw32/include/c++/algorithm:62,
from C:/Program Files/R/R-3.5.1/library/RcppEigen/include/Eigen/Core:285,
from C:/Program Files/R/R-3.5.1/library/RcppEigen/include/Eigen/Dense:1,
from C:/Program Files/R/R-3.5.1/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4,
from C:/Program Files/R/R-3.5.1/library/StanHeaders/include/stan/math/prim/mat/fun/mean.hpp:5,
from chains.cpp:19:
C:/Rtools/mingw_64/x86_64-w64-mingw32/include/c++/bits/random.h:106:26: error: expected unqualified-id before ‘__int128’
{ typedef unsigned __int128 type; };
^
make: *** [C:/PROGRA~1/R/R-35~1.1/etc/i386/Makeconf:215: chains.o] Error 1
ERROR: compilation failed for package ‘rstan’

removing ‘C:/Program Files/R/R-3.5.1/library/rstan’
restoring previous ‘C:/Program Files/R/R-3.5.1/library/rstan’
In R CMD INSTALL
Error in i.p(…) :
(converted from warning) installation of package ‘C:/Users/ARMAND~1/AppData/Local/Temp/RtmpqQEarM/file104433e81814/rstan_2.18.2.tar.gz’ had non-zero exit status
In addition: Warning message:
In utils::untar(tarfile, …) :
‘tar.exe -zxf “C:\Users\ARMAND~1\AppData\Local\Temp\RtmpqQEarM\file104478623cc9.tar.gz” -C “C:/Users/ARMAND~1/AppData/Local/Temp/RtmpqQEarM/remotes104449fe556c”’ returned error code 2

bgoodri · October 24, 2018, 5:10am

I was running into this error before, but it went away when I got the 3.5 toolchain setup right. But your setup looks like my setup now. What is your Sys.getenv("BINPREF")?

armando · October 24, 2018, 4:59pm

[1] “C:/Rtools/mingw_64/bin/”

Change to C:/Rtools/bin ?

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Compilation ERROR - brms and stan model

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