Modeling failed Warnings: 'C:/Users/R-34~1.3/rtools40/usr/mingw_/bin/g++' not found Errors: Multiple results for CXX14FLAGS found, something is wrong.FALSE

Interfaces RStan
,
41

The output is still huge… I am just copying the last few lines again.

In file included from \server/userhome/students4/My Documents/R/win-library/4.0/StanHeaders/include/stan/math/rev/core.hpp:46,
from ./stan/model/model_base.hpp:5,
from …/inst/include/rstan_next/stan_fit.hpp:7,
from stan_fit.cpp:1:
\server/userhome/students4/My Documents/R/win-library/4.0/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp: At global scope:
\server/userhome/students4/My Documents/R/win-library/4.0/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp:14:13: warning: ‘void stan::math::set_zero_all_adjoints()’ defined but not used [-Wunused-function]
static void set_zero_all_adjoints() {
^~~~~~~~~~~~~~~~~~~~~
C:/Users/R-3.4.3/rtools40/mingw32/bin/ar -rs …/inst/lib//i386/libStanServices.a stan_fit.o stan_fit_base.o
C:\Users\R-3.4.3\rtools40\mingw32\bin\ar.exe: creating …/inst/lib//i386/libStanServices.a
no DLL was created
ERROR: compilation failed for package ‘rstan’

  • removing ‘\server/userhome/students4/My Documents/R/win-library/4.0/rstan’
    Warning in install.packages :
    installation of package ‘rstan’ had non-zero exit status
42

This is certainly being much trickier than usual, sorry about all this!

First, we can cut down the output a bit more by adding -Wno-unused-function to Makevars.win file, in the same way you did before.

Next, I’ll get you to remove the StanHeaders package: remove.packages("StanHeaders"), and restart R.

Let’s double check that you can compile c++ from R. Can you post the output from:

system("touch foo.cpp")
system("R CMD SHLIB foo.cpp")
43

system(“touch foo.cpp”)
[1] 0
system(“R CMD SHLIB foo.cpp”)
C:/Users/R-3.4.3/rtools40/mingw64/bin/g++ -std=gnu++11 -I"C:/Users/R/R-40~1.3/include" -DNDEBUG -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c foo.cpp -o foo.o
C:/Users/R-3.4.3/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o foo.dll tmp.def foo.o -LC:/Users/R/R-40~1.3/bin/x64 -lR
[1] 0

44

Great! So it’s compiling C and C++ without issue, so it’s not a toolchain issue. For now, can you just install RStan regularly (not from source), and then try the example model:

install.packages("rstan")
library(rstan)
example(stan_model,run.dontrun=T)
45

Good news rstan and stan headers got installed with no errors. But the example gave the following error.

Compilation ERROR, function(s)/method(s) not created!
Error in compileCode(f, code, language = language, verbose = verbose) : 
  cc1plus.exe: fatal error: \server/userhome/students4/My Documents/R/win-library/4.0/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp: No such file or directorycompilation terminated.make: *** [C:/Users/R/R-40~1.3/etc/x64/Makeconf:229: file29e05485510a.o] Error 1
In addition: Warning message:
In system(paste(CXX, ARGS), ignore.stdout = TRUE, ignore.stderr = TRUE) :
  'C:/Users/R-34~1.3/rtools40/usr/mingw_/bin/g++' not found
46

Alright, I think this is happening because the rstan and StanHeaders packages are installed on a networked drive.

First, double-check that the file is definitely there by running:

length(list.files("~/R/win-library/4.0/StanHeaders/include/stan/math/prim/mat/fun/"))

It should return 215.

If that’s all fine, then you’ll need to remove rstan and StanHeaders and install them in a local directory on your computer (not on the network drive). Did you need information on how to do that?

47

That’s strange, because I am saving them in to the local folder I have access to in the C drive. What do you mean by a network driver? Is it the server location? I am sorry I am not tech savvy.
Here is the output from the line you gave me.

length(list.files(“~/R/win-library/4.0/StanHeaders/include/stan/math/prim/mat/fun/”))
[1] 215

48

It’s because when you install a package via install.packages it installs into a folder on \server/userhome/students4/My Documents/, which is located a networked drive, not a drive on your computer. This can cause issues for RStan with accessing files

Let’s try this, first restart R. Then remove the rstan and StanHeaders packages:

remove.packages(c("rstan","StanHeaders"))

Then, install them to your local library (taken from an earlier post):

install.packages("rstan",lib="C:/Users/R/R-4.0.3/library")

Does that install without erroring?

49

Yes. Install happened without errors. What shall I do now?

50

Can you try the example model from above again?

51

Sadly I got the following error.
Compilation ERROR, function(s)/method(s) not created!
Error in compileCode(f, code, language = language, verbose = verbose) :
cc1plus.exe: fatal error: \server/userhome/students4/My Documents/R/win-library/4.0/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp: No such file or directorycompilation terminated.make: *** [C:/Users/R/R-40~1.3/etc/x64/Makeconf:229: file5ea43a8f64e0.o] Error 1
In addition: Warning message:
In system(paste(CXX, ARGS), ignore.stdout = TRUE, ignore.stderr = TRUE) :
‘C:/Users/R-34~1.3/rtools40/usr/mingw_/bin/g++’ not found

52

Do you think there is a reason why it can’t locate “C:/Users/R-34~1.3/rtools40/usr/mingw_/bin/g++’ not found” ??
Unfortunately its getting late here for me. So I might retire since its late here. I shall be able to reply again tomorrow morning.

53

Yes, but don’t worry about it.

54

Alright, let’s try moving the entire package installation directory to your local drive (i.e., all R packages will get installed to a folder on your computer, rather than the network drive).

First we need to remove those RStan and StanHeaders packages:

remove.packages(c("rstan","StanHeaders"))

And restart R.

Given that we know you have permissions to the C:/Users/R folder, we’ll create a folder there which your packages will be installed into:

dir.create("C:/Users/R/win-library/4.0", recursive = T)

Next, we need to tell R to install and load R packages from this directory. We can do this by setting the R_LIBS_USER environment variable using your .Renviron file:

cat("R_LIBS_USER = \"C:/Users/R/win-library/4.0\"",
    file="~/.Renviron", append=TRUE)

And then restart R. If you look at the ‘Packages’ pane in RStudio, you should only see packages listed under ‘System Library’. Next, we’ll copy R packages from your old directory to this new one (otherwise you’ll have to re-install them all):

file.copy(from="~/R/win-library/4.0/",to="C:/Users/R/win-library/",recursive = T)

Depending on how many packages you have installed, this could take a few minutes. Then restart R again.

If all of the above ran without any errors (fingers crossed), then try to install RStan and run the example model again:

install.packages("rstan")
library(rstan)
example(stan_model, run.dontrun=T)
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55

Thanks Andrjohns. I did all the steps, and after I ran the model
I got this

Warning message:
In system(paste(CXX, ARGS), ignore.stdout = TRUE, ignore.stderr = TRUE) :
‘C:/Users/R-34~1.3/rtools40/usr/mingw_/bin/g++’ not found

56

That warning is completely safe to ignore, it will be fixed in the next release. Did everything run and finish sampling?

57

Yes! I am super thankful!!! You have been such a great help on this, I sincerely appreciate it!!!

2 Likes
58

Fantastic news! Thanks for hanging in there with the debugging, and sorry that it’s been such a journey.

1 Like
59

Not at all, actually this has been the quickest debugging I have ever had! So I am super thankful, and you gave me insights on the problem which I had no idea about.

2 Likes
60

Glad it’s working now @ASaeed!

And seriously thanks to you @andrjohns for hanging in there and helping them get everything sorted out. That was quite the debugging journey!

2 Likes