I’m trying to install CmdStan 2.18 on my Win10 machine.
When I type make build I’m was getting an error from cpplint about Python2 not existing. Downloaded Python 2, added to PATH and that solved that.
Now I’m getting the error:
make build
> make: *** No rule to make target 'build'. Stop.
Any suggestions please ?
When you typed make build, what directory were you in? That error message usually means that the make command can’t find a Makefile.
I was in the directory stan-develop - so the same directory where the files are. I can see a file called makefile in the directory
You need to be in the directory in which CmdStan was extracted, not the subdirectory in which Stan was extracted. If everything’s unpacked properly, there should be a cmdstan directory from which you can run make build. The cmdstan directory should contain a subdirectory cmdstan/stan with the common Stan C++ core, but you don’t need to deal with that directly when working with CmdStan.
Hi bob. Ok some of those things were not in my extracted files, so I started over. This time make build is running but I’m getting a bunch of errors. FYI I don’t know if it matters but I’m using a Threadripper machine not intel.
Edit: removed the -j4 option to make things more clear:
C:\CmdStan\cmdstan-2.18.0>make build
uname: not found
uname: not found
g++ -Wall -I . -isystem stan/lib/stan_math/lib/eigen_3.3.3 -isystem stan/lib/stan_math/lib/boost_1.66.0 -isystem stan/lib/stan_math/lib/sundials_3.1.0/include -std=c++1y -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -Wno-unused-function -Wno-uninitialized -I src -isystem stan/src -isystem stan/lib/stan_math/ -DFUSION_MAX_VECTOR_SIZE=12 -Wno-unused-local-typedefs -DEIGEN_NO_DEBUG -m64 -Wno-unused-but-set-variable -DNO_FPRINTF_OUTPUT -pipe -c src/cmdstan/stanc.cpp -O3 -o bin/cmdstan/stanc.o
Assembler messages:
Fatal error: no compiled in support for x86_64src/cmdstan/stanc.cpp:1:0: sorry, unimplemented: 64-bit mode not compiled in
#include <stan/command/stanc_helper.hpp>
^
make: *** [bin/cmdstan/stanc.o] Error 1I have no idea what that means. Which g++ are you using?
The make target seems busted anyway—shouldn’t that be making cmdstan/bin/stanc.o? I don’t know why it would be trying to put it above the directory you’re in.
My machine has an AMD Threadripper 1920X processor (12 cores/24 threads), instead of an intel processor. It shouldn’t be important but just thought I should mention it in case it is!
I checked my g++ version and it says gcc 4.9.3. Are g++ and gcc versions the same?
I can’t answer the other questions! Its my first time trying to install CmdStan so this is all new to me
Can you cut and paste the output of “g++ --version” (without the quotes)?
Sure here you go:
C:\CmdStan\cmdstan-2.18.0>g++ --version
g++ (i686-posix-dwarf, Built by MinGW-W64 project) 4.9.3
Copyright (C) 2015 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
As far as I can figure this was installed by Rtools 3.4
Ok I just removed Rtools 3.4 and then updated to R 3.5.1, RTools 3.5 and latest RStudio and it seems to be working now. Its working away I’ll update this post with the result!
Update:
Argh -failed. This time I got many messages while it was working until I hit an error.
C:\CmdStan\cmdstan-2.18.0>make build
g++ -Wall -I . -isystem stan/lib/stan_math/lib/eigen_3.3.3 -isystem stan/lib/stan_math/lib/boost_1.66.0 -isystem stan/lib/stan_math/lib/sundials_3.1.0/include -std=c++1y -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -Wno-unused-function -Wno-uninitialized -I src -isystem stan/src -isystem stan/lib/stan_math/ -DFUSION_MAX_VECTOR_SIZE=12 -Wno-unused-local-typedefs -DEIGEN_NO_DEBUG -DNO_FPRINTF_OUTPUT -pipe -c src/cmdstan/stanc.cpp -O3 -o bin/cmdstan/stanc.o
g++ -Wall -I . -isystem stan/lib/stan_math/lib/eigen_3.3.3 -isystem stan/lib/stan_math/lib/boost_1.66.0 -isystem stan/lib/stan_math/lib/sundials_3.1.0/include -std=c++1y -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -Wno-unused-function -Wno-uninitialized -I src -isystem stan/src -isystem stan/lib/stan_math/ -DFUSION_MAX_VECTOR_SIZE=12 -Wno-unused-local-typedefs -DEIGEN_NO_DEBUG -DNO_FPRINTF_OUTPUT -pipe -c -O3 -o bin/stan/lang/grammars/bare_type_grammar_inst.o stan/src/stan/lang/grammars/bare_type_grammar_inst.cpp
g++ -Wall -I . -isystem stan/lib/stan_math/lib/eigen_3.3.3 -isystem stan/lib/stan_math/lib/boost_1.66.0 -isystem stan/lib/stan_math/lib/sundials_3.1.0/include -std=c++1y -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -Wno-unused-function -Wno-uninitialized -I src -isystem stan/src -isystem stan/lib/stan_math/ -DFUSION_MAX_VECTOR_SIZE=12 -Wno-unused-local-typedefs -DEIGEN_NO_DEBUG -DNO_FPRINTF_OUTPUT -pipe -c -O3 -o bin/stan/lang/grammars/expression07_grammar_inst.o stan/src/stan/lang/grammars/expression07_grammar_inst.cpp
g++ -Wall -I . -isystem stan/lib/stan_math/lib/eigen_3.3.3 -isystem stan/lib/stan_math/lib/boost_1.66.0 -isystem stan/lib/stan_math/lib/sundials_3.1.0/include -std=c++1y -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -Wno-unused-function -Wno-uninitialized -I src -isystem stan/src -isystem stan/lib/stan_math/ -DFUSION_MAX_VECTOR_SIZE=12 -Wno-unused-local-typedefs -DEIGEN_NO_DEBUG -DNO_FPRINTF_OUTPUT -pipe -c -O3 -o bin/stan/lang/grammars/expression_grammar_inst.o stan/src/stan/lang/grammars/expression_grammar_inst.cpp
g++ -Wall -I . -isystem stan/lib/stan_math/lib/eigen_3.3.3 -isystem stan/lib/stan_math/lib/boost_1.66.0 -isystem stan/lib/stan_math/lib/sundials_3.1.0/include -std=c++1y -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -Wno-unused-function -Wno-uninitialized -I src -isystem stan/src -isystem stan/lib/stan_math/ -DFUSION_MAX_VECTOR_SIZE=12 -Wno-unused-local-typedefs -DEIGEN_NO_DEBUG -DNO_FPRINTF_OUTPUT -pipe -c -O3 -o bin/stan/lang/grammars/functions_grammar_inst.o stan/src/stan/lang/grammars/functions_grammar_inst.cpp
g++ -Wall -I . -isystem stan/lib/stan_math/lib/eigen_3.3.3 -isystem stan/lib/stan_math/lib/boost_1.66.0 -isystem stan/lib/stan_math/lib/sundials_3.1.0/include -std=c++1y -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -Wno-unused-function -Wno-uninitialized -I src -isystem stan/src -isystem stan/lib/stan_math/ -DFUSION_MAX_VECTOR_SIZE=12 -Wno-unused-local-typedefs -DEIGEN_NO_DEBUG -DNO_FPRINTF_OUTPUT -pipe -c -O3 -o bin/stan/lang/grammars/indexes_grammar_inst.o stan/src/stan/lang/grammars/indexes_grammar_inst.cpp
g++ -Wall -I . -isystem stan/lib/stan_math/lib/eigen_3.3.3 -isystem stan/lib/stan_math/lib/boost_1.66.0 -isystem stan/lib/stan_math/lib/sundials_3.1.0/include -std=c++1y -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -Wno-unused-function -Wno-uninitialized -I src -isystem stan/src -isystem stan/lib/stan_math/ -DFUSION_MAX_VECTOR_SIZE=12 -Wno-unused-local-typedefs -DEIGEN_NO_DEBUG -DNO_FPRINTF_OUTPUT -pipe -c -O3 -o bin/stan/lang/grammars/program_grammar_inst.o stan/src/stan/lang/grammars/program_grammar_inst.cpp
g++ -Wall -I . -isystem stan/lib/stan_math/lib/eigen_3.3.3 -isystem stan/lib/stan_math/lib/boost_1.66.0 -isystem stan/lib/stan_math/lib/sundials_3.1.0/include -std=c++1y -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -Wno-unused-function -Wno-uninitialized -I src -isystem stan/src -isystem stan/lib/stan_math/ -DFUSION_MAX_VECTOR_SIZE=12 -Wno-unused-local-typedefs -DEIGEN_NO_DEBUG -DNO_FPRINTF_OUTPUT -pipe -c -O3 -o bin/stan/lang/grammars/statement_2_grammar_inst.o stan/src/stan/lang/grammars/statement_2_grammar_inst.cpp
g++ -Wall -I . -isystem stan/lib/stan_math/lib/eigen_3.3.3 -isystem stan/lib/stan_math/lib/boost_1.66.0 -isystem stan/lib/stan_math/lib/sundials_3.1.0/include -std=c++1y -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -Wno-unused-function -Wno-uninitialized -I src -isystem stan/src -isystem stan/lib/stan_math/ -DFUSION_MAX_VECTOR_SIZE=12 -Wno-unused-local-typedefs -DEIGEN_NO_DEBUG -DNO_FPRINTF_OUTPUT -pipe -c -O3 -o bin/stan/lang/grammars/statement_grammar_inst.o stan/src/stan/lang/grammars/statement_grammar_inst.cpp
g++ -Wall -I . -isystem stan/lib/stan_math/lib/eigen_3.3.3 -isystem stan/lib/stan_math/lib/boost_1.66.0 -isystem stan/lib/stan_math/lib/sundials_3.1.0/include -std=c++1y -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -Wno-unused-function -Wno-uninitialized -I src -isystem stan/src -isystem stan/lib/stan_math/ -DFUSION_MAX_VECTOR_SIZE=12 -Wno-unused-local-typedefs -DEIGEN_NO_DEBUG -DNO_FPRINTF_OUTPUT -pipe -c -O3 -o bin/stan/lang/grammars/term_grammar_inst.o stan/src/stan/lang/grammars/term_grammar_inst.cpp
g++ -Wall -I . -isystem stan/lib/stan_math/lib/eigen_3.3.3 -isystem stan/lib/stan_math/lib/boost_1.66.0 -isystem stan/lib/stan_math/lib/sundials_3.1.0/include -std=c++1y -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -Wno-unused-function -Wno-uninitialized -I src -isystem stan/src -isystem stan/lib/stan_math/ -DFUSION_MAX_VECTOR_SIZE=12 -Wno-unused-local-typedefs -DEIGEN_NO_DEBUG -DNO_FPRINTF_OUTPUT -pipe -c -O3 -o bin/stan/lang/grammars/var_decls_grammar_inst.o stan/src/stan/lang/grammars/var_decls_grammar_inst.cpp
g++ -Wall -I . -isystem stan/lib/stan_math/lib/eigen_3.3.3 -isystem stan/lib/stan_math/lib/boost_1.66.0 -isystem stan/lib/stan_math/lib/sundials_3.1.0/include -std=c++1y -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -Wno-unused-function -Wno-uninitialized -I src -isystem stan/src -isystem stan/lib/stan_math/ -DFUSION_MAX_VECTOR_SIZE=12 -Wno-unused-local-typedefs -DEIGEN_NO_DEBUG -DNO_FPRINTF_OUTPUT -pipe -c -O3 -o bin/stan/lang/grammars/whitespace_grammar_inst.o stan/src/stan/lang/grammars/whitespace_grammar_inst.cpp
g++ -Wall -I . -isystem stan/lib/stan_math/lib/eigen_3.3.3 -isystem stan/lib/stan_math/lib/boost_1.66.0 -isystem stan/lib/stan_math/lib/sundials_3.1.0/include -std=c++1y -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -Wno-unused-function -Wno-uninitialized -I src -isystem stan/src -isystem stan/lib/stan_math/ -DFUSION_MAX_VECTOR_SIZE=12 -Wno-unused-local-typedefs -DEIGEN_NO_DEBUG -DNO_FPRINTF_OUTPUT -pipe -c -O3 -o bin/stan/lang/ast_def.o stan/src/stan/lang/ast_def.cpp
g++ -Wall -I . -isystem stan/lib/stan_math/lib/eigen_3.3.3 -isystem stan/lib/stan_math/lib/boost_1.66.0 -isystem stan/lib/stan_math/lib/sundials_3.1.0/include -std=c++1y -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -Wno-unused-function -Wno-uninitialized -I src -isystem stan/src -isystem stan/lib/stan_math/ -DFUSION_MAX_VECTOR_SIZE=12 -Wno-unused-local-typedefs -DEIGEN_NO_DEBUG -DNO_FPRINTF_OUTPUT -pipe -c -O3 -o bin/stan/lang/grammars/semantic_actions_def.o stan/src/stan/lang/grammars/semantic_actions_def.cpp
ar -rs bin/libstanc.a bin/stan/lang/grammars/bare_type_grammar_inst.o bin/stan/lang/grammars/expression07_grammar_inst.o bin/stan/lang/grammars/expression_grammar_inst.o bin/stan/lang/grammars/functions_grammar_inst.o bin/stan/lang/grammars/indexes_grammar_inst.o bin/stan/lang/grammars/program_grammar_inst.o bin/stan/lang/grammars/statement_2_grammar_inst.o bin/stan/lang/grammars/statement_grammar_inst.o bin/stan/lang/grammars/term_grammar_inst.o bin/stan/lang/grammars/var_decls_grammar_inst.o bin/stan/lang/grammars/whitespace_grammar_inst.o bin/stan/lang/ast_def.o bin/stan/lang/grammars/semantic_actions_def.o
C:\Rtools\mingw_32\bin\ar.exe: creating bin/libstanc.a
g++ -Wall -I . -isystem stan/lib/stan_math/lib/eigen_3.3.3 -isystem stan/lib/stan_math/lib/boost_1.66.0 -isystem stan/lib/stan_math/lib/sundials_3.1.0/include -std=c++1y -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -Wno-unused-function -Wno-uninitialized -I src -isystem stan/src -isystem stan/lib/stan_math/ -DFUSION_MAX_VECTOR_SIZE=12 -Wno-unused-local-typedefs -DEIGEN_NO_DEBUG -DNO_FPRINTF_OUTPUT -pipe -O3 -o bin/stanc.exe bin/cmdstan/stanc.o -Lbin -lstanc
g++ -Wall -I . -isystem stan/lib/stan_math/lib/eigen_3.3.3 -isystem stan/lib/stan_math/lib/boost_1.66.0 -isystem stan/lib/stan_math/lib/sundials_3.1.0/include -std=c++1y -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -Wno-unused-function -Wno-uninitialized -I src -isystem stan/src -isystem stan/lib/stan_math/ -DFUSION_MAX_VECTOR_SIZE=12 -Wno-unused-local-typedefs -DEIGEN_NO_DEBUG -DNO_FPRINTF_OUTPUT -pipe -c src/cmdstan/stansummary.cpp -O3 -o bin/cmdstan/stansummary.o
g++ -Wall -I . -isystem stan/lib/stan_math/lib/eigen_3.3.3 -isystem stan/lib/stan_math/lib/boost_1.66.0 -isystem stan/lib/stan_math/lib/sundials_3.1.0/include -std=c++1y -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -Wno-unused-function -Wno-uninitialized -I src -isystem stan/src -isystem stan/lib/stan_math/ -DFUSION_MAX_VECTOR_SIZE=12 -Wno-unused-local-typedefs -DEIGEN_NO_DEBUG -DNO_FPRINTF_OUTPUT -pipe -O3 -o bin/stansummary.exe bin/cmdstan/stansummary.o
g++ -Wall -I . -isystem stan/lib/stan_math/lib/eigen_3.3.3 -isystem stan/lib/stan_math/lib/boost_1.66.0 -isystem stan/lib/stan_math/lib/sundials_3.1.0/include -std=c++1y -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -Wno-unused-function -Wno-uninitialized -I src -isystem stan/src -isystem stan/lib/stan_math/ -DFUSION_MAX_VECTOR_SIZE=12 -Wno-unused-local-typedefs -DEIGEN_NO_DEBUG -DNO_FPRINTF_OUTPUT -pipe -c src/cmdstan/print.cpp -O3 -o bin/cmdstan/print.o
g++ -Wall -I . -isystem stan/lib/stan_math/lib/eigen_3.3.3 -isystem stan/lib/stan_math/lib/boost_1.66.0 -isystem stan/lib/stan_math/lib/sundials_3.1.0/include -std=c++1y -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -Wno-unused-function -Wno-uninitialized -I src -isystem stan/src -isystem stan/lib/stan_math/ -DFUSION_MAX_VECTOR_SIZE=12 -Wno-unused-local-typedefs -DEIGEN_NO_DEBUG -DNO_FPRINTF_OUTPUT -pipe -O3 -o bin/print.exe bin/cmdstan/print.o
g++ -Wall -I . -isystem stan/lib/stan_math/lib/eigen_3.3.3 -isystem stan/lib/stan_math/lib/boost_1.66.0 -isystem stan/lib/stan_math/lib/sundials_3.1.0/include -std=c++1y -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -Wno-unused-function -Wno-uninitialized -I src -isystem stan/src -isystem stan/lib/stan_math/ -DFUSION_MAX_VECTOR_SIZE=12 -Wno-unused-local-typedefs -DEIGEN_NO_DEBUG -DNO_FPRINTF_OUTPUT -pipe -c src/cmdstan/diagnose.cpp -O3 -o bin/cmdstan/diagnose.o
g++ -Wall -I . -isystem stan/lib/stan_math/lib/eigen_3.3.3 -isystem stan/lib/stan_math/lib/boost_1.66.0 -isystem stan/lib/stan_math/lib/sundials_3.1.0/include -std=c++1y -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -Wno-unused-function -Wno-uninitialized -I src -isystem stan/src -isystem stan/lib/stan_math/ -DFUSION_MAX_VECTOR_SIZE=12 -Wno-unused-local-typedefs -DEIGEN_NO_DEBUG -DNO_FPRINTF_OUTPUT -pipe -O3 -o bin/diagnose.exe bin/cmdstan/diagnose.o
cc -DNO_FPRINTF_OUTPUT -pipe -c -x c -O3 -include stan/lib/stan_math/lib/sundials_3.1.0/include/stan_sundials_printf_override.hpp -isystem stan/lib/stan_math/lib/sundials_3.1.0/include stan/lib/stan_math/lib/sundials_3.1.0/src/nvec_ser/nvector_serial.c -o stan/lib/stan_math/lib/sundials_3.1.0/src/nvec_ser/nvector_serial.o
make: cc: Command not found
make: *** [stan/lib/stan_math/make/libraries:38: stan/lib/stan_math/lib/sundials_3.1.0/src/nvec_ser/nvector_serial.o] Error 127So I eventually fixed this very simply by creating a copy of the file ‘gcc.exe’ and renaming it to ‘cc.exe’.
I’m sure there is a smarter way to fix this but this worked and Stan built successfully
What happens if you remove that cc.exe and then create a file make/local in the CmdStan directory with the contents “CC = gcc” (without the quotes)?
So I deleted the file cc.exe, and to test that that broke things again, I tried running the commands before making the change you recommend and everything just works still without ‘make/local’.
I am at a loss to explain it.