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ImperialCollegeLondon / covid19model

Code for modelling estimated deaths and cases for COVID19.
MIT License
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Docker image run on MacOS ends up in error #73

Closed usptact closed 4 years ago

usptact commented 4 years ago

Describe the bug A clear and concise description of what the bug is.

To Reproduce Steps to reproduce the behavior: $ docker run covid19model

Expected behavior Expected results folder populated and figures generated.

Screenshots Error in compileCode(f, code, language = language, verbose = verbose) : Compilation ERROR, function(s)/method(s) not created! In file included from /usr/lib/R/site-library/RcppEigen/include/Eigen/Core:392, from /usr/lib/R/site-library/RcppEigen/include/Eigen/Dense:1, from /usr/lib/R/site-library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13, from : /usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:60:39: warning: ignoring attributes on template argument ‘m128’ {aka ‘vector(4) float’} [-Wignored-attributes] 60 template<> struct is_arithmetic<__m128> { enum { value = true }; }; ^ /usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:61:40: warning: ignoring attributes on template argument ‘m128i’ {aka ‘vector(2) long long int’} [-Wignored-attributes] 61 template<> struct is_arithmetic<__m128i> { enum { value = true }; };

Calls: stan_model ... cxxfunctionplus -> -> cxxfunction -> compileCode In addition: Warning message: In system(cmd, intern = !verbose) : running command '/usr/lib/R/bin/R CMD SHLIB file6f80ddb.cpp 2> file6f80ddb.cpp.err.txt' had status 1 Error in sink(type = "output") : invalid connection Calls: stan_model -> cxxfunctionplus -> sink

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Additional context N/A

jmbrowne26 commented 4 years ago

I am getting the same issue when using conda to create the environment and then running base.r in Rstudio in Windows 10.

s-mishra commented 4 years ago

Hi @usptact, look here Stan has issues with MacOD Catalina https://github.com/stan-dev/rstan/wiki/Catalina-problems

s-mishra commented 4 years ago

Hi @jmbrowne26 , Can you give details of the issue not just a single line

jmbrowne26 commented 4 years ago

Hi @s-mishra this is the error I get when running in the terminal: Error in compileCode(f, code, language = language, verbose = verbose) : Compilation ERROR, function(s)/method(s) not created! 2 [main] make 15816 fork: child 8608 - died waiting for dll loa ding, errno 11 make: fork: Resource temporarily unavailable Calls: stan_model ... -> -> force -> cxxfunction -> compileCode In addition: Warning message: In system(cmd, intern = !verbose) : running command 'C:/Users/j.browne/Documents/R/R-3.6.3/bin/x64/R CMD SHLIB file2c287ef35b3c.cpp 2> file2c287ef35b3c.cpp.err .txt' had status 1 Error in sink(type = "output") : invalid connection Calls: stan_model -> cxxfunctionplus -> sink Execution halted

and when running in the console I get: Error in compileCode(f, code, language = language, verbose = verbose) : Compilation ERROR, function(s)/method(s) not created! file398030ec2db2.cpp:6:36: warning: ISO C99 requires whitespace after the macro name

define STANSERVICESCOMMAND_HPP#include <boost/integer/integer_log2.hpp>

                                ^

make: *** [C:/Users/J5116~1.BRO/DOCUME~1/R/R-36~1.3/share/make/winshlib.mk:13: file398030ec2db2.dll] Error 127 In addition: Warning message: In system(cmd, intern = !verbose) : running command 'C:/Users/J5116~1.BRO/DOCUME~1/R/R-36~1.3/bin/x64/R CMD SHLIB file398030ec2db2.cpp 2> file398030ec2db2.cpp.err.txt' had status 1 Error in sink(type = "output") : invalid connection

dsjoerg commented 4 years ago

I had a similar issue. I worked around it by launching a Linux VM on AWS EC2 and running Docker there. :(