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eyzhao / SignIT

Mutation Signatures in Individual Tumours Deciphered by MCMC
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install failture on mac os x #1

Open ipstone opened 5 years ago

ipstone commented 5 years ago

Hi Eric,

thank you for this package, however, as I am trying to install it on mac, I got the following errors. Is this package only working on linux? Thanks! - Isaac


─  preparing ‘signit’:
✔  checking DESCRIPTION meta-information ...
─  cleaning src
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  looking to see if a ‘data/datalist’ file should be added
─  building ‘signit_1.0.1.tar.gz’
   Warning: invalid uid value replaced by that for user 'nobody'
   Warning: invalid gid value replaced by that for user 'nobody'

* installing *source* package ‘signit’ ...
** libs
"/Library/Frameworks/R.framework/Resources/bin/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/population_model.stan
Wrote C++ file "stan_files/population_model.cc"
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"`"/Library/Frameworks/R.framework/Resources/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=ignore_error -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/rstan/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c stan_files/population_model.cc -o stan_files/population_model.o
In file included from stan_files/population_model.cc:3:
In file included from stan_files/population_model.hpp:18:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rstan/include/rstan/stan_fit.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/random/additive_combine.hpp:27:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/random/linear_congruential.hpp:30:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/random/detail/const_mod.hpp:23:```
eyzhao commented 5 years ago

Hello @ipstone, thanks for your interest in SignIT. It should be working on Mac. I don't actually see an error traceback in your quoted section, however. The lines looking like

In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/random/detail/const_mod.hpp:23:

look like compiler warnings. As per Stan documentation: "These simply say there is some part of the Stan library that is being compiled but not used; it has nothing to do with your model specifically. You can safely ignore these compiler warnings".

Was there maybe more to the error message that you did not quote there?