Comments (9)
vissarion
commented on August 30, 2024
Which of the following commands yield that error? Could you share more information about the error returned?
EDIT: do you have similar problems with the CRAN package?
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vaithak
commented on August 30, 2024
I get the error after running devtools::install(), error log:
copula.cpp:11:ed from
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/RcppEigenForward.h:40:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:51:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
copula.cpp:13:10: fatal error: 'ellipsoids.h' file not found
#include "ellipsoids.h"
^~~~~~~~~~~~~~
17 warnings and 1 error generated.
make: *** [copula.o] Error 1
ERROR: compilation failed for package ‘volesti’
* removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/volesti’
Error in (function (command = NULL, args = character(), error_on_status = TRUE, :
System command error
I have not yet tried with CRAN package.
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vissarion
commented on August 30, 2024
Are trying to build the develop branch ? Which compiler/version? (it seems you are using clang)
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vaithak
commented on August 30, 2024
Yes, I am compiling the develop branch.
Compiler: Apple clang version 11.0.0 (clang-1100.0.33.8)
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TolisChal
commented on August 30, 2024
Please open with R studio the file volesti.Rproj in 'root/R-proj` file to be sure that the working directory has been set correctly and then run:
Rcpp::compileAttributes()
library(devtools)
devtools::build()
devtools::install()
library(volesti)
Please report possible errors.
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vaithak
commented on August 30, 2024
Same errors:
In file included from copula.cpp:11:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/RcppEigenForward.h:40:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:51:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
copula.cpp:13:10: fatal error: 'ellipsoids.h' file not found
#include "ellipsoids.h"
^~~~~~~~~~~~~~
17 warnings and 1 error generated.
make: *** [copula.o] Error 1
ERROR: compilation failed for package ‘volesti’
* removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/volesti’
Error in (function (command = NULL, args = character(), error_on_status = TRUE, :
System command error
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vaithak
commented on August 30, 2024
Hi, I tried building the package again, this time with gcc but still same error. I think this is an error in devtools which was introduced in macOS Mojave or Catalina.
A point to note is that, if I run the following command from bash in src folder, then there is no error, but the same command when ran through devtools::build gives error.
g++ -std=c++11 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../../external/boost -I../../external/LPsolve_src/run_headers -I../../external/minimum_ellipsoid -I../../include -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I/usr/local/include -lm -ldl -Wno-ignored-attributes -DBOOST_NO_AUTO_PTR -DDISABLE_NLP_ORACLES -fPIC -Wall -g -O2 -c copula.cpp -o copula.o
I tried changing the -I path in Makevars file from relative to absolute path, then there was no error.
PKG_CPPFLAGS= -I$(HOME)/volume_approximation/external/boost -I$(HOME)/volume_approximation/external/LPsolve_src/run_headers -I$(HOME)/volume_approximation/external/minimum_ellipsoid -I$(HOME)/volume_approximation/include
I think this can solve the issue but is there a way of using the absolute path without hardcoding it in the Makevars like above.
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vissarion
commented on August 30, 2024
@vaithak does #137 solves your issue?
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vaithak
commented on August 30, 2024
I debugged this issue properly today, #137 helped a little, but the main issue was with macOS. Firstly, I had to follow the steps here: https://cmichel.io/fixing-cpp-compilation-bugs-for-the-mac-os-catalina-upgrade/ to fix the issue with Catalina. Other than this, GCC was not using the colamd.h in external/LPsolve_src/include but instead using the system installed one in /usr/local/include which had some issues. After fixing this, it worked fine :)
Closing the issue now.
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