Compiling CGAL programs on mac, installed using macports - c++

I am working on a project that requires CGAL running on a mac and am very new to C++ in general. I installed CGAL using macports using the command
sudo port install cgal
The installation completed and the .h files were placed in
/opt/local/include/cgal
I copied the tutorial program into a .cpp file and compiled using
g++ -lcgal -I/opt/local/include/ vec.cpp
This returns the error
ld: library not found for -lcgal
clang: error: linker command failed with exit code 1 (use -v to see invocation)
g++ -lcgal -v -I/opt/local/include/ vec.cpp returns
Apple LLVM version 5.1 (clang-503.0.40) (based on LLVM 3.4svn)
Target: x86_64-apple-darwin13.2.0
Thread model: posix
"/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/clang" -cc1 -triple x86_64-apple-macosx10.9.0 -emit-obj -mrelax-all -disable-free -disable-llvm-verifier -main-file-name vec.cpp -mrelocation-model pic -pic-level 2 -mdisable-fp-elim -masm-verbose -munwind-tables -target-cpu core2 -target-linker-version 236.3 -v -resource-dir /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.1 -I /opt/local/include -stdlib=libc++ -fdeprecated-macro -fdebug-compilation-dir /Users/sujeath/C practice -ferror-limit 19 -fmessage-length 80 -stack-protector 1 -mstackrealign -fblocks -fobjc-runtime=macosx-10.9.0 -fencode-extended-block-signature -fcxx-exceptions -fexceptions -fdiagnostics-show-option -fcolor-diagnostics -vectorize-slp -o /var/folders/tm/bgg4k0xs4v36pzwxvsrqtsb00000gn/T/vec-0a56fb.o -x c++ vec.cpp
clang -cc1 version 5.1 based upon LLVM 3.4svn default target x86_64-apple-darwin13.2.0
ignoring nonexistent directory "/usr/include/c++/v1"
\#include "..." search starts here:
\#include search starts here:
/opt/local/include
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1
/usr/local/include
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.1/include
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include
/usr/include
/System/Library/Frameworks (framework directory)
/Library/Frameworks (framework directory)
End of search list.
"/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld" -demangle -dynamic -arch x86_64 -macosx_version_min 10.9.0 -o a.out /var/folders/tm/bgg4k0xs4v36pzwxvsrqtsb00000gn/T/vec-0a56fb.o -lcgal -lc++ -lSystem /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.1/lib/darwin/libclang_rt.osx.a
ld: library not found for -lcgal
clang: error: linker command failed with exit code 1 (use -v to see invocation)
I am using Mavericks BTW and gnu gcc
Thanks!

so, first of all, I'm new on stackoverflow and actually would have preferred to add a comment rather then posting an answer as I'm pretty new to the C++/Mac world too.
Stated this disclaimer I would like to point out a two things that I saw "parsing" the output you posted:
You're calling g++, however, you're using clang to compile (default on OS X Mavericks) as /usr/bin/g++ points to /usr/bin/clang++
I think the cgal library is not on your search path. Marc Glisse pointed you to the -L option of the ld command that let you define further search directories. Probably -L/opt/local/lib might work for you using Macports (I didn't use Macports for a long time so I'm not sure if that's the correct path for the libraries).
Hope this helps.

Related

Compiler error of clang++ 8.0 -- Segmentation fault -- on Mac OSX Sierra 10.12.3

I recently upgraded my OSX from El Capitan to Sierra. The upgrade starts generating compiler errors when using clang++ for one of my projects. I tried it on other projects which do not generate the same errors. Here's the error message.
clang++ -v -O3 -std=c++11 -stdlib=libc++ -g -Wall -I/Users/kevincha/projects/git_hub/DRAMPower/src -I/usr/local/include -I/usr/local/Cellar/boost/1.63.0/include -DRAMULATOR -o ramulator src/Main.cpp obj/ALDRAM.o obj/Cache.o obj/Config.o obj/Controller.o obj/DDR3.o obj/DDR4.o obj/DSARP.o obj/GDDR5.o obj/HBM.o obj/LPDDR4.o obj/Packet.o obj/Processor.o obj/Refresh.o obj/SALP.o obj/StatType.o obj/TLDRAM.o obj/WideIO.o obj/WideIO2.o
Apple LLVM version 8.0.0 (clang-800.0.42.1)
Target: x86_64-apple-darwin16.4.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
"/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/clang" -cc1 -triple x86_64-apple-macosx10.12.0 -Wdeprecated-objc-isa-usage -Werror=deprecated-objc-isa-usage -emit-obj -disable-free -disable-llvm-verifier -discard-value-names -main-file-name Main.cpp -mrelocation-model pic -pic-level 2 -mthread-model posix -mdisable-fp-elim -masm-verbose -munwind-tables -target-cpu penryn -target-linker-version 274.2 -v -dwarf-column-info -debug-info-kind=standalone -dwarf-version=2 -debugger-tuning=lldb -resource-dir /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/8.0.0 -I /Users/kevincha/projects/git_hub/DRAMPower/src -I /usr/local/include -I /usr/local/Cellar/boost/1.63.0/include -D RAMULATOR -stdlib=libc++ -O3 -Wall -std=c++11 -fdeprecated-macro -fdebug-compilation-dir /Users/kevincha/projects/git_hub/ramulator_power -ferror-limit 19 -fmessage-length 270 -stack-protector 1 -fblocks -fobjc-runtime=macosx-10.12.0 -fencode-extended-block-signature -fcxx-exceptions -fexceptions -fmax-type-align=16 -fdiagnostics-show-option -fcolor-diagnostics -vectorize-loops -vectorize-slp -o /var/folders/cn/jclpg1w53fd_gbsnwtjzsc7w0000gn/T/Main-4d31a3.o -x c++ src/Main.cpp
clang -cc1 version 8.0.0 (clang-800.0.42.1) default target x86_64-apple-darwin16.4.0
ignoring nonexistent directory "/usr/include/c++/v1"
ignoring duplicate directory "/usr/local/include"
as it is a non-system directory that duplicates a system directory
#include "..." search starts here:
#include <...> search starts here:
/Users/kevincha/projects/git_hub/DRAMPower/src
/usr/local/Cellar/boost/1.63.0/include
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1
/usr/local/include
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/8.0.0/include
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include
/usr/include
/System/Library/Frameworks (framework directory)
/Library/Frameworks (framework directory)
End of search list.
clang: error: unable to execute command: Segmentation fault: 11
clang: error: clang frontend command failed due to signal (use -v to see invocation)
Apple LLVM version 8.0.0 (clang-800.0.42.1)
Target: x86_64-apple-darwin16.4.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
clang: note: diagnostic msg: PLEASE submit a bug report to http://developer.apple.com/bugreporter/ and include the crash backtrace, preprocessed source, and associated run script.
clang: note: diagnostic msg:
********************
PLEASE ATTACH THE FOLLOWING FILES TO THE BUG REPORT:
Preprocessed source(s) and associated run script(s) are located at:
clang: note: diagnostic msg: /var/folders/cn/jclpg1w53fd_gbsnwtjzsc7w0000gn/T/Main-ae92f3.cpp
clang: note: diagnostic msg: /var/folders/cn/jclpg1w53fd_gbsnwtjzsc7w0000gn/T/Main-ae92f3.sh
clang: note: diagnostic msg:
********************
make: *** [ramulator] Error 254
This was a clang compiler bug, now fixed in the latest (beta) Xcode:
Xcode 8.3 beta 3 (8W132p)
Posted Date: Feb 20th, 2017
↳ https://developer.apple.com/download/

C++ libraries on mac not compiling with g++ my_program.cpp -o my_program

I have recently attempted to download (using Homebrew) Eigen (a C++ library) and compile the example program on Eigen's website https://eigen.tuxfamily.org/dox/GettingStarted.html.
I get a error in terminal that is:
EigenExample1.cpp:10:10: fatal error: 'Eigen/Dense' file not found #include < Eigen/Dense >
I have double checked to make sure homebrew was updated and the eigen3 folder does exist in /usr/local/include. In addition I do have command line tools installed and cpp -v returns:
Apple LLVM version 8.0.0 (clang-800.0.42.1)
Target: x86_64-apple-darwin16.3.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
"/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/clang" -cc1 -triple x86_64-apple-macosx10.12.0 -Wdeprecated-objc-isa-usage -Werror=deprecated-objc-isa-usage -E -disable-free -disable-llvm-verifier -discard-value-names -main-file-name - -mrelocation-model pic -pic-level 2 -mthread-model posix -mdisable-fp-elim -masm-verbose -munwind-tables -target-cpu penryn -target-linker-version 274.2 -v -dwarf-column-info -debugger-tuning=lldb -resource-dir /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/8.0.0 -I /usr/include -fdebug-compilation-dir /Users/name/MNISTNeuralNetwork/Eigen -ferror-limit 19 -fmessage-length 80 -stack-protector 1 -fblocks -fobjc-runtime=macosx-10.12.0 -fencode-extended-block-signature -fmax-type-align=16 -fdiagnostics-show-option -fcolor-diagnostics -traditional-cpp -o - -x c -
clang -cc1 version 8.0.0 (clang-800.0.42.1) default target x86_64-apple-darwin16.3.0
ignoring duplicate directory "/usr/include"
as it is a non-system directory that duplicates a system directory
\#include "..." search starts here:
\#include <...> search starts here:
/usr/local/include
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/8.0.0/include
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include
/usr/include
/System/Library/Frameworks (framework directory)
/Library/Frameworks (framework directory)
End of search list.
When you install using Homebrew, the Eigen directory is nested inside include/eigen3. You should be able to compile with the following flags:
g++ -I "$(brew --prefix eigen)/include/eigen3" my_program.cpp -o my_program
Indeed, this is how the Homebrew installation is tested.

Issue with executing a.out file (C++) MacOS Sierra 10.12.1

I just updated to Sierra and it seems my compiler fell apart for some reason.
The code I wrote worked fine before the update, so I'm sure its not an issue there but now it just isn't working what so ever when I try to execute it.
Here is the output.
$ g++ source.cpp
$ ./a.out
dyld: mach-o, but built for simulator (not macOS)
Abort trap: 6
Running G++ with verbose for #NulledPointer
$ g++ --verbose source.cpp
Apple LLVM version 8.0.0 (clang-800.0.38)
Target: x86_64-apple-darwin16.1.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
"/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/clang" -cc1 -triple x86_64-apple-ios7.0.0 -Wdeprecated-objc-isa-usage -Werror=deprecated-objc-isa-usage -Werror=implicit-function-declaration -emit-obj -mrelax-all -disable-free -disable-llvm-verifier -discard-value-names -main-file-name source.cpp -mrelocation-model pic -pic-level 2 -mthread-model posix -mdisable-fp-elim -masm-verbose -munwind-tables -target-cpu core2 -target-linker-version 274.1 -v -dwarf-column-info -debugger-tuning=lldb -resource-dir /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/8.0.0 -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/iPhoneSimulator.platform/Developer/SDKs/iPhoneSimulator10.0.sdk -stdlib=libc++ -Wno-error -fdeprecated-macro -fdebug-compilation-dir /Users/USERNAME/FILE_DIRECTORY/ -ferror-limit 19 -fmessage-length 130 -stack-protector 1 -fblocks -fobjc-runtime=ios-7.0.0 -fencode-extended-block-signature -fcxx-exceptions -fexceptions -fmax-type-align=16 -fdiagnostics-show-option -fcolor-diagnostics -o /var/folders/kr/tvqfrgdx2w32m0c9fq96zddc0000gn/T/source-355902.o -x c++ source.cpp
clang -cc1 version 8.0.0 (clang-800.0.38) default target x86_64-apple-darwin16.1.0
ignoring nonexistent directory "/Applications/Xcode.app/Contents/Developer/Platforms/iPhoneSimulator.platform/Developer/SDKs/iPhoneSimulator10.0.sdk/usr/include/c++/v1"
ignoring nonexistent directory "/Applications/Xcode.app/Contents/Developer/Platforms/iPhoneSimulator.platform/Developer/SDKs/iPhoneSimulator10.0.sdk/usr/local/include"
#include "..." search starts here:
#include <...> search starts here:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/8.0.0/include
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include
/Applications/Xcode.app/Contents/Developer/Platforms/iPhoneSimulator.platform/Developer/SDKs/iPhoneSimulator10.0.sdk/usr/include
/Applications/Xcode.app/Contents/Developer/Platforms/iPhoneSimulator.platform/Developer/SDKs/iPhoneSimulator10.0.sdk/System/Library/Frameworks (framework directory)
/Applications/Xcode.app/Contents/Developer/Platforms/iPhoneSimulator.platform/Developer/SDKs/iPhoneSimulator10.0.sdk/Library/Frameworks (framework directory)
End of search list.
"/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld" -demangle -dynamic -arch x86_64 -ios_simulator_version_min 7.0.0 -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/iPhoneSimulator.platform/Developer/SDKs/iPhoneSimulator10.0.sdk -o a.out /var/folders/kr/tvqfrgdx2w32m0c9fq96zddc0000gn/T/source-355902.o -lc++ -lSystem /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/8.0.0/lib/darwin/libclang_rt.ios.a
Error from running that command NulledPointer posted.
clang: warning: no such sysroot directory: '/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk'
clang: warning: using sysroot for 'MacOSX' but targeting 'iPhone'
In file included from source.cpp:10:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/iostream:38:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/ios:215:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/iosfwd:90:10: fatal error:
'wchar.h' file not found
#include <wchar.h> // for mbstate_t
^
1 error generated.
There are multiple options:
Try installing missing tools (if any) using xcode-select --install and try compiling. If that fails,
Try running gcc -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk source.cpp. This obviously assuming you have SDK installed in that location. Replace with whatever location exist there.

Compile error when including boost/thread.hpp

I'm trying to use threads in C++, using boost's thread library. Clang is giving me an error and I don't know how to interpret it. The file I'm trying to compile is about as minimal as it can get:
#include <iostream>
#include <boost/thread.hpp>
using namespace std;
int main() {
return 0;
}
Here's the transcript:
$ clang++ -std=c++11 -o 4.4 4.4.cpp -v
Apple clang version 4.1 (tags/Apple/clang-421.11.66) (based on LLVM 3.1svn)
Target: x86_64-apple-darwin12.2.1
Thread model: posix
"/usr/bin/clang" -cc1 -triple x86_64-apple-macosx10.8.0 -emit-obj -mrelax-all -disable-free -disable-llvm-verifier -main-file-name 4.4.cpp -pic-level 1 -mdisable-fp-elim -relaxed-aliasing -masm-verbose -munwind-tables -target-cpu core2 -target-linker-version 134.9 -v -resource-dir /usr/bin/../lib/clang/4.1 -fmodule-cache-path /var/folders/mt/k4dhhm7d7_7_q6drl3zkjj4r0000gn/T/clang-module-cache -std=c++11 -fdeprecated-macro -fdebug-compilation-dir /Users/thinkpad20/Documents/workspace/cpp/homework4 -ferror-limit 19 -fmessage-length 100 -stack-protector 1 -mstackrealign -fblocks -fobjc-runtime-has-arc -fobjc-runtime-has-weak -fobjc-dispatch-method=mixed -fobjc-default-synthesize-properties -fcxx-exceptions -fexceptions -fdiagnostics-show-option -fcolor-diagnostics -o /var/folders/mt/k4dhhm7d7_7_q6drl3zkjj4r0000gn/T/4-49j8fE.o -x c++ 4.4.cpp
clang -cc1 version 4.1 based upon LLVM 3.1svn default target x86_64-apple-darwin12.2.1
ignoring nonexistent directory "/usr/include/c++/4.2.1/i686-apple-darwin10/x86_64"
ignoring nonexistent directory "/usr/include/c++/4.0.0"
ignoring nonexistent directory "/usr/include/c++/4.0.0/i686-apple-darwin8/"
ignoring nonexistent directory "/usr/include/c++/4.0.0/backward"
ignoring nonexistent directory "/usr/local/include"
#include "..." search starts here:
#include <...> search starts here:
/usr/include/c++/4.2.1
/usr/include/c++/4.2.1/backward
/usr/bin/../lib/clang/4.1/include
/usr/include
/System/Library/Frameworks (framework directory)
/Library/Frameworks (framework directory)
End of search list.
"/usr/bin/ld" -demangle -dynamic -arch x86_64 -macosx_version_min 10.8.0 -o 4.4 /var/folders/mt/k4dhhm7d7_7_q6drl3zkjj4r0000gn/T/4-49j8fE.o -lstdc++ -lSystem /usr/bin/../lib/clang/4.1/lib/darwin/libclang_rt.osx.a
Undefined symbols for architecture x86_64:
"boost::system::system_category()", referenced from:
___cxx_global_var_init3 in 4-49j8fE.o
"boost::system::generic_category()", referenced from:
___cxx_global_var_init1 in 4-49j8fE.o
___cxx_global_var_init2 in 4-49j8fE.o
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
Any help is appreciated! :)
You need to tell clang which libraries to link against. In your case, this is boost_system (that's what the error message tells you) and (as soon as you actually get around to using some threading stuff in your program) boost_thread as well, so compile it like this:
clang++ -std=c++11 -o myapp myfile.cpp -lboost_system -lboost_thread

clang-2.9 crt1 not found error

Just compiled clang-2.9 release and it can't link an hello world example. There is the error:
crt1.o: No such file: No such file or directory
LLVM is configured as default + --enable-shared. The llvm-2.8 build with same options works normally on the same machine.
$ clang -v a.c
clang version 2.9 (tags/RELEASE_29/final)
Target: i386-pc-linux-gnu
Thread model: posix
"/root/bin/clang" -cc1 -triple i386-pc-linux-gnu -emit-obj -mrelax-all -disable-free -disable-llvm-verifier -main-file-name a.c -mrelocation-model static -mdisable-fp-elim -masm-verbose -mconstructor-aliases -target-cpu pentium4 -target-linker-version 2.18 -momit-leaf-frame-pointer -v -resource-dir /root/lib/clang/2.9 -ferror-limit 19 -fmessage-length 157 -fgnu-runtime -fdiagnostics-show-option -fcolor-diagnostics -o /tmp/cc-2ueoYy.o -x c a.c
clang -cc1 version 2.9 based upon llvm 2.9 hosted on i386-pc-linux-gnu
ignoring nonexistent directory "/usr/local/include"
#include "..." search starts here:
#include <...> search starts here:
/root/lib/clang/2.9/include
/usr/include
End of search list.
a.c:1:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int]
main(){}
^~~~
1 warning generated.
"/usr/bin/ld" --eh-frame-hdr -m elf_i386 -dynamic-linker /lib/ld-linux.so.2 -o a.out crt1.o crti.o crtbegin.o -L -L/../../.. /tmp/cc-2ueoYy.o -lgcc --as-needed -lgcc_s --no-as-needed -lc -lgcc --as-needed -lgcc_s --no-as-needed crtend.o crtn.o
/usr/bin/ld: crt1.o: No such file: No such file or directory
clang: error: linker command failed with exit code 1 (use -v to see invocation)
The same error was here http://permalink.gmane.org/gmane.comp.compilers.clang.devel/12101
and http://comments.gmane.org/gmane.comp.compilers.clang.devel/14269 and http://permalink.gmane.org/gmane.comp.compilers.llvm.bugs/11352
What I can learn while comparing with llvm-2.8 -- newer version tries to assemble file itself, and older version calls gcc to do assemble and link steps.
Please, this is not a duplicate of clang linker problem as I can't edit sources of LLVM, so the accepted solution isn't useful to me.
As suggested at http://permalink.gmane.org/gmane.comp.compilers.llvm.bugs/11352 (llvm bug 8897) this is because
gcc used to build clang is not in a standard location
or
system gcc is not listed in the ToolChains.cpp GccVersions list:
./tools/clang/lib/Driver/ToolChains.cpp: const char* GccVersions[] = {"4.5.2", "4.5.1", "4.5", "4.4.5", "4.4.4",
./tools/clang/lib/Driver/ToolChains.cpp- "4.4.3", "4.4", "4.3.4", "4.3.3", "4.3.2",
./tools/clang/lib/Driver/ToolChains.cpp- "4.3", "4.2.4", "4.2.3", "4.2.2", "4.2.1",
./tools/clang/lib/Driver/ToolChains.cpp- "4.2"};
Both cases are true for my installation.
To fix this, I'll try to add my version of gcc into list GccVersions[].
This helps me.