Error attempting to install on OSX
I am attempting to (make) install proteinortho on OSX 10.14.6. I was receiving the '-fopenmp' error. I seemed to fix that by directing the CC= and CXX= lines in the makefile to point toward the gcc-9 I installed from brew. I now get the confusing errors provided below. Googling of these errors has yet to produce any relevant results and I am feeling stumped. Any assistance would be greatly appreciated.
Thank you for your time.
sudo make clean && make
rm -rf src/BUILD test/C.faa.* test/E.faa.* test/C2.faa.* test/L.faa.* test/M.faa.*
rm -rf src/lapack-3.8.0/
Creating build directory ...
[ 10%] Prepare proteinortho_clustering ...
[ 20%] Building **proteinortho_clustering** with LAPACK (dynamic linking)
/usr/local/bin/g++-9 -O2 -fopenmp -march=native -mtune=native -o src/BUILD/Darwin_x86_64/proteinortho_clustering src/proteinortho_clustering.cpp -llapack -lblas -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/wchar.h:90,
from /usr/local/Cellar/gcc@9/9.3.0_1/include/c++/9.3.0/cwchar:44,
from /usr/local/Cellar/gcc@9/9.3.0_1/include/c++/9.3.0/bits/postypes.h:40,
from /usr/local/Cellar/gcc@9/9.3.0_1/include/c++/9.3.0/iosfwd:40,
from /usr/local/Cellar/gcc@9/9.3.0_1/include/c++/9.3.0/ios:38,
from /usr/local/Cellar/gcc@9/9.3.0_1/include/c++/9.3.0/ostream:38,
from /usr/local/Cellar/gcc@9/9.3.0_1/include/c++/9.3.0/iostream:39,
from src/proteinortho_clustering.cpp:16:
/usr/local/Cellar/gcc@9/9.3.0_1/lib/gcc/9/gcc/x86_64-apple-darwin18/9.3.0/include-fixed/stdio.h:219:10: fatal error: _ctermid.h: No such file or directory
219 | #include <_ctermid.h>
| ^~~~~~~~~~~~
compilation terminated.
......-march=native -mtune=native failed, I try without them again.
/usr/local/bin/g++-9 -O2 -fopenmp -o src/BUILD/Darwin_x86_64/proteinortho_clustering src/proteinortho_clustering.cpp -llapack -lblas -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/wchar.h:90,
from /usr/local/Cellar/gcc@9/9.3.0_1/include/c++/9.3.0/cwchar:44,
from /usr/local/Cellar/gcc@9/9.3.0_1/include/c++/9.3.0/bits/postypes.h:40,
from /usr/local/Cellar/gcc@9/9.3.0_1/include/c++/9.3.0/iosfwd:40,
from /usr/local/Cellar/gcc@9/9.3.0_1/include/c++/9.3.0/ios:38,
from /usr/local/Cellar/gcc@9/9.3.0_1/include/c++/9.3.0/ostream:38,
from /usr/local/Cellar/gcc@9/9.3.0_1/include/c++/9.3.0/iostream:39,
from src/proteinortho_clustering.cpp:16:
/usr/local/Cellar/gcc@9/9.3.0_1/lib/gcc/9/gcc/x86_64-apple-darwin18/9.3.0/include-fixed/stdio.h:219:10: fatal error: _ctermid.h: No such file or directory
219 | #include <_ctermid.h>
| ^~~~~~~~~~~~
compilation terminated.
......dynamic linking failed too, now I try dynamic linking without -WL,-whole-archive (this should now work for OSX).
/usr/local/bin/g++-9 -O2 -fopenmp -o src/BUILD/Darwin_x86_64/proteinortho_clustering src/proteinortho_clustering.cpp -llapack -lblas -pthread -lpthread
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/wchar.h:90,
from /usr/local/Cellar/gcc@9/9.3.0_1/include/c++/9.3.0/cwchar:44,
from /usr/local/Cellar/gcc@9/9.3.0_1/include/c++/9.3.0/bits/postypes.h:40,
from /usr/local/Cellar/gcc@9/9.3.0_1/include/c++/9.3.0/iosfwd:40,
from /usr/local/Cellar/gcc@9/9.3.0_1/include/c++/9.3.0/ios:38,
from /usr/local/Cellar/gcc@9/9.3.0_1/include/c++/9.3.0/ostream:38,
from /usr/local/Cellar/gcc@9/9.3.0_1/include/c++/9.3.0/iostream:39,
from src/proteinortho_clustering.cpp:16:
/usr/local/Cellar/gcc@9/9.3.0_1/lib/gcc/9/gcc/x86_64-apple-darwin18/9.3.0/include-fixed/stdio.h:219:10: fatal error: _ctermid.h: No such file or directory
219 | #include <_ctermid.h>
| ^~~~~~~~~~~~
compilation terminated.
......dynamic linking failed (without -WL,-whole-archive) too too, now I try to openblas.
/usr/local/bin/g++-9 -O2 -fopenmp -o src/BUILD/Darwin_x86_64/proteinortho_clustering src/proteinortho_clustering.cpp -lopenblas -pthread -lpthread
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/wchar.h:90,
from /usr/local/Cellar/gcc@9/9.3.0_1/include/c++/9.3.0/cwchar:44,
from /usr/local/Cellar/gcc@9/9.3.0_1/include/c++/9.3.0/bits/postypes.h:40,
from /usr/local/Cellar/gcc@9/9.3.0_1/include/c++/9.3.0/iosfwd:40,
from /usr/local/Cellar/gcc@9/9.3.0_1/include/c++/9.3.0/ios:38,
from /usr/local/Cellar/gcc@9/9.3.0_1/include/c++/9.3.0/ostream:38,
from /usr/local/Cellar/gcc@9/9.3.0_1/include/c++/9.3.0/iostream:39,
from src/proteinortho_clustering.cpp:16:
/usr/local/Cellar/gcc@9/9.3.0_1/lib/gcc/9/gcc/x86_64-apple-darwin18/9.3.0/include-fixed/stdio.h:219:10: fatal error: _ctermid.h: No such file or directory
219 | #include <_ctermid.h>
| ^~~~~~~~~~~~
compilation terminated.
......last linking failed too too too, now I try to recompile lapack (v.3.8.0) and then compile proteinortho_clustering with dynamic linking.
......[ 33%] Extracting the LAPACK library
cd src; tar -xzvf lapack-3.8.0.tar.gz
......[ 66%] Compiling the LAPACK library (using cmake + make)
mkdir src/lapack-3.8.0/build; cd src/lapack-3.8.0/build; cmake .. -DCMAKE_CXX_COMPILER=/usr/local/bin/g++-9 > /dev/null; make all -j4
CMake Warning:
Manually-specified variables were not used by the project:
CMAKE_CXX_COMPILER
......[ 99%] Building **proteinortho_clustering** with LAPACK (dynamic linking)
/usr/local/bin/g++-9 -O2 -fopenmp -o src/BUILD/Darwin_x86_64/proteinortho_clustering src/proteinortho_clustering.cpp -Isrc/lapack-3.8.0/build/include/ -Lsrc/lapack-3.8.0/build/lib/ -llapack -lblas -lgfortran
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/wchar.h:90,
from /usr/local/Cellar/gcc@9/9.3.0_1/include/c++/9.3.0/cwchar:44,
from /usr/local/Cellar/gcc@9/9.3.0_1/include/c++/9.3.0/bits/postypes.h:40,
from /usr/local/Cellar/gcc@9/9.3.0_1/include/c++/9.3.0/iosfwd:40,
from /usr/local/Cellar/gcc@9/9.3.0_1/include/c++/9.3.0/ios:38,
from /usr/local/Cellar/gcc@9/9.3.0_1/include/c++/9.3.0/ostream:38,
from /usr/local/Cellar/gcc@9/9.3.0_1/include/c++/9.3.0/iostream:39,
from src/proteinortho_clustering.cpp:16:
/usr/local/Cellar/gcc@9/9.3.0_1/lib/gcc/9/gcc/x86_64-apple-darwin18/9.3.0/include-fixed/stdio.h:219:10: fatal error: _ctermid.h: No such file or directory
219 | #include <_ctermid.h>
| ^~~~~~~~~~~~
compilation terminated.
proteinortho_clustering compilation failed. Please visit https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Codes
make: *** [src/BUILD/Darwin_x86_64/proteinortho_clustering] Error 1
Edited by Paul Klemm