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It took me hours to figure out the way to install liftover. I just write it here in case someone has the same problem.
OS: centOS6
I got this while I was trying to install lifterover using 'pip install liftover':
Building wheels for collected packages: liftover
Building wheel for liftover (PEP 517) ... error
ERROR: Command errored out with exit status 1:
command: /gs/gsfs0/users/yizhao/miniconda2/bin/python /gs/gsfs0/users/yizhao/miniconda2/lib/python2.7/site-packages/pip/_vendor/pep517/_in_process.py build_wheel /tmp/tmpMBscfO
cwd: /tmp/pip-install-HWwAKR/liftover
Complete output (19 lines):
running bdist_wheel
running build
running build_py
creating build
creating build/lib.linux-x86_64-2.7
creating build/lib.linux-x86_64-2.7/liftover
copying liftover/lifter.py -> build/lib.linux-x86_64-2.7/liftover
copying liftover/init.py -> build/lib.linux-x86_64-2.7/liftover
copying liftover/download_file.py -> build/lib.linux-x86_64-2.7/liftover
running build_ext
building 'liftover.chain_file' extension
creating build/temp.linux-x86_64-2.7
creating build/temp.linux-x86_64-2.7/liftover
creating build/temp.linux-x86_64-2.7/src
creating build/temp.linux-x86_64-2.7/src/gzstream
gcc -pthread -B /gs/gsfs0/users/yizhao/miniconda2/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Isrc/ -Isrc/gzstream/ -Isrc/intervaltree/ -I/gs/gsfs0/users/yizhao/miniconda2/include/python2.7 -c liftover/chain_file.cpp -o build/temp.linux-x86_64-2.7/liftover/chain_file.o -std=c++11
cc1plus: warning: command line option "-Wstrict-prototypes" is valid for Ada/C/ObjC but not for C++
cc1plus: error: unrecognized command line option "-std=c++11"
error: command 'gcc' failed with exit status 1
ERROR: Failed building wheel for liftover
Running setup.py clean for liftover
Failed to build liftover
ERROR: Could not build wheels for liftover which use PEP 517 and cannot be installed directly
So I check my gcc version is 4.4.7. And google told me to use c++11 it need to be at lease 4.7.x. After I upgraded my gcc to 4.7.4, it was installed successfully.
The text was updated successfully, but these errors were encountered:
It took me hours to figure out the way to install liftover. I just write it here in case someone has the same problem.
OS: centOS6
I got this while I was trying to install lifterover using 'pip install liftover':
Building wheels for collected packages: liftover
Building wheel for liftover (PEP 517) ... error
ERROR: Command errored out with exit status 1:
command: /gs/gsfs0/users/yizhao/miniconda2/bin/python /gs/gsfs0/users/yizhao/miniconda2/lib/python2.7/site-packages/pip/_vendor/pep517/_in_process.py build_wheel /tmp/tmpMBscfO
cwd: /tmp/pip-install-HWwAKR/liftover
Complete output (19 lines):
running bdist_wheel
running build
running build_py
creating build
creating build/lib.linux-x86_64-2.7
creating build/lib.linux-x86_64-2.7/liftover
copying liftover/lifter.py -> build/lib.linux-x86_64-2.7/liftover
copying liftover/init.py -> build/lib.linux-x86_64-2.7/liftover
copying liftover/download_file.py -> build/lib.linux-x86_64-2.7/liftover
running build_ext
building 'liftover.chain_file' extension
creating build/temp.linux-x86_64-2.7
creating build/temp.linux-x86_64-2.7/liftover
creating build/temp.linux-x86_64-2.7/src
creating build/temp.linux-x86_64-2.7/src/gzstream
gcc -pthread -B /gs/gsfs0/users/yizhao/miniconda2/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Isrc/ -Isrc/gzstream/ -Isrc/intervaltree/ -I/gs/gsfs0/users/yizhao/miniconda2/include/python2.7 -c liftover/chain_file.cpp -o build/temp.linux-x86_64-2.7/liftover/chain_file.o -std=c++11
cc1plus: warning: command line option "-Wstrict-prototypes" is valid for Ada/C/ObjC but not for C++
cc1plus: error: unrecognized command line option "-std=c++11"
error: command 'gcc' failed with exit status 1
ERROR: Failed building wheel for liftover
Running setup.py clean for liftover
Failed to build liftover
ERROR: Could not build wheels for liftover which use PEP 517 and cannot be installed directly
So I check my gcc version is 4.4.7. And google told me to use c++11 it need to be at lease 4.7.x. After I upgraded my gcc to 4.7.4, it was installed successfully.
The text was updated successfully, but these errors were encountered: