unable to install on Mac running El Capitan

[proukakis]

Hello, I am a novice so any help welcome

trying from zip file

Christoss-MacBook-Pro:~ christos$ cd /Volumes/SD/svelter-master
Christoss-MacBook-Pro:svelter-master christos$ python setup.py install --user
running install
error: can't combine user with prefix, exec_prefix/home, or install_(plat)base

[xuefzhao]

Hi,
would u like to try this and see if it works ?
http://stackoverflow.com/questions/4495120/combine-user-with-prefix-error-with-setup-py-install

[proukakis]

_**hi, many thanks

It doesnt quite solve it. Not sure if I can specify the gcc somehow to overcome this . Probably my paths are all messed up**_

Christoss-MacBook-Pro:svelter-master christos$ python setup.py install --user --prefix=
running install
running bdist_egg
running egg_info
creating SVelter.egg-info
writing SVelter.egg-info/PKG-INFO
writing top-level names to SVelter.egg-info/top_level.txt
writing dependency_links to SVelter.egg-info/dependency_links.txt
writing manifest file 'SVelter.egg-info/SOURCES.txt'
reading manifest file 'SVelter.egg-info/SOURCES.txt'
writing manifest file 'SVelter.egg-info/SOURCES.txt'
installing library code to build/bdist.macosx-10.11-x86_64/egg
running install_lib
running build_py
creating build
creating build/lib.macosx-10.11-x86_64-2.7
creating build/lib.macosx-10.11-x86_64-2.7/svelter_sv
copying svelter_sv/init.py -> build/lib.macosx-10.11-x86_64-2.7/svelter_sv
copying svelter_sv/svelter.py -> build/lib.macosx-10.11-x86_64-2.7/svelter_sv
running build_ext
building 'svelter_sv.function' extension
creating build/temp.macosx-10.11-x86_64-2.7
creating build/temp.macosx-10.11-x86_64-2.7/svelter_sv
gcc-4.8” export PATH=/Users/christos/opt/cross/bin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/usr/local/ncbi/blast/bin:/Library/TeX/texbin export PATH=/Users/christos/.delly/bin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/usr/local/ncbi/blast/bin:/Library/TeX/texbin export PATH=/Users/christos/.lofreq/bin:?? -fno-strict-aliasing -fno-common -dynamic -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/include -I/usr/local/opt/openssl/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python/2.7.11/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c svelter_sv/function.c -o build/temp.macosx-10.11-x86_64-2.7/svelter_sv/function.o
unable to execute 'gcc-4.8\xe2\x80\x9d': No such file or directory
error: command 'gcc-4.8\xe2\x80\x9d' failed with exit status 1

I thought I had also added the git clone results which are even more puzzling to me- here they are

Christoss-MacBook-Pro:SD christos$ git clone https://github.com/mills-lab/svelter.git
Cloning into 'svelter'...
remote: Counting objects: 1346, done.
remote: Total 1346 (delta 0), reused 0 (delta 0), pack-reused 1346
Receiving objects: 100% (1346/1346), 44.05 MiB | 2.35 MiB/s, done.
Resolving deltas: 100% (792/792), done.
git-lfs smudge 'Support/ref-index/GRCh37/genome.GC_Content': git-lfs: command not found
error: external filter git-lfs smudge %f failed -1
error: external filter git-lfs smudge %f failed
fatal: Support/ref-index/GRCh37/genome.GC_Content: smudge filter lfs failed
warning: Clone succeeded, but checkout failed.
You can inspect what was checked out with 'git status'
and retry the checkout with 'git checkout -f HEAD'

Do let me know if you have any other ideas, otherwise I will try next week on our main server (currently out if action)
thanks
christos

[xuefzhao]

the other option here is to try pip:
pip install --user --install-option="--prefix=" .
see if it works ?

[proukakis]

still not quite...

Christoss-MacBook-Pro:svelter-master christos$ pip install --user --install-option="--prefix=" .
/usr/local/lib/python2.7/site-packages/pip/commands/install.py:194: UserWarning: Disabling all use of wheels due to the use of --build-options / --global-options / --install-options.
cmdoptions.check_install_build_global(options)
Processing /Users/christos/Desktop/svelter-master
Skipping bdist_wheel for SVelter, due to binaries being disabled for it.
Installing collected packages: SVelter
Running setup.py install for SVelter ... error
Complete output from command /usr/local/opt/python/bin/python2.7 -u -c "import setuptools, tokenize;file='/private/var/folders/b5/rjhzb5y563z1ybwjqjtr71m40000gn/T/pip-qdFGiy-build/setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" install --record /var/folders/b5/rjhzb5y563z1ybwjqjtr71m40000gn/T/pip-3TDRq5-record/install-record.txt --single-version-externally-managed --compile --prefix= --user --prefix=:
running install
running build
running build_py
creating build
creating build/lib.macosx-10.11-x86_64-2.7
creating build/lib.macosx-10.11-x86_64-2.7/svelter_sv
copying svelter_sv/init.py -> build/lib.macosx-10.11-x86_64-2.7/svelter_sv
copying svelter_sv/svelter.py -> build/lib.macosx-10.11-x86_64-2.7/svelter_sv
running build_ext
building 'svelter_sv.function' extension
creating build/temp.macosx-10.11-x86_64-2.7
creating build/temp.macosx-10.11-x86_64-2.7/svelter_sv
gcc-4.8” export PATH=/Users/christos/opt/cross/bin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/usr/local/ncbi/blast/bin:/Library/TeX/texbin export PATH=/Users/christos/.delly/bin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/usr/local/ncbi/blast/bin:/Library/TeX/texbin export PATH=/Users/christos/.lofreq/bin:?? -fno-strict-aliasing -fno-common -dynamic -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/include -I/usr/local/opt/openssl/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python/2.7.11/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c svelter_sv/function.c -o build/temp.macosx-10.11-x86_64-2.7/svelter_sv/function.o
unable to execute 'gcc-4.8\xe2\x80\x9d': No such file or directory
error: command 'gcc-4.8\xe2\x80\x9d' failed with exit status 1

----------------------------------------

Command "/usr/local/opt/python/bin/python2.7 -u -c "import setuptools, tokenize;file='/private/var/folders/b5/rjhzb5y563z1ybwjqjtr71m40000gn/T/pip-qdFGiy-build/setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" install --record /var/folders/b5/rjhzb5y563z1ybwjqjtr71m40000gn/T/pip-3TDRq5-record/install-record.txt --single-version-externally-managed --compile --prefix= --user --prefix=" failed with error code 1 in /private/var/folders/b5/rjhzb5y563z1ybwjqjtr71m40000gn/T/pip-qdFGiy-build/