missing file?

[gilfunk]

when i try to install im getting this error: error: [Errno 2] No such file or directory: 'porechop/cpp_functions.so'

file does not appear to exist on github either?

( i had a colleague send me an old version of the repo which installed without this issue )

[punkrockscience]

Same issue here. (Except the part about getting an old version of the repo, which I don't have.)

[gilfunk]

[update ] : i got the installation to work with the 'make' command, then was able to run from that dir by calling ./porechop-runner.py

[rrwick]

I'm glad you got it working, but I'm not sure where things went wrong. The cpp_functions.so file is created by make. How did you install - with python3 setup.py install? That command should run make just like you did manually, so I don't know why your manual make succeeded but the setup make failed. Did it display any error messages while installing?

Sorry I can't be more help... let me know if you have any more info on the matter!

Ryan

[gilfunk]

just the error message mentioned above :

" error: [Errno 2] No such file or directory: 'porechop/cpp_functions.so' "

[rrwick]

Sorry, perhaps (if it's not a bother) can you give me the entire output of installing? I suspect the compilation step may be hitting an error, failing to make the cpp_functions.so file, which then leads to the final error you gave. But it's the compilation error I'm interested in...

[bc2zb]

I also just ran into this error. Any of these help?

running install
running build
running build_py
creating build
creating build/lib
creating build/lib/porechop
copying porechop/nanopore_read.py -> build/lib/porechop
copying porechop/version.py -> build/lib/porechop
copying porechop/porechop.py -> build/lib/porechop
copying porechop/adapters.py -> build/lib/porechop
copying porechop/misc.py -> build/lib/porechop
copying porechop/cpp_function_wrappers.py -> build/lib/porechop
copying porechop/__init__.py -> build/lib/porechop
Cleaning previous compilation: make clean
rm -f porechop/src/adapter_align.o porechop/src/alignment.o
Compiling Porechop: make -j 8
g++ -std=c++14 -Iporechop/include -fPIC -O3 -D NDEBUG -Wall -Wextra -pedantic -mtune=native -c -o porechop/src/adapter_align.o porechop/src/adapter_align.cpp
cc1plus: error: unrecognized command line option "-std=c++14"
g++ -std=c++14 -Iporechop/include -fPIC -O3 -D NDEBUG -Wall -Wextra -pedantic -mtune=native -c -o porechop/src/alignment.o porechop/src/alignment.cpp
make: *** [porechop/src/adapter_align.o] Error 1
make: *** Waiting for unfinished jobs....
cc1plus: error: unrecognized command line option "-std=c++14"
make: *** [porechop/src/alignment.o] Error 1
running install_lib
copying build/lib/porechop/nanopore_read.py -> ~/miniconda3/envs/albacore/lib/python3.6/site-packages/porechop
copying build/lib/porechop/version.py -> ~/miniconda3/envs/albacore/lib/python3.6/site-packages/porechop
copying build/lib/porechop/porechop.py -> ~/miniconda3/envs/albacore/lib/python3.6/site-packages/porechop
copying build/lib/porechop/adapters.py -> ~/miniconda3/envs/albacore/lib/python3.6/site-packages/porechop
copying build/lib/porechop/misc.py -> ~/miniconda3/envs/albacore/lib/python3.6/site-packages/porechop
copying build/lib/porechop/cpp_function_wrappers.py -> ~/miniconda3/envs/albacore/lib/python3.6/site-packages/porechop
copying build/lib/porechop/__init__.py -> ~/miniconda3/envs/albacore/lib/python3.6/site-packages/porechop
byte-compiling ~/miniconda3/envs/albacore/lib/python3.6/site-packages/porechop/nanopore_read.py to nanopore_read.cpython-36.pyc
byte-compiling ~/miniconda3/envs/albacore/lib/python3.6/site-packages/porechop/version.py to version.cpython-36.pyc
byte-compiling ~/miniconda3/envs/albacore/lib/python3.6/site-packages/porechop/porechop.py to porechop.cpython-36.pyc
byte-compiling ~/miniconda3/envs/albacore/lib/python3.6/site-packages/porechop/adapters.py to adapters.cpython-36.pyc
byte-compiling ~/miniconda3/envs/albacore/lib/python3.6/site-packages/porechop/misc.py to misc.cpython-36.pyc
byte-compiling ~/miniconda3/envs/albacore/lib/python3.6/site-packages/porechop/cpp_function_wrappers.py to cpp_function_wrappers.cpython-36.pyc
byte-compiling ~/miniconda3/envs/albacore/lib/python3.6/site-packages/porechop/__init__.py to __init__.cpython-36.pyc
running install_egg_info
running egg_info
creating porechop.egg-info
writing porechop.egg-info/PKG-INFO
writing dependency_links to porechop.egg-info/dependency_links.txt
writing entry points to porechop.egg-info/entry_points.txt
writing top-level names to porechop.egg-info/top_level.txt
writing manifest file 'porechop.egg-info/SOURCES.txt'
reading manifest file 'porechop.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
writing manifest file 'porechop.egg-info/SOURCES.txt'
removing '~/miniconda3/envs/albacore/lib/python3.6/site-packages/porechop-0.2.2-py3.6.egg-info' (and everything under it)
Copying porechop.egg-info to ~/miniconda3/envs/albacore/lib/python3.6/site-packages/porechop-0.2.2-py3.6.egg-info
running install_scripts
Installing porechop script to ~/miniconda3/envs/albacore/bin
error: [Errno 2] No such file or directory: 'porechop/cpp_functions.so'

[rrwick]

Thanks for the full output! I can see that in your case, the problem is that GCC doesn't know how to interpret -std=c++14. I suspect that means you're using an older version of GCC. Porechop needs v4.9.1 or later, any of which should compile without error.

Let me know if that solves it for you!

Ryan

[bc2zb]

@rrwick Sorry to take so long, updating GCC worked like a charm. Thanks!

[rrwick]

Great - thanks for letting me know!