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rrwick / Porechop

adapter trimmer for Oxford Nanopore reads
GNU General Public License v3.0
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error: [Errno 2] No such file or directory: 'porechop/cpp_functions.so' #23

Closed stefanprost closed 7 years ago

stefanprost commented 7 years ago

Hi,

I tried to compile several versions of Porechop on my Ubuntu server and always get the same error:

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

Help would be much appreciated!

Cheers, Stefan

rrwick commented 7 years ago

Hi Stefan,

What command gives you that error? I'm wondering if the problem is with the compilation (i.e. cpp_functions.so is never being built) or the installation (i.e. cpp_functions.so isn't being copied to the correct place).

Can you try this installation-free test:

git clone https://github.com/rrwick/Porechop.git
cd Porechop
make
./porechop-runner.py -h

If that fails, then the compilation is the problem, and could you give me any error messages it prints?

If it succeeds, then I suspect the problem is in the setup.py installation. Let me know!

Ryan

stefanprost commented 7 years ago

Hi,

That worked, thanks!

Cheers,

Stefan

From: Ryan Wick notifications@github.com Sent: Sunday, July 23, 2017 7:33:39 PM To: rrwick/Porechop Cc: Stefan Prost; Author Subject: Re: [rrwick/Porechop] error: [Errno 2] No such file or directory: 'porechop/cpp_functions.so' (#23)

Hi Stefan,

What command gives you that error? I'm wondering if the problem is with the compilation (i.e. cpp_functions.so is never being built) or the installation (i.e. cpp_functions.so isn't being copied to the correct place).

Can you try this installation-free test:

git clone https://github.com/rrwick/Porechop.git cd Porechop make ./porechop-runner.py -h

If that fails, then the compilation is the problem, and could you give me any error messages it prints?

If it succeeds, then I suspect the problem is in the setup.py installation. Let me know!

Ryan

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/rrwick/Porechop/issues/23#issuecomment-317304794, or mute the threadhttps://github.com/notifications/unsubscribe-auth/ATdm9IH__qgolb6KYvDgD4x-v8aUJ1cqks5sRAKDgaJpZM4OcPEo.

rrwick commented 7 years ago

Glad to hear it!

punkrockscience commented 6 years ago

Similar problem here, but the installation-free test doesn't work for me. I get the following error from the make: `(porechop) user@test:~/Porechop$ make 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

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

g++ -std=c++14 -Iporechop/include -fPIC -O3 -D NDEBUG -Wall -Wextra -pedantic -mtune=native -shared -Wl,-soname,porechop/cpp_functions.so -o porechop/cpp_functions.so porechop/src/alignment.o porechop/src/adapter_align.o

/usr/bin/ld: /home/user/miniconda3/envs/porechop/bin/../lib/gcc/x86_64-pc-linux-gnu/6.2.0/crtbeginS.o: unrecognized relocation (0x2a) in section `.text'

/usr/bin/ld: final link failed: Bad value

collect2: error: ld returned 1 exit status

make: *** [porechop/cpp_functions.so] Error 1`

Any insights?

rrwick commented 6 years ago

I have never seen this one before! I did a little bit of Googling, and it seems like an issue with libc versions or something. This comment describes a common theme: a mismatch between GCC version and library version.

I see in the error message that it's trying to link against a v6.2.0 library. Could you run g++ --version to see if your compiler is also v6.2.0? If not, then I suspect that's your problem.

I'm afraid that I'm not very savvy with C++ compilation stuff, so I'm probably not much more help in troubleshooting. Is this on your computer or a big server? If it's the latter, is there a sys admin who knows the configuration?

My only other thought is that Miniconda might be fiddling with environment variables in some odd way. You could try running make outside of Miniconda and see if that works.

Ryan

punkrockscience commented 6 years ago

I am using v6.2.0 (in a brand-new conda environment with nothing else in it). Thank you for your help! I'll do some googling of my own and update here if I find a solution.

punkrockscience commented 6 years ago

Downgrading g++ to 5.2.0 seems to have worked. Thanks again!

lab-rat-kid commented 4 years ago

I'm having the same problem, but compiling in g++ 5.2 did not work. When I try the installation-free test above I get:

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"
make: *** [porechop/src/adapter_align.o] Error 1