pip install cutadapt: build fails

• Cutadapt and Python version Cutadapt 1.16, Python 3.7.0

Build fails with pip install cutadapt. The pertinent lines for the build failure:

src/cutadapt/_seqio.c: In function '__Pyx__ExceptionSwap':
src/cutadapt/_seqio.c:9589:22: error: 'PyThreadState {aka struct _ts}' has no member named 'exc_type'
     tmp_type = tstate->exc_type;
                      ^
src/cutadapt/_seqio.c:9590:23: error: 'PyThreadState {aka struct _ts}' has no member named 'exc_value'
     tmp_value = tstate->exc_value;
                       ^
src/cutadapt/_seqio.c:9591:20: error: 'PyThreadState {aka struct _ts}' has no member named 'exc_traceback'
     tmp_tb = tstate->exc_traceback;
                    ^
src/cutadapt/_seqio.c:9592:11: error: 'PyThreadState {aka struct _ts}' has no member named 'exc_type'
     tstate->exc_type = *type;
           ^
src/cutadapt/_seqio.c:9593:11: error: 'PyThreadState {aka struct _ts}' has no member named 'exc_value'
     tstate->exc_value = *value;
           ^
src/cutadapt/_seqio.c:9594:11: error: 'PyThreadState {aka struct _ts}' has no member named 'exc_traceback'
     tstate->exc_traceback = *tb;
           ^
error: command 'gcc-5' failed with exit status 1

    ----------------------------------------
Command "/home/linuxbrew/.linuxbrew/opt/python/bin/python3.7 -u -c "import setuptools, tokenize;__file__='/tmp/pip-install-zi5go87_/cutadapt/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-record-6fb855w2/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /tmp/pip-install-zi5go87_/cutadapt/

[marcelm]

I’ve just released Cutadapt 1.17, which should fix the problem. I’ve also created binary packages (wheels) for Python 3.7 so you don’t even have a compilation step anymore. You’ll get them automatically when you pip3 install --upgrade cutadapt.

Thanks again for reporting!

[marcelm]

Thanks a lot, I can confirm this. Installing the developer version works, which is why I haven’t seen this.

I will need to re-generate the included _seqio.c with a more recent Cython version.