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biocore / qiime

Official QIIME 1 software repository. QIIME 2 (https://qiime2.org) has succeeded QIIME 1 as of January 2018.
GNU General Public License v2.0
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biom-format does not pip install on python3.7 #2216

Closed rwst closed 6 years ago

rwst commented 6 years ago

I'm installing outside of qiime but certainly you're interested in this?

    running egg_info
    writing biom_format.egg-info/PKG-INFO
    writing dependency_links to biom_format.egg-info/dependency_links.txt
    writing entry points to biom_format.egg-info/entry_points.txt
    writing requirements to biom_format.egg-info/requires.txt
    writing top-level names to biom_format.egg-info/top_level.txt
    reading manifest file 'biom_format.egg-info/SOURCES.txt'
    reading manifest template 'MANIFEST.in'
    warning: no directories found matching 'support_files'
    no previously-included directories found matching 'docs/_build'
    warning: no previously-included files matching '*.pyc' found anywhere in distribution
    warning: no previously-included files matching '*.pyo' found anywhere in distribution
    warning: no previously-included files matching '.git' found anywhere in distribution
    warning: no previously-included files matching '*.so' found anywhere in distribution
    warning: no previously-included files matching '.*.swp' found anywhere in distribution
    writing manifest file 'biom_format.egg-info/SOURCES.txt'
    copying biom/_filter.c -> build/lib.linux-x86_64-3.7/biom
    copying biom/_filter.pyx -> build/lib.linux-x86_64-3.7/biom
    copying biom/_subsample.c -> build/lib.linux-x86_64-3.7/biom
    copying biom/_subsample.pyx -> build/lib.linux-x86_64-3.7/biom
    copying biom/_transform.c -> build/lib.linux-x86_64-3.7/biom
    copying biom/_transform.pyx -> build/lib.linux-x86_64-3.7/biom
    creating build/lib.linux-x86_64-3.7/biom/assets
    copying biom/assets/exercise_api.py -> build/lib.linux-x86_64-3.7/biom/assets
    copying biom/assets/exercise_cli.sh -> build/lib.linux-x86_64-3.7/biom/assets
    running build_ext
    building 'biom._filter' extension
    creating build/temp.linux-x86_64-3.7
    creating build/temp.linux-x86_64-3.7/biom
    gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -fmessage-length=0 -grecord-gcc-switches -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -DOPENSSL_LOAD_CONF -fmessage-length=0 -grecord-gcc-switches -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -fmessage-length=0 -grecord-gcc-switches -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -fPIC -I/usr/lib64/python3.7/site-packages/numpy/core/include -I/usr/lib64/python3.7/site-packages/numpy/core/include -I/usr/include/python3.7m -c biom/_filter.c -o build/temp.linux-x86_64-3.7/biom/_filter.o
    In file included from /usr/lib64/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1821:0,
                     from /usr/lib64/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18,
                     from /usr/lib64/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                     from biom/_filter.c:435:
    /usr/lib64/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
     #warning "Using deprecated NumPy API, disable it by " \
      ^
    biom/_filter.c: In function ‘__Pyx_PyCFunction_FastCall’:
    biom/_filter.c:7492:5: error: too many arguments to function ‘(struct PyObject * (*)(struct PyObject *, struct PyObject * const*, Py_ssize_t))meth’
         return (*((__Pyx_PyCFunctionFast)meth)) (self, args, nargs, NULL);
         ^
    biom/_filter.c: In function ‘__Pyx__ExceptionSave’:
    biom/_filter.c:8393:19: error: ‘PyThreadState’ has no member named ‘exc_type’
         *type = tstate->exc_type;
                       ^
    biom/_filter.c:8394:20: error: ‘PyThreadState’ has no member named ‘exc_value’
         *value = tstate->exc_value;
                        ^
    biom/_filter.c:8395:17: error: ‘PyThreadState’ has no member named ‘exc_traceback’
         *tb = tstate->exc_traceback;
                     ^
    biom/_filter.c: In function ‘__Pyx__ExceptionReset’:
    biom/_filter.c:8402:22: error: ‘PyThreadState’ has no member named ‘exc_type’
         tmp_type = tstate->exc_type;
                          ^
    biom/_filter.c:8403:23: error: ‘PyThreadState’ has no member named ‘exc_value’
         tmp_value = tstate->exc_value;
                           ^
    biom/_filter.c:8404:20: error: ‘PyThreadState’ has no member named ‘exc_traceback’
         tmp_tb = tstate->exc_traceback;
                        ^
    biom/_filter.c:8405:11: error: ‘PyThreadState’ has no member named ‘exc_type’
         tstate->exc_type = type;
               ^
    biom/_filter.c:8406:11: error: ‘PyThreadState’ has no member named ‘exc_value’
         tstate->exc_value = value;
               ^
    biom/_filter.c:8407:11: error: ‘PyThreadState’ has no member named ‘exc_traceback’
         tstate->exc_traceback = tb;
               ^
    biom/_filter.c: In function ‘__Pyx__GetException’:
    biom/_filter.c:8462:22: error: ‘PyThreadState’ has no member named ‘exc_type’
         tmp_type = tstate->exc_type;
                          ^
    biom/_filter.c:8463:23: error: ‘PyThreadState’ has no member named ‘exc_value’
         tmp_value = tstate->exc_value;
                           ^
    biom/_filter.c:8464:20: error: ‘PyThreadState’ has no member named ‘exc_traceback’
         tmp_tb = tstate->exc_traceback;
                        ^
    biom/_filter.c:8465:11: error: ‘PyThreadState’ has no member named ‘exc_type’
         tstate->exc_type = local_type;
               ^
    biom/_filter.c:8466:11: error: ‘PyThreadState’ has no member named ‘exc_value’
         tstate->exc_value = local_value;
               ^
    biom/_filter.c:8467:11: error: ‘PyThreadState’ has no member named ‘exc_traceback’
         tstate->exc_traceback = local_tb;
               ^
    error: command 'gcc' failed with exit status 1

    ----------------------------------------
Command "/usr/bin/python3.7 -u -c "import setuptools, tokenize;__file__='/tmp/pip-install-y9fu1azn/biom-format/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-igp7prsi/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /tmp/pip-install-y9fu1azn/biom-format/
wasade commented 6 years ago

@rwst, the tracker for this issue is with the BIOM-Format project (https://github.com/biocore/biom-format), would it be possible to open the issue there? As its maintainer, we haven't done testing yet on 3.7, so thank you for identifying and reporting. If this is blocking you, the traceback suggests regenerating the Cython outputs.

As a heads up, QIIME1 is deprecated. Please see (http://qiime.org) for more information.