installation error (implicit declaration invalid)

[mauricelanghinrichs]

Hi,

first, thanks very much for this effort to provide open facs analysis tools! We are in need for some of the transformation functions (e.g., Logicle), offered in the higher-level module flowkit. However I got an error message in the installation process. The error is caused by the flowutils installation. The relevant line might be:

flowutils/logicle_c_ext/_logicle.c:120:5: error: implicit declaration of function 'hyperlog_inverse' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
        hyperlog_inverse(t, w, m, a, xc, n);

Do you know what's going on here and can help us out? Thanks a lot in advance. The full error message is below. My system is macOS Catalina, python 3.8.8, numpy 1.19.2.

Collecting flowutils
  Using cached FlowUtils-0.9.1.tar.gz (11 kB)
Requirement already satisfied: numpy>=1.7 in ./opt/anaconda3/envs/sc_env/lib/python3.8/site-packages (from flowutils) (1.19.2)
Building wheels for collected packages: flowutils
  Building wheel for flowutils (setup.py) ... error
  ERROR: Command errored out with exit status 1:
   command: /Users/user/opt/anaconda3/envs/sc_env/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/d6/cn_12s513fj8dymm3xy_tdy9mskn84/T/pip-install-4ev728v7/flowutils_c66ffa7ac87d488f9f05705abe9735a0/setup.py'"'"'; __file__='"'"'/private/var/folders/d6/cn_12s513fj8dymm3xy_tdy9mskn84/T/pip-install-4ev728v7/flowutils_c66ffa7ac87d488f9f05705abe9735a0/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /private/var/folders/d6/cn_12s513fj8dymm3xy_tdy9mskn84/T/pip-wheel-dpauxvfu
       cwd: /private/var/folders/d6/cn_12s513fj8dymm3xy_tdy9mskn84/T/pip-install-4ev728v7/flowutils_c66ffa7ac87d488f9f05705abe9735a0/
  Complete output (31 lines):
  running bdist_wheel
  running build
  running build_py
  creating build
  creating build/lib.macosx-10.9-x86_64-3.8
  creating build/lib.macosx-10.9-x86_64-3.8/flowutils
  copying flowutils/transforms.py -> build/lib.macosx-10.9-x86_64-3.8/flowutils
  copying flowutils/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/flowutils
  copying flowutils/compensate.py -> build/lib.macosx-10.9-x86_64-3.8/flowutils
  running build_ext
  building 'flowutils.logicle_c' extension
  creating build/temp.macosx-10.9-x86_64-3.8
  creating build/temp.macosx-10.9-x86_64-3.8/flowutils
  creating build/temp.macosx-10.9-x86_64-3.8/flowutils/logicle_c_ext
  gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/user/opt/anaconda3/envs/sc_env/include -arch x86_64 -I/Users/user/opt/anaconda3/envs/sc_env/include -arch x86_64 -I/Users/user/opt/anaconda3/envs/sc_env/lib/python3.8/site-packages/numpy/core/include -Iflowutils/logicle_c_ext -I/Users/user/opt/anaconda3/envs/sc_env/include/python3.8 -c flowutils/logicle_c_ext/_logicle.c -o build/temp.macosx-10.9-x86_64-3.8/flowutils/logicle_c_ext/_logicle.o -std=c99
  In file included from flowutils/logicle_c_ext/_logicle.c:2:
  In file included from /Users/user/opt/anaconda3/envs/sc_env/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:4:
  In file included from /Users/user/opt/anaconda3/envs/sc_env/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
  In file included from /Users/user/opt/anaconda3/envs/sc_env/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822:
  /Users/user/opt/anaconda3/envs/sc_env/lib/python3.8/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with "          "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
  #warning "Using deprecated NumPy API, disable it with " \
   ^
  flowutils/logicle_c_ext/_logicle.c:120:5: error: implicit declaration of function 'hyperlog_inverse' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
      hyperlog_inverse(t, w, m, a, xc, n);
      ^
  flowutils/logicle_c_ext/_logicle.c:120:5: note: did you mean 'wrap_hyperlog_inverse'?
  flowutils/logicle_c_ext/_logicle.c:95:18: note: 'wrap_hyperlog_inverse' declared here
  static PyObject *wrap_hyperlog_inverse(PyObject *self, PyObject *args) {
                   ^
  1 warning and 1 error generated.
  error: command 'gcc' failed with exit status 1
  ----------------------------------------
  ERROR: Failed building wheel for flowutils
  Running setup.py clean for flowutils
Failed to build flowutils
Installing collected packages: flowutils
    Running setup.py install for flowutils ... error
    ERROR: Command errored out with exit status 1:
     command: /Users/user/opt/anaconda3/envs/sc_env/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/d6/cn_12s513fj8dymm3xy_tdy9mskn84/T/pip-install-4ev728v7/flowutils_c66ffa7ac87d488f9f05705abe9735a0/setup.py'"'"'; __file__='"'"'/private/var/folders/d6/cn_12s513fj8dymm3xy_tdy9mskn84/T/pip-install-4ev728v7/flowutils_c66ffa7ac87d488f9f05705abe9735a0/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /private/var/folders/d6/cn_12s513fj8dymm3xy_tdy9mskn84/T/pip-record-jq9qby7j/install-record.txt --single-version-externally-managed --compile --install-headers /Users/user/opt/anaconda3/envs/sc_env/include/python3.8/flowutils
         cwd: /private/var/folders/d6/cn_12s513fj8dymm3xy_tdy9mskn84/T/pip-install-4ev728v7/flowutils_c66ffa7ac87d488f9f05705abe9735a0/
    Complete output (31 lines):
    running install
    running build
    running build_py
    creating build
    creating build/lib.macosx-10.9-x86_64-3.8
    creating build/lib.macosx-10.9-x86_64-3.8/flowutils
    copying flowutils/transforms.py -> build/lib.macosx-10.9-x86_64-3.8/flowutils
    copying flowutils/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/flowutils
    copying flowutils/compensate.py -> build/lib.macosx-10.9-x86_64-3.8/flowutils
    running build_ext
    building 'flowutils.logicle_c' extension
    creating build/temp.macosx-10.9-x86_64-3.8
    creating build/temp.macosx-10.9-x86_64-3.8/flowutils
    creating build/temp.macosx-10.9-x86_64-3.8/flowutils/logicle_c_ext
    gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/user/opt/anaconda3/envs/sc_env/include -arch x86_64 -I/Users/user/opt/anaconda3/envs/sc_env/include -arch x86_64 -I/Users/user/opt/anaconda3/envs/sc_env/lib/python3.8/site-packages/numpy/core/include -Iflowutils/logicle_c_ext -I/Users/user/opt/anaconda3/envs/sc_env/include/python3.8 -c flowutils/logicle_c_ext/_logicle.c -o build/temp.macosx-10.9-x86_64-3.8/flowutils/logicle_c_ext/_logicle.o -std=c99
    In file included from flowutils/logicle_c_ext/_logicle.c:2:
    In file included from /Users/user/opt/anaconda3/envs/sc_env/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:4:
    In file included from /Users/user/opt/anaconda3/envs/sc_env/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
    In file included from /Users/user/opt/anaconda3/envs/sc_env/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822:
    /Users/user/opt/anaconda3/envs/sc_env/lib/python3.8/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with "          "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
    #warning "Using deprecated NumPy API, disable it with " \
     ^
    flowutils/logicle_c_ext/_logicle.c:120:5: error: implicit declaration of function 'hyperlog_inverse' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
        hyperlog_inverse(t, w, m, a, xc, n);
        ^
    flowutils/logicle_c_ext/_logicle.c:120:5: note: did you mean 'wrap_hyperlog_inverse'?
    flowutils/logicle_c_ext/_logicle.c:95:18: note: 'wrap_hyperlog_inverse' declared here
    static PyObject *wrap_hyperlog_inverse(PyObject *self, PyObject *args) {
                     ^
    1 warning and 1 error generated.
    error: command 'gcc' failed with exit status 1
    ----------------------------------------
ERROR: Command errored out with exit status 1: /Users/user/opt/anaconda3/envs/sc_env/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/d6/cn_12s513fj8dymm3xy_tdy9mskn84/T/pip-install-4ev728v7/flowutils_c66ffa7ac87d488f9f05705abe9735a0/setup.py'"'"'; __file__='"'"'/private/var/folders/d6/cn_12s513fj8dymm3xy_tdy9mskn84/T/pip-install-4ev728v7/flowutils_c66ffa7ac87d488f9f05705abe9735a0/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /private/var/folders/d6/cn_12s513fj8dymm3xy_tdy9mskn84/T/pip-record-jq9qby7j/install-record.txt --single-version-externally-managed --compile --install-headers /Users/user/opt/anaconda3/envs/sc_env/include/python3.8/flowutils Check the logs for full command output.

[mauricelanghinrichs]

ok I think I got it fixed... adding the line

void hyperlog_inverse(double t, double w, double m, double a, double* x, int n);

in the logicle.h file did the job for me. You have already initialised the other functions there, so maybe hyperlog_inverse was just forgotten.

[andreas-wilm]

Same problem here. Fix worked for me as well

[lorenzgerber]

Here too, fixe worked.

[whitews]

Hi all,

Sorry to be late to this thread, I never got a notification from GitHub. Indeed, this was a simple omission on my part. I'll create a new minor release today with this fix.

Thanks for reporting this and submitting the PR fix! All the feedback and contributions are very much appreciated, Scott