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.