Problems Installing

[tmgreenfield1101]

Hi,

I'm having trouble installing PlateFlex. I have created the anaconda environment as suggested in the installation instructions but the installation throws a large amount amount of errors. I'm a little stuck at the moment and don't really understand where the error is coming from.

Any help would be great - even if it's to say that you don't know and its something wrong with my system.

Tim

p.s. I've included the terminal output below

(pflex) tg286@circinus:/space/tg286/PlateFlex$ python -m pip install .
Processing /space/tg286/PlateFlex
Requirement already satisfied: numpy>=1.15 in /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages (from plateflex==0.1.0) (1.17.5)
Requirement already satisfied: pymc3 in /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages (from plateflex==0.1.0) (3.8)
Requirement already satisfied: matplotlib in /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages (from plateflex==0.1.0) (3.1.2)
Requirement already satisfied: seaborn in /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages (from plateflex==0.1.0) (0.9.0)
Requirement already satisfied: arviz>=0.4.1 in /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages (from pymc3->plateflex==0.1.0) (0.6.1)
Requirement already satisfied: theano>=1.0.4 in /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages (from pymc3->plateflex==0.1.0) (1.0.4)
Requirement already satisfied: tqdm>=4.8.4 in /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages (from pymc3->plateflex==0.1.0) (4.41.1)
Requirement already satisfied: h5py>=2.7.0 in /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages (from pymc3->plateflex==0.1.0) (2.10.0)
Requirement already satisfied: pandas>=0.18.0 in /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages (from pymc3->plateflex==0.1.0) (0.25.3)
Requirement already satisfied: patsy>=0.4.0 in /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages (from pymc3->plateflex==0.1.0) (0.5.1)
Requirement already satisfied: scipy>=0.18.1 in /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages (from pymc3->plateflex==0.1.0) (1.4.1)
Requirement already satisfied: kiwisolver>=1.0.1 in /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages (from matplotlib->plateflex==0.1.0) (1.1.0)
Requirement already satisfied: cycler>=0.10 in /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages (from matplotlib->plateflex==0.1.0) (0.10.0)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages (from matplotlib->plateflex==0.1.0) (2.4.6)
Requirement already satisfied: python-dateutil>=2.1 in /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages (from matplotlib->plateflex==0.1.0) (2.8.1)
Requirement already satisfied: packaging in /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages (from arviz>=0.4.1->pymc3->plateflex==0.1.0) (20.0)
Requirement already satisfied: netcdf4 in /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages (from arviz>=0.4.1->pymc3->plateflex==0.1.0) (1.5.3)
Requirement already satisfied: xarray>=0.11 in /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages (from arviz>=0.4.1->pymc3->plateflex==0.1.0) (0.14.1)
Requirement already satisfied: six>=1.9.0 in /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages (from theano>=1.0.4->pymc3->plateflex==0.1.0) (1.14.0)
Requirement already satisfied: pytz>=2017.2 in /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages (from pandas>=0.18.0->pymc3->plateflex==0.1.0) (2019.3)
Requirement already satisfied: setuptools in /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages (from kiwisolver>=1.0.1->matplotlib->plateflex==0.1.0) (45.1.0.post20200119)
Requirement already satisfied: cftime in /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages (from netcdf4->arviz>=0.4.1->pymc3->plateflex==0.1.0) (1.0.4.2)
Building wheels for collected packages: plateflex
Building wheel for plateflex (setup.py) ... error
ERROR: Command errored out with exit status 1:
command: /space/tg286/miniconda_alt/envs/pflex/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-req-build-4_zm7t8a/setup.py'"'"'; file='"'"'/tmp/pip-req-build-4_zm7t8a/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 /tmp/pip-wheel-bvv4pwnc --python-tag cp37
cwd: /tmp/pip-req-build-4_zm7t8a/
Complete output (114 lines):
running bdist_wheel
running build
running config_cc
unifing config_cc, config, build_clib, build_ext, build commands --compiler options
running config_fc
unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
running build_src
build_src
building extension "plateflex.cpwt" sources
f2py options: []
adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex/fortranobject.c' to sources.
adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex' to include_dirs.
adding 'build/src.linux-x86_64-3.7/plateflex/cpwt-f2pywrappers2.f90' to sources.
building extension "plateflex.flex" sources
f2py options: []
adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex/fortranobject.c' to sources.
adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex' to include_dirs.
adding 'build/src.linux-x86_64-3.7/plateflex/flex-f2pywrappers2.f90' to sources.
build_src: building npy-pkg config files
running build_py
creating build/lib.linux-x86_64-3.7
creating build/lib.linux-x86_64-3.7/plateflex
copying plateflex/estimate.py -> build/lib.linux-x86_64-3.7/plateflex
copying plateflex/init.py -> build/lib.linux-x86_64-3.7/plateflex
copying plateflex/doc.py -> build/lib.linux-x86_64-3.7/plateflex
copying plateflex/classes.py -> build/lib.linux-x86_64-3.7/plateflex
copying plateflex/plotting.py -> build/lib.linux-x86_64-3.7/plateflex
copying plateflex/conf.py -> build/lib.linux-x86_64-3.7/plateflex
creating build/lib.linux-x86_64-3.7/plateflex/examples
copying plateflex/examples/data.zip -> build/lib.linux-x86_64-3.7/plateflex/examples
creating build/lib.linux-x86_64-3.7/plateflex/examples/Notebooks
copying plateflex/examples/Notebooks/Ex2_wavelet_analysis.ipynb -> build/lib.linux-x86_64-3.7/plateflex/examples/Notebooks
copying plateflex/examples/Notebooks/Ex7_full_suite_NW_Pacific.ipynb -> build/lib.linux-x86_64-3.7/plateflex/examples/Notebooks
copying plateflex/examples/Notebooks/Ex5_estimate_flex_parameters_grid.ipynb -> build/lib.linux-x86_64-3.7/plateflex/examples/Notebooks
copying plateflex/examples/Notebooks/Ex1_making_grids.ipynb -> build/lib.linux-x86_64-3.7/plateflex/examples/Notebooks
copying plateflex/examples/Notebooks/Ex3_admittance_coherence.ipynb -> build/lib.linux-x86_64-3.7/plateflex/examples/Notebooks
copying plateflex/examples/Notebooks/Ex4_estimate_flex_parameters_cell.ipynb -> build/lib.linux-x86_64-3.7/plateflex/examples/Notebooks
copying plateflex/examples/Notebooks/Ex6_full_suite_North_America.ipynb -> build/lib.linux-x86_64-3.7/plateflex/examples/Notebooks
running build_ext
customize UnixCCompiler
C compiler: /space/tg286/miniconda_alt/envs/pflex/bin/x86_64-conda_cos6-linux-gnu-cc -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -Wstrict-prototypes -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /space/tg286/miniconda_alt/envs/pflex/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /space/tg286/miniconda_alt/envs/pflex/include -fPIC

creating /tmp/tmpiylvn2_z/tmp
creating /tmp/tmpiylvn2_z/tmp/tmpiylvn2_z
compile options: '-MMD -MF /tmp/tmpiylvn2_z/file.c.d -c'
x86_64-conda_cos6-linux-gnu-cc: /tmp/tmpiylvn2_z/file.c
customize UnixCCompiler using build_ext
get_default_fcompiler: matching types: '['gnu95', 'intel', 'lahey', 'pg', 'absoft', 'nag', 'vast', 'compaq', 'intele', 'intelem', 'gnu', 'g95', 'pathf95', 'nagfor']'
customize Gnu95FCompiler
Found executable /usr/bin/gfortran
Found executable /space/tg286/miniconda_alt/envs/pflex/bin/x86_64-conda_cos6-linux-gnu-ld
Found executable /space/tg286/miniconda_alt/envs/pflex/bin/x86_64-conda_cos6-linux-gnu-ar
Found executable /space/tg286/miniconda_alt/envs/pflex/bin/x86_64-conda_cos6-linux-gnu-ranlib
/space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages/numpy/distutils/fcompiler/init.py:530: UserWarning: LDFLAGS is used as is, not appended to flags already defined by numpy.distutils! Use NPY_DISTUTILS_APPEND_FLAGS=1 to obtain appending behavior instead (this behavior will become default in a future release).
linker_so_flags = self.flag_vars.linker_so
/space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages/numpy/distutils/fcompiler/init.py:540: UserWarning: LDFLAGS is used as is, not appended to flags already defined by numpy.distutils! Use NPY_DISTUTILS_APPEND_FLAGS=1 to obtain appending behavior instead (this behavior will become default in a future release).
linker_exe_flags = self.flag_vars.linker_exe
customize Gnu95FCompiler
customize Gnu95FCompiler using build_ext
building 'plateflex.cpwt' extension
compiling C sources
C compiler: /space/tg286/miniconda_alt/envs/pflex/bin/x86_64-conda_cos6-linux-gnu-cc -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -Wstrict-prototypes -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /space/tg286/miniconda_alt/envs/pflex/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /space/tg286/miniconda_alt/envs/pflex/include -fPIC

creating build/temp.linux-x86_64-3.7/build
creating build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7
creating build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex
creating build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/build
creating build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7
creating build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex
compile options: '-Ibuild/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex -I/space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages/numpy/core/include -I/space/tg286/miniconda_alt/envs/pflex/include/python3.7m -c'
x86_64-conda_cos6-linux-gnu-cc: build/src.linux-x86_64-3.7/plateflex/cpwtmodule.cx86_64-conda_cos6-linux-gnu-cc: build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex/fortranobject.c

In file included from /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1830:0,
from /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex/fortranobject.h:13,
from build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex/fortranobject.c:2:
/space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
#warning "Using deprecated NumPy API, disable it with "
^~~~~~~
In file included from /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1830:0,
from /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex/fortranobject.h:13,
from build/src.linux-x86_64-3.7/plateflex/cpwtmodule.c:16:
/space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
#warning "Using deprecated NumPy API, disable it with "
^~~~~~~
build/src.linux-x86_64-3.7/plateflex/cpwtmodule.c:148:12: warning: 'f2py_size' defined but not used [-Wunused-function]
static int f2py_size(PyArrayObject* var, ...)
^~~~~~~~~
compiling Fortran 90 module sources
creating build/temp.linux-x86_64-3.7/plateflex
Fortran f77 compiler: /usr/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -fPIC -O3 -funroll-loops
Fortran f90 compiler: /usr/bin/gfortran -Wall -g -fno-second-underscore -fPIC -O3 -funroll-loops
Fortran fix compiler: /usr/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -Wall -g -fno-second-underscore -fPIC -O3 -funroll-loops
creating build/temp.linux-x86_64-3.7/src
creating build/temp.linux-x86_64-3.7/src/cpwt
compile options: '-Ibuild/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex -I/space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages/numpy/core/include -I/space/tg286/miniconda_alt/envs/pflex/include/python3.7m -c'
extra options: '-Jbuild/temp.linux-x86_64-3.7/plateflex -Ibuild/temp.linux-x86_64-3.7/plateflex'
gfortran:f90: src/cpwt/cpwt.f90
compiling Fortran sources
Fortran f77 compiler: /usr/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -fPIC -O3 -funroll-loops
Fortran f90 compiler: /usr/bin/gfortran -Wall -g -fno-second-underscore -fPIC -O3 -funroll-loops
Fortran fix compiler: /usr/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -Wall -g -fno-second-underscore -fPIC -O3 -funroll-loops
compile options: '-Ibuild/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex -I/space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages/numpy/core/include -I/space/tg286/miniconda_alt/envs/pflex/include/python3.7m -c'
extra options: '-Jbuild/temp.linux-x86_64-3.7/plateflex -Ibuild/temp.linux-x86_64-3.7/plateflex'
gfortran:f90: src/cpwt/cpwt_sub.f90
gfortran:f90: build/src.linux-x86_64-3.7/plateflex/cpwt-f2pywrappers2.f90
/usr/bin/gfortran -Wall -g -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/space/tg286/miniconda_alt/envs/pflex/lib -Wl,-rpath-link,/space/tg286/miniconda_alt/envs/pflex/lib -L/space/tg286/miniconda_alt/envs/pflex/lib build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex/cpwtmodule.o build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex/fortranobject.o build/temp.linux-x86_64-3.7/src/cpwt/cpwt.o build/temp.linux-x86_64-3.7/src/cpwt/cpwt_sub.o build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex/cpwt-f2pywrappers2.o -L/usr/lib/gcc/x86_64-linux-gnu/7 -L/usr/lib/gcc/x86_64-linux-gnu/7 -lgfortran -lgfortran -o build/lib.linux-x86_64-3.7/plateflex/cpwt.cpython-37m-x86_64-linux-gnu.so
/usr/lib/gcc/x86_64-linux-gnu/7/../../../x86_64-linux-gnu/Scrt1.o: In function _start': (.text+0x20): undefined reference to main'
collect2: error: ld returned 1 exit status
error: Command "/usr/bin/gfortran -Wall -g -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/space/tg286/miniconda_alt/envs/pflex/lib -Wl,-rpath-link,/space/tg286/miniconda_alt/envs/pflex/lib -L/space/tg286/miniconda_alt/envs/pflex/lib build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex/cpwtmodule.o build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex/fortranobject.o build/temp.linux-x86_64-3.7/src/cpwt/cpwt.o build/temp.linux-x86_64-3.7/src/cpwt/cpwt_sub.o build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex/cpwt-f2pywrappers2.o -L/usr/lib/gcc/x86_64-linux-gnu/7 -L/usr/lib/gcc/x86_64-linux-gnu/7 -lgfortran -lgfortran -o build/lib.linux-x86_64-3.7/plateflex/cpwt.cpython-37m-x86_64-linux-gnu.so" failed with exit status 1

ERROR: Failed building wheel for plateflex
Running setup.py clean for plateflex
Failed to build plateflex
Installing collected packages: plateflex
Running setup.py install for plateflex ... error
ERROR: Command errored out with exit status 1:
command: /space/tg286/miniconda_alt/envs/pflex/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-req-build-4_zm7t8a/setup.py'"'"'; file='"'"'/tmp/pip-req-build-4_zm7t8a/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-ka0tb788/install-record.txt --single-version-externally-managed --compile
cwd: /tmp/pip-req-build-4_zm7t8a/
Complete output (114 lines):
running install
running build
running config_cc
unifing config_cc, config, build_clib, build_ext, build commands --compiler options
running config_fc
unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
running build_src
build_src
building extension "plateflex.cpwt" sources
f2py options: []
adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex/fortranobject.c' to sources.
adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex' to include_dirs.
adding 'build/src.linux-x86_64-3.7/plateflex/cpwt-f2pywrappers2.f90' to sources.
building extension "plateflex.flex" sources
f2py options: []
adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex/fortranobject.c' to sources.
adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex' to include_dirs.
adding 'build/src.linux-x86_64-3.7/plateflex/flex-f2pywrappers2.f90' to sources.
build_src: building npy-pkg config files
running build_py
creating build/lib.linux-x86_64-3.7
creating build/lib.linux-x86_64-3.7/plateflex
copying plateflex/estimate.py -> build/lib.linux-x86_64-3.7/plateflex
copying plateflex/init.py -> build/lib.linux-x86_64-3.7/plateflex
copying plateflex/doc.py -> build/lib.linux-x86_64-3.7/plateflex
copying plateflex/classes.py -> build/lib.linux-x86_64-3.7/plateflex
copying plateflex/plotting.py -> build/lib.linux-x86_64-3.7/plateflex
copying plateflex/conf.py -> build/lib.linux-x86_64-3.7/plateflex
creating build/lib.linux-x86_64-3.7/plateflex/examples
copying plateflex/examples/data.zip -> build/lib.linux-x86_64-3.7/plateflex/examples
creating build/lib.linux-x86_64-3.7/plateflex/examples/Notebooks
copying plateflex/examples/Notebooks/Ex2_wavelet_analysis.ipynb -> build/lib.linux-x86_64-3.7/plateflex/examples/Notebooks
copying plateflex/examples/Notebooks/Ex7_full_suite_NW_Pacific.ipynb -> build/lib.linux-x86_64-3.7/plateflex/examples/Notebooks
copying plateflex/examples/Notebooks/Ex5_estimate_flex_parameters_grid.ipynb -> build/lib.linux-x86_64-3.7/plateflex/examples/Notebooks
copying plateflex/examples/Notebooks/Ex1_making_grids.ipynb -> build/lib.linux-x86_64-3.7/plateflex/examples/Notebooks
copying plateflex/examples/Notebooks/Ex3_admittance_coherence.ipynb -> build/lib.linux-x86_64-3.7/plateflex/examples/Notebooks
copying plateflex/examples/Notebooks/Ex4_estimate_flex_parameters_cell.ipynb -> build/lib.linux-x86_64-3.7/plateflex/examples/Notebooks
copying plateflex/examples/Notebooks/Ex6_full_suite_North_America.ipynb -> build/lib.linux-x86_64-3.7/plateflex/examples/Notebooks
running build_ext
customize UnixCCompiler
C compiler: /space/tg286/miniconda_alt/envs/pflex/bin/x86_64-conda_cos6-linux-gnu-cc -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -Wstrict-prototypes -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /space/tg286/miniconda_alt/envs/pflex/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /space/tg286/miniconda_alt/envs/pflex/include -fPIC

creating /tmp/tmp75p4d3k_/tmp
creating /tmp/tmp75p4d3k_/tmp/tmp75p4d3k_
compile options: '-MMD -MF /tmp/tmp75p4d3k_/file.c.d -c'
x86_64-conda_cos6-linux-gnu-cc: /tmp/tmp75p4d3k_/file.c
customize UnixCCompiler using build_ext
get_default_fcompiler: matching types: '['gnu95', 'intel', 'lahey', 'pg', 'absoft', 'nag', 'vast', 'compaq', 'intele', 'intelem', 'gnu', 'g95', 'pathf95', 'nagfor']'
customize Gnu95FCompiler
Found executable /usr/bin/gfortran
Found executable /space/tg286/miniconda_alt/envs/pflex/bin/x86_64-conda_cos6-linux-gnu-ld
Found executable /space/tg286/miniconda_alt/envs/pflex/bin/x86_64-conda_cos6-linux-gnu-ar
Found executable /space/tg286/miniconda_alt/envs/pflex/bin/x86_64-conda_cos6-linux-gnu-ranlib
/space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages/numpy/distutils/fcompiler/__init__.py:530: UserWarning: LDFLAGS is used as is, not appended to flags already defined by numpy.distutils! Use NPY_DISTUTILS_APPEND_FLAGS=1 to obtain appending behavior instead (this behavior will become default in a future release).
  linker_so_flags = self.flag_vars.linker_so
/space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages/numpy/distutils/fcompiler/__init__.py:540: UserWarning: LDFLAGS is used as is, not appended to flags already defined by numpy.distutils! Use NPY_DISTUTILS_APPEND_FLAGS=1 to obtain appending behavior instead (this behavior will become default in a future release).
  linker_exe_flags = self.flag_vars.linker_exe
customize Gnu95FCompiler
customize Gnu95FCompiler using build_ext
building 'plateflex.cpwt' extension
compiling C sources
C compiler: /space/tg286/miniconda_alt/envs/pflex/bin/x86_64-conda_cos6-linux-gnu-cc -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -Wstrict-prototypes -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /space/tg286/miniconda_alt/envs/pflex/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /space/tg286/miniconda_alt/envs/pflex/include -fPIC

creating build/temp.linux-x86_64-3.7/build
creating build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7
creating build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex
creating build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/build
creating build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7
creating build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex
compile options: '-Ibuild/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex -I/space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages/numpy/core/include -I/space/tg286/miniconda_alt/envs/pflex/include/python3.7m -c'
x86_64-conda_cos6-linux-gnu-cc: build/src.linux-x86_64-3.7/plateflex/cpwtmodule.c
x86_64-conda_cos6-linux-gnu-cc: build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex/fortranobject.c
In file included from /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1830:0,
                 from /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex/fortranobject.h:13,
                 from build/src.linux-x86_64-3.7/plateflex/cpwtmodule.c:16:
/space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
 #warning "Using deprecated NumPy API, disable it with " \
  ^~~~~~~
In file included from /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1830:0,
                 from /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex/fortranobject.h:13,
                 from build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex/fortranobject.c:2:
/space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
 #warning "Using deprecated NumPy API, disable it with " \
  ^~~~~~~
build/src.linux-x86_64-3.7/plateflex/cpwtmodule.c:148:12: warning: 'f2py_size' defined but not used [-Wunused-function]
 static int f2py_size(PyArrayObject* var, ...)
            ^~~~~~~~~
compiling Fortran 90 module sources
creating build/temp.linux-x86_64-3.7/plateflex
Fortran f77 compiler: /usr/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -fPIC -O3 -funroll-loops
Fortran f90 compiler: /usr/bin/gfortran -Wall -g -fno-second-underscore -fPIC -O3 -funroll-loops
Fortran fix compiler: /usr/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -Wall -g -fno-second-underscore -fPIC -O3 -funroll-loops
creating build/temp.linux-x86_64-3.7/src
creating build/temp.linux-x86_64-3.7/src/cpwt
compile options: '-Ibuild/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex -I/space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages/numpy/core/include -I/space/tg286/miniconda_alt/envs/pflex/include/python3.7m -c'
extra options: '-Jbuild/temp.linux-x86_64-3.7/plateflex -Ibuild/temp.linux-x86_64-3.7/plateflex'
gfortran:f90: src/cpwt/cpwt.f90
compiling Fortran sources
Fortran f77 compiler: /usr/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -fPIC -O3 -funroll-loops
Fortran f90 compiler: /usr/bin/gfortran -Wall -g -fno-second-underscore -fPIC -O3 -funroll-loops
Fortran fix compiler: /usr/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -Wall -g -fno-second-underscore -fPIC -O3 -funroll-loops
compile options: '-Ibuild/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex -I/space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages/numpy/core/include -I/space/tg286/miniconda_alt/envs/pflex/include/python3.7m -c'
extra options: '-Jbuild/temp.linux-x86_64-3.7/plateflex -Ibuild/temp.linux-x86_64-3.7/plateflex'
gfortran:f90: src/cpwt/cpwt_sub.f90
gfortran:f90: build/src.linux-x86_64-3.7/plateflex/cpwt-f2pywrappers2.f90
/usr/bin/gfortran -Wall -g -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/space/tg286/miniconda_alt/envs/pflex/lib -Wl,-rpath-link,/space/tg286/miniconda_alt/envs/pflex/lib -L/space/tg286/miniconda_alt/envs/pflex/lib build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex/cpwtmodule.o build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex/fortranobject.o build/temp.linux-x86_64-3.7/src/cpwt/cpwt.o build/temp.linux-x86_64-3.7/src/cpwt/cpwt_sub.o build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex/cpwt-f2pywrappers2.o -L/usr/lib/gcc/x86_64-linux-gnu/7 -L/usr/lib/gcc/x86_64-linux-gnu/7 -lgfortran -lgfortran -o build/lib.linux-x86_64-3.7/plateflex/cpwt.cpython-37m-x86_64-linux-gnu.so
/usr/lib/gcc/x86_64-linux-gnu/7/../../../x86_64-linux-gnu/Scrt1.o: In function `_start':
(.text+0x20): undefined reference to `main'
collect2: error: ld returned 1 exit status
error: Command "/usr/bin/gfortran -Wall -g -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/space/tg286/miniconda_alt/envs/pflex/lib -Wl,-rpath-link,/space/tg286/miniconda_alt/envs/pflex/lib -L/space/tg286/miniconda_alt/envs/pflex/lib build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex/cpwtmodule.o build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex/fortranobject.o build/temp.linux-x86_64-3.7/src/cpwt/cpwt.o build/temp.linux-x86_64-3.7/src/cpwt/cpwt_sub.o build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex/cpwt-f2pywrappers2.o -L/usr/lib/gcc/x86_64-linux-gnu/7 -L/usr/lib/gcc/x86_64-linux-gnu/7 -lgfortran -lgfortran -o build/lib.linux-x86_64-3.7/plateflex/cpwt.cpython-37m-x86_64-linux-gnu.so" failed with exit status 1
----------------------------------------

ERROR: Command errored out with exit status 1: /space/tg286/miniconda_alt/envs/pflex/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-req-build-4_zm7t8a/setup.py'"'"'; file='"'"'/tmp/pip-req-build-4_zm7t8a/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-ka0tb788/install-record.txt --single-version-externally-managed --compile Check the logs for full command output.

[paudetseis]

@tmgreenfield1101 Thank you for reporting this. I see that the problem comes from linking the librairies with your system-wide fortran compiler. The installer detected a /usr/bin/gfortran compiler but the f2py librairies seem to be incompatible with the compiler. Here is a quick work around.

To make a clean install, remove the build directory in the PlateFlex folder, then delete the pflex environment: conda env remove --name pflex. Now you can re-create the environment with the requirements and activate it. Before installing the software, I suggest you install the gfortran compiler provided via anaconda, which would ensure the librairies are compatible. Since you are in a conda environment, this won't affect your system-wide gfortran. If you are working on a linux OS, type conda install -c anaconda gfortran_linux-64, or if you are on a Mac OS, type conda install -c anaconda gfortran_osx-64.

Once gfortran is installed in the pflex environment, you can install the software with python -m pip install ..

Let me know if this works.

[tmgreenfield1101]

Thanks for your quick reply. I have followed your instructions but I’ve had no luck I’m afraid. The original error has disappeared, only to be replaced with another. I have included the full command line output below. However, after some extensive googling I ran the command ‘export LDFLAGS+=" -shared"’ before using pip install and everything seems to have compiled correctly. This solution was found here (https://groups.google.com/a/continuum.io/forum/#!topic/anaconda/Xw57CjIcBIU). I don’t necessarily understand it – but I’m happy your package seems to have installed. I’m working remotely at the moment, but when I get back to the UK next week I’ll check everything out more fully. As an aside – I couldn’t get plateflex to install at all on a mac. I am running Catalina at the moment and the main problem appears to be inconsistencies between the gfortran compiler (the homebrew version I’ve install, or the anaconda native version I installed after your initial suggestion) and the system linker (something to do with LLVM?). Even installing the anaconda linker (through ‘conda install binutils’) didn’t produce better results. I suspect this is something wrong with the most recent version of xcode tools and my mac setup overall. But I am not too worried about fixing it as I prefer to work on my desktop linux machine. (pflex) tg286@circinus:/space/tg286/PlateFlex$ python -m pip install . Processing /space/tg286/PlateFlex Requirement already satisfied: numpy>=1.15 in /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages (from plateflex==0.1.0) (1.17.5) Requirement already satisfied: pymc3 in /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages (from plateflex==0.1.0) (3.8) Requirement already satisfied: matplotlib in /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages (from plateflex==0.1.0) (3.1.2) Requirement already satisfied: seaborn in /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages (from plateflex==0.1.0) (0.9.0) Requirement already satisfied: patsy>=0.4.0 in /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages (from pymc3->plateflex==0.1.0) (0.5.1) Requirement already satisfied: scipy>=0.18.1 in /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages (from pymc3->plateflex==0.1.0) (1.4.1) Requirement already satisfied: pandas>=0.18.0 in /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages (from pymc3->plateflex==0.1.0) (0.25.3) Requirement already satisfied: arviz>=0.4.1 in /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages (from pymc3->plateflex==0.1.0) (0.6.1) Requirement already satisfied: h5py>=2.7.0 in /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages (from pymc3->plateflex==0.1.0) (2.10.0) Requirement already satisfied: tqdm>=4.8.4 in /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages (from pymc3->plateflex==0.1.0) (4.42.0) Requirement already satisfied: theano>=1.0.4 in /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages (from pymc3->plateflex==0.1.0) (1.0.4) Requirement already satisfied: python-dateutil>=2.1 in /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages (from matplotlib->plateflex==0.1.0) (2.8.1) Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages (from matplotlib->plateflex==0.1.0) (2.4.6) Requirement already satisfied: kiwisolver>=1.0.1 in /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages (from matplotlib->plateflex==0.1.0) (1.1.0) Requirement already satisfied: cycler>=0.10 in /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages (from matplotlib->plateflex==0.1.0) (0.10.0) Requirement already satisfied: six in /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages (from patsy>=0.4.0->pymc3->plateflex==0.1.0) (1.14.0) Requirement already satisfied: pytz>=2017.2 in /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages (from pandas>=0.18.0->pymc3->plateflex==0.1.0) (2019.3) Requirement already satisfied: xarray>=0.11 in /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages (from arviz>=0.4.1->pymc3->plateflex==0.1.0) (0.14.1) Requirement already satisfied: netcdf4 in /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages (from arviz>=0.4.1->pymc3->plateflex==0.1.0) (1.5.3) Requirement already satisfied: packaging in /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages (from arviz>=0.4.1->pymc3->plateflex==0.1.0) (20.1) Requirement already satisfied: setuptools in /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages (from kiwisolver>=1.0.1->matplotlib->plateflex==0.1.0) (45.1.0.post20200119) Requirement already satisfied: cftime in /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages (from netcdf4->arviz>=0.4.1->pymc3->plateflex==0.1.0) (1.0.4.2) Building wheels for collected packages: plateflex Building wheel for plateflex (setup.py) ... error ERROR: Command errored out with exit status 1: command: /space/tg286/miniconda_alt/envs/pflex/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-req-build-y0zu5db9/setup.py'"'"'; __file__='"'"'/tmp/pip-req-build-y0zu5db9/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 /tmp/pip-wheel-pc662p3z cwd: /tmp/pip-req-build-y0zu5db9/ Complete output (116 lines): running bdist_wheel running build running config_cc unifing config_cc, config, build_clib, build_ext, build commands --compiler options running config_fc unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options running build_src build_src building extension "plateflex.cpwt" sources f2py options: [] adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex/fortranobject.c' to sources. adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex' to include_dirs. adding 'build/src.linux-x86_64-3.7/plateflex/cpwt-f2pywrappers2.f90' to sources. building extension "plateflex.flex" sources f2py options: [] adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex/fortranobject.c' to sources. adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex' to include_dirs. adding 'build/src.linux-x86_64-3.7/plateflex/flex-f2pywrappers2.f90' to sources. build_src: building npy-pkg config files running build_py creating build/lib.linux-x86_64-3.7 creating build/lib.linux-x86_64-3.7/plateflex copying plateflex/estimate.py -> build/lib.linux-x86_64-3.7/plateflex copying plateflex/__init__.py -> build/lib.linux-x86_64-3.7/plateflex copying plateflex/doc.py -> build/lib.linux-x86_64-3.7/plateflex copying plateflex/classes.py -> build/lib.linux-x86_64-3.7/plateflex copying plateflex/plotting.py -> build/lib.linux-x86_64-3.7/plateflex copying plateflex/conf.py -> build/lib.linux-x86_64-3.7/plateflex creating build/lib.linux-x86_64-3.7/plateflex/examples copying plateflex/examples/data.zip -> build/lib.linux-x86_64-3.7/plateflex/examples creating build/lib.linux-x86_64-3.7/plateflex/examples/Notebooks copying plateflex/examples/Notebooks/Ex2_wavelet_analysis.ipynb -> build/lib.linux-x86_64-3.7/plateflex/examples/Notebooks copying plateflex/examples/Notebooks/Ex7_full_suite_NW_Pacific.ipynb -> build/lib.linux-x86_64-3.7/plateflex/examples/Notebooks copying plateflex/examples/Notebooks/Ex5_estimate_flex_parameters_grid.ipynb -> build/lib.linux-x86_64-3.7/plateflex/examples/Notebooks copying plateflex/examples/Notebooks/Ex1_making_grids.ipynb -> build/lib.linux-x86_64-3.7/plateflex/examples/Notebooks copying plateflex/examples/Notebooks/Ex3_admittance_coherence.ipynb -> build/lib.linux-x86_64-3.7/plateflex/examples/Notebooks copying plateflex/examples/Notebooks/Ex4_estimate_flex_parameters_cell.ipynb -> build/lib.linux-x86_64-3.7/plateflex/examples/Notebooks copying plateflex/examples/Notebooks/Ex6_full_suite_North_America.ipynb -> build/lib.linux-x86_64-3.7/plateflex/examples/Notebooks running build_ext customize UnixCCompiler C compiler: /space/tg286/miniconda_alt/envs/pflex/bin/x86_64-conda_cos6-linux-gnu-cc -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -Wstrict-prototypes -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /space/tg286/miniconda_alt/envs/pflex/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /space/tg286/miniconda_alt/envs/pflex/include -fPIC creating /tmp/tmpvr9iyakc/tmp creating /tmp/tmpvr9iyakc/tmp/tmpvr9iyakc compile options: '-MMD -MF /tmp/tmpvr9iyakc/file.c.d -c' x86_64-conda_cos6-linux-gnu-cc: /tmp/tmpvr9iyakc/file.c customize UnixCCompiler using build_ext get_default_fcompiler: matching types: '['gnu95', 'intel', 'lahey', 'pg', 'absoft', 'nag', 'vast', 'compaq', 'intele', 'intelem', 'gnu', 'g95', 'pathf95', 'nagfor']' customize Gnu95FCompiler Found executable /space/tg286/miniconda_alt/envs/pflex/bin/x86_64-conda_cos6-linux-gnu-gfortran Found executable /space/tg286/miniconda_alt/envs/pflex/bin/x86_64-conda_cos6-linux-gnu-ld Found executable /space/tg286/miniconda_alt/envs/pflex/bin/x86_64-conda_cos6-linux-gnu-ar Found executable /space/tg286/miniconda_alt/envs/pflex/bin/x86_64-conda_cos6-linux-gnu-ranlib /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages/numpy/distutils/fcompiler/__init__.py:517: UserWarning: FFLAGS is used as is, not appended to flags already defined by numpy.distutils! Use NPY_DISTUTILS_APPEND_FLAGS=1 to obtain appending behavior instead (this behavior will become default in a future release). fflags = self.flag_vars.flags + dflags + oflags + aflags /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages/numpy/distutils/fcompiler/__init__.py:530: UserWarning: LDFLAGS is used as is, not appended to flags already defined by numpy.distutils! Use NPY_DISTUTILS_APPEND_FLAGS=1 to obtain appending behavior instead (this behavior will become default in a future release). linker_so_flags = self.flag_vars.linker_so /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages/numpy/distutils/fcompiler/__init__.py:540: UserWarning: LDFLAGS is used as is, not appended to flags already defined by numpy.distutils! Use NPY_DISTUTILS_APPEND_FLAGS=1 to obtain appending behavior instead (this behavior will become default in a future release). linker_exe_flags = self.flag_vars.linker_exe customize Gnu95FCompiler customize Gnu95FCompiler using build_ext building 'plateflex.cpwt' extension compiling C sources C compiler: /space/tg286/miniconda_alt/envs/pflex/bin/x86_64-conda_cos6-linux-gnu-cc -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -Wstrict-prototypes -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /space/tg286/miniconda_alt/envs/pflex/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /space/tg286/miniconda_alt/envs/pflex/include -fPIC creating build/temp.linux-x86_64-3.7/build creating build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7 creating build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex creating build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/build creating build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7 creating build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex compile options: '-Ibuild/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex -I/space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages/numpy/core/include -I/space/tg286/miniconda_alt/envs/pflex/include/python3.7m -c' x86_64-conda_cos6-linux-gnu-cc: build/src.linux-x86_64-3.7/plateflex/cpwtmodule.cx86_64-conda_cos6-linux-gnu-cc: build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex/fortranobject.c In file included from /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1830:0, from /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex/fortranobject.h:13, from build/src.linux-x86_64-3.7/plateflex/cpwtmodule.c:16: /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ In file included from /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1830:0, from /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex/fortranobject.h:13, from build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex/fortranobject.c:2: /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ build/src.linux-x86_64-3.7/plateflex/cpwtmodule.c:148:12: warning: 'f2py_size' defined but not used [-Wunused-function] static int f2py_size(PyArrayObject* var, ...) ^~~~~~~~~ compiling Fortran 90 module sources creating build/temp.linux-x86_64-3.7/plateflex Fortran f77 compiler: /space/tg286/miniconda_alt/envs/pflex/bin/x86_64-conda_cos6-linux-gnu-gfortran -Wall -g -ffixed-form -fno-second-underscore -fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /space/tg286/miniconda_alt/envs/pflex/include -O3 -funroll-loops Fortran f90 compiler: /space/tg286/miniconda_alt/envs/pflex/bin/x86_64-conda_cos6-linux-gnu-gfortran -Wall -g -fno-second-underscore -fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /space/tg286/miniconda_alt/envs/pflex/include -O3 -funroll-loops Fortran fix compiler: /space/tg286/miniconda_alt/envs/pflex/bin/x86_64-conda_cos6-linux-gnu-gfortran -Wall -g -ffixed-form -fno-second-underscore -Wall -g -fno-second-underscore -fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /space/tg286/miniconda_alt/envs/pflex/include -O3 -funroll-loops creating build/temp.linux-x86_64-3.7/src creating build/temp.linux-x86_64-3.7/src/cpwt compile options: '-Ibuild/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex -I/space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages/numpy/core/include -I/space/tg286/miniconda_alt/envs/pflex/include/python3.7m -c' extra options: '-Jbuild/temp.linux-x86_64-3.7/plateflex -Ibuild/temp.linux-x86_64-3.7/plateflex' x86_64-conda_cos6-linux-gnu-gfortran:f90: src/cpwt/cpwt.f90 compiling Fortran sources Fortran f77 compiler: /space/tg286/miniconda_alt/envs/pflex/bin/x86_64-conda_cos6-linux-gnu-gfortran -Wall -g -ffixed-form -fno-second-underscore -fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /space/tg286/miniconda_alt/envs/pflex/include -O3 -funroll-loops Fortran f90 compiler: /space/tg286/miniconda_alt/envs/pflex/bin/x86_64-conda_cos6-linux-gnu-gfortran -Wall -g -fno-second-underscore -fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /space/tg286/miniconda_alt/envs/pflex/include -O3 -funroll-loops Fortran fix compiler: /space/tg286/miniconda_alt/envs/pflex/bin/x86_64-conda_cos6-linux-gnu-gfortran -Wall -g -ffixed-form -fno-second-underscore -Wall -g -fno-second-underscore -fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /space/tg286/miniconda_alt/envs/pflex/include -O3 -funroll-loops compile options: '-Ibuild/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex -I/space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages/numpy/core/include -I/space/tg286/miniconda_alt/envs/pflex/include/python3.7m -c' extra options: '-Jbuild/temp.linux-x86_64-3.7/plateflex -Ibuild/temp.linux-x86_64-3.7/plateflex' x86_64-conda_cos6-linux-gnu-gfortran:f90: src/cpwt/cpwt_sub.f90 x86_64-conda_cos6-linux-gnu-gfortran:f90: build/src.linux-x86_64-3.7/plateflex/cpwt-f2pywrappers2.f90 /space/tg286/miniconda_alt/envs/pflex/bin/x86_64-conda_cos6-linux-gnu-gfortran -Wall -g -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/space/tg286/miniconda_alt/envs/pflex/lib -Wl,-rpath-link,/space/tg286/miniconda_alt/envs/pflex/lib -L/space/tg286/miniconda_alt/envs/pflex/lib build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex/cpwtmodule.o build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex/fortranobject.o build/temp.linux-x86_64-3.7/src/cpwt/cpwt.o build/temp.linux-x86_64-3.7/src/cpwt/cpwt_sub.o build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex/cpwt-f2pywrappers2.o -L/space/tg286/miniconda_alt/envs/pflex/bin/../x86_64-conda_cos6-linux-gnu/sysroot/lib/../lib -L/space/tg286/miniconda_alt/envs/pflex/bin/../x86_64-conda_cos6-linux-gnu/sysroot/lib/../lib -lgfortran -lgfortran -o build/lib.linux-x86_64-3.7/plateflex/cpwt.cpython-37m-x86_64-linux-gnu.so /space/tg286/miniconda_alt/envs/pflex/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /space/tg286/miniconda_alt/envs/pflex/bin/../x86_64-conda_cos6-linux-gnu/sysroot/usr/lib/../lib/Scrt1.o: in function `_start': /home/conda/feedstock_root/build_artifacts/ctng-compilers_1578638345833/work/.build/src/glibc-2.12.2/csu/../sysdeps/x86_64/elf/start.S:99: undefined reference to `main' collect2: error: ld returned 1 exit status error: Command "/space/tg286/miniconda_alt/envs/pflex/bin/x86_64-conda_cos6-linux-gnu-gfortran -Wall -g -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/space/tg286/miniconda_alt/envs/pflex/lib -Wl,-rpath-link,/space/tg286/miniconda_alt/envs/pflex/lib -L/space/tg286/miniconda_alt/envs/pflex/lib build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex/cpwtmodule.o build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex/fortranobject.o build/temp.linux-x86_64-3.7/src/cpwt/cpwt.o build/temp.linux-x86_64-3.7/src/cpwt/cpwt_sub.o build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex/cpwt-f2pywrappers2.o -L/space/tg286/miniconda_alt/envs/pflex/bin/../x86_64-conda_cos6-linux-gnu/sysroot/lib/../lib -L/space/tg286/miniconda_alt/envs/pflex/bin/../x86_64-conda_cos6-linux-gnu/sysroot/lib/../lib -lgfortran -lgfortran -o build/lib.linux-x86_64-3.7/plateflex/cpwt.cpython-37m-x86_64-linux-gnu.so" failed with exit status 1

…

---------------------------------------- ERROR: Failed building wheel for plateflex Running setup.py clean for plateflex Failed to build plateflex Installing collected packages: plateflex Running setup.py install for plateflex ... error ERROR: Command errored out with exit status 1: command: /space/tg286/miniconda_alt/envs/pflex/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-req-build-y0zu5db9/setup.py'"'"'; __file__='"'"'/tmp/pip-req-build-y0zu5db9/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-8wuhf96u/install-record.txt --single-version-externally-managed --compile --install-headers /space/tg286/miniconda_alt/envs/pflex/include/python3.7m/plateflex cwd: /tmp/pip-req-build-y0zu5db9/ Complete output (116 lines): running install running build running config_cc unifing config_cc, config, build_clib, build_ext, build commands --compiler options running config_fc unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options running build_src build_src building extension "plateflex.cpwt" sources f2py options: [] adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex/fortranobject.c' to sources. adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex' to include_dirs. adding 'build/src.linux-x86_64-3.7/plateflex/cpwt-f2pywrappers2.f90' to sources. building extension "plateflex.flex" sources f2py options: [] adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex/fortranobject.c' to sources. adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex' to include_dirs. adding 'build/src.linux-x86_64-3.7/plateflex/flex-f2pywrappers2.f90' to sources. build_src: building npy-pkg config files running build_py creating build/lib.linux-x86_64-3.7 creating build/lib.linux-x86_64-3.7/plateflex copying plateflex/estimate.py -> build/lib.linux-x86_64-3.7/plateflex copying plateflex/__init__.py -> build/lib.linux-x86_64-3.7/plateflex copying plateflex/doc.py -> build/lib.linux-x86_64-3.7/plateflex copying plateflex/classes.py -> build/lib.linux-x86_64-3.7/plateflex copying plateflex/plotting.py -> build/lib.linux-x86_64-3.7/plateflex copying plateflex/conf.py -> build/lib.linux-x86_64-3.7/plateflex creating build/lib.linux-x86_64-3.7/plateflex/examples copying plateflex/examples/data.zip -> build/lib.linux-x86_64-3.7/plateflex/examples creating build/lib.linux-x86_64-3.7/plateflex/examples/Notebooks copying plateflex/examples/Notebooks/Ex2_wavelet_analysis.ipynb -> build/lib.linux-x86_64-3.7/plateflex/examples/Notebooks copying plateflex/examples/Notebooks/Ex7_full_suite_NW_Pacific.ipynb -> build/lib.linux-x86_64-3.7/plateflex/examples/Notebooks copying plateflex/examples/Notebooks/Ex5_estimate_flex_parameters_grid.ipynb -> build/lib.linux-x86_64-3.7/plateflex/examples/Notebooks copying plateflex/examples/Notebooks/Ex1_making_grids.ipynb -> build/lib.linux-x86_64-3.7/plateflex/examples/Notebooks copying plateflex/examples/Notebooks/Ex3_admittance_coherence.ipynb -> build/lib.linux-x86_64-3.7/plateflex/examples/Notebooks copying plateflex/examples/Notebooks/Ex4_estimate_flex_parameters_cell.ipynb -> build/lib.linux-x86_64-3.7/plateflex/examples/Notebooks copying plateflex/examples/Notebooks/Ex6_full_suite_North_America.ipynb -> build/lib.linux-x86_64-3.7/plateflex/examples/Notebooks running build_ext customize UnixCCompiler C compiler: /space/tg286/miniconda_alt/envs/pflex/bin/x86_64-conda_cos6-linux-gnu-cc -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -Wstrict-prototypes -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /space/tg286/miniconda_alt/envs/pflex/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /space/tg286/miniconda_alt/envs/pflex/include -fPIC creating /tmp/tmpeowhicoz/tmp creating /tmp/tmpeowhicoz/tmp/tmpeowhicoz compile options: '-MMD -MF /tmp/tmpeowhicoz/file.c.d -c' x86_64-conda_cos6-linux-gnu-cc: /tmp/tmpeowhicoz/file.c customize UnixCCompiler using build_ext get_default_fcompiler: matching types: '['gnu95', 'intel', 'lahey', 'pg', 'absoft', 'nag', 'vast', 'compaq', 'intele', 'intelem', 'gnu', 'g95', 'pathf95', 'nagfor']' customize Gnu95FCompiler Found executable /space/tg286/miniconda_alt/envs/pflex/bin/x86_64-conda_cos6-linux-gnu-gfortran Found executable /space/tg286/miniconda_alt/envs/pflex/bin/x86_64-conda_cos6-linux-gnu-ld Found executable /space/tg286/miniconda_alt/envs/pflex/bin/x86_64-conda_cos6-linux-gnu-ar Found executable /space/tg286/miniconda_alt/envs/pflex/bin/x86_64-conda_cos6-linux-gnu-ranlib /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages/numpy/distutils/fcompiler/__init__.py:517: UserWarning: FFLAGS is used as is, not appended to flags already defined by numpy.distutils! Use NPY_DISTUTILS_APPEND_FLAGS=1 to obtain appending behavior instead (this behavior will become default in a future release). fflags = self.flag_vars.flags + dflags + oflags + aflags /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages/numpy/distutils/fcompiler/__init__.py:530: UserWarning: LDFLAGS is used as is, not appended to flags already defined by numpy.distutils! Use NPY_DISTUTILS_APPEND_FLAGS=1 to obtain appending behavior instead (this behavior will become default in a future release). linker_so_flags = self.flag_vars.linker_so /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages/numpy/distutils/fcompiler/__init__.py:540: UserWarning: LDFLAGS is used as is, not appended to flags already defined by numpy.distutils! Use NPY_DISTUTILS_APPEND_FLAGS=1 to obtain appending behavior instead (this behavior will become default in a future release). linker_exe_flags = self.flag_vars.linker_exe customize Gnu95FCompiler customize Gnu95FCompiler using build_ext building 'plateflex.cpwt' extension compiling C sources C compiler: /space/tg286/miniconda_alt/envs/pflex/bin/x86_64-conda_cos6-linux-gnu-cc -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -Wstrict-prototypes -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /space/tg286/miniconda_alt/envs/pflex/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /space/tg286/miniconda_alt/envs/pflex/include -fPIC creating build/temp.linux-x86_64-3.7/build creating build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7 creating build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex creating build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/build creating build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7 creating build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex compile options: '-Ibuild/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex -I/space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages/numpy/core/include -I/space/tg286/miniconda_alt/envs/pflex/include/python3.7m -c' x86_64-conda_cos6-linux-gnu-cc: build/src.linux-x86_64-3.7/plateflex/cpwtmodule.c x86_64-conda_cos6-linux-gnu-cc: build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex/fortranobject.c In file included from /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1830:0, from /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex/fortranobject.h:13, from build/src.linux-x86_64-3.7/plateflex/cpwtmodule.c:16: /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ In file included from /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1830:0, from /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex/fortranobject.h:13, from build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex/fortranobject.c:2: /space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ build/src.linux-x86_64-3.7/plateflex/cpwtmodule.c:148:12: warning: 'f2py_size' defined but not used [-Wunused-function] static int f2py_size(PyArrayObject* var, ...) ^~~~~~~~~ compiling Fortran 90 module sources creating build/temp.linux-x86_64-3.7/plateflex Fortran f77 compiler: /space/tg286/miniconda_alt/envs/pflex/bin/x86_64-conda_cos6-linux-gnu-gfortran -Wall -g -ffixed-form -fno-second-underscore -fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /space/tg286/miniconda_alt/envs/pflex/include -O3 -funroll-loops Fortran f90 compiler: /space/tg286/miniconda_alt/envs/pflex/bin/x86_64-conda_cos6-linux-gnu-gfortran -Wall -g -fno-second-underscore -fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /space/tg286/miniconda_alt/envs/pflex/include -O3 -funroll-loops Fortran fix compiler: /space/tg286/miniconda_alt/envs/pflex/bin/x86_64-conda_cos6-linux-gnu-gfortran -Wall -g -ffixed-form -fno-second-underscore -Wall -g -fno-second-underscore -fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /space/tg286/miniconda_alt/envs/pflex/include -O3 -funroll-loops creating build/temp.linux-x86_64-3.7/src creating build/temp.linux-x86_64-3.7/src/cpwt compile options: '-Ibuild/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex -I/space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages/numpy/core/include -I/space/tg286/miniconda_alt/envs/pflex/include/python3.7m -c' extra options: '-Jbuild/temp.linux-x86_64-3.7/plateflex -Ibuild/temp.linux-x86_64-3.7/plateflex' x86_64-conda_cos6-linux-gnu-gfortran:f90: src/cpwt/cpwt.f90 compiling Fortran sources Fortran f77 compiler: /space/tg286/miniconda_alt/envs/pflex/bin/x86_64-conda_cos6-linux-gnu-gfortran -Wall -g -ffixed-form -fno-second-underscore -fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /space/tg286/miniconda_alt/envs/pflex/include -O3 -funroll-loops Fortran f90 compiler: /space/tg286/miniconda_alt/envs/pflex/bin/x86_64-conda_cos6-linux-gnu-gfortran -Wall -g -fno-second-underscore -fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /space/tg286/miniconda_alt/envs/pflex/include -O3 -funroll-loops Fortran fix compiler: /space/tg286/miniconda_alt/envs/pflex/bin/x86_64-conda_cos6-linux-gnu-gfortran -Wall -g -ffixed-form -fno-second-underscore -Wall -g -fno-second-underscore -fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /space/tg286/miniconda_alt/envs/pflex/include -O3 -funroll-loops compile options: '-Ibuild/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex -I/space/tg286/miniconda_alt/envs/pflex/lib/python3.7/site-packages/numpy/core/include -I/space/tg286/miniconda_alt/envs/pflex/include/python3.7m -c' extra options: '-Jbuild/temp.linux-x86_64-3.7/plateflex -Ibuild/temp.linux-x86_64-3.7/plateflex' x86_64-conda_cos6-linux-gnu-gfortran:f90: src/cpwt/cpwt_sub.f90 x86_64-conda_cos6-linux-gnu-gfortran:f90: build/src.linux-x86_64-3.7/plateflex/cpwt-f2pywrappers2.f90 /space/tg286/miniconda_alt/envs/pflex/bin/x86_64-conda_cos6-linux-gnu-gfortran -Wall -g -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/space/tg286/miniconda_alt/envs/pflex/lib -Wl,-rpath-link,/space/tg286/miniconda_alt/envs/pflex/lib -L/space/tg286/miniconda_alt/envs/pflex/lib build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex/cpwtmodule.o build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex/fortranobject.o build/temp.linux-x86_64-3.7/src/cpwt/cpwt.o build/temp.linux-x86_64-3.7/src/cpwt/cpwt_sub.o build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex/cpwt-f2pywrappers2.o -L/space/tg286/miniconda_alt/envs/pflex/bin/../x86_64-conda_cos6-linux-gnu/sysroot/lib/../lib -L/space/tg286/miniconda_alt/envs/pflex/bin/../x86_64-conda_cos6-linux-gnu/sysroot/lib/../lib -lgfortran -lgfortran -o build/lib.linux-x86_64-3.7/plateflex/cpwt.cpython-37m-x86_64-linux-gnu.so /space/tg286/miniconda_alt/envs/pflex/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /space/tg286/miniconda_alt/envs/pflex/bin/../x86_64-conda_cos6-linux-gnu/sysroot/usr/lib/../lib/Scrt1.o: in function `_start': /home/conda/feedstock_root/build_artifacts/ctng-compilers_1578638345833/work/.build/src/glibc-2.12.2/csu/../sysdeps/x86_64/elf/start.S:99: undefined reference to `main' collect2: error: ld returned 1 exit status error: Command "/space/tg286/miniconda_alt/envs/pflex/bin/x86_64-conda_cos6-linux-gnu-gfortran -Wall -g -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/space/tg286/miniconda_alt/envs/pflex/lib -Wl,-rpath-link,/space/tg286/miniconda_alt/envs/pflex/lib -L/space/tg286/miniconda_alt/envs/pflex/lib build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex/cpwtmodule.o build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex/fortranobject.o build/temp.linux-x86_64-3.7/src/cpwt/cpwt.o build/temp.linux-x86_64-3.7/src/cpwt/cpwt_sub.o build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/plateflex/cpwt-f2pywrappers2.o -L/space/tg286/miniconda_alt/envs/pflex/bin/../x86_64-conda_cos6-linux-gnu/sysroot/lib/../lib -L/space/tg286/miniconda_alt/envs/pflex/bin/../x86_64-conda_cos6-linux-gnu/sysroot/lib/../lib -lgfortran -lgfortran -o build/lib.linux-x86_64-3.7/plateflex/cpwt.cpython-37m-x86_64-linux-gnu.so" failed with exit status 1

---------------------------------------- ERROR: Command errored out with exit status 1: /space/tg286/miniconda_alt/envs/pflex/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-req-build-y0zu5db9/setup.py'"'"'; __file__='"'"'/tmp/pip-req-build-y0zu5db9/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-8wuhf96u/install-record.txt --single-version-externally-managed --compile --install-headers /space/tg286/miniconda_alt/envs/pflex/include/python3.7m/plateflex Check the logs for full command output.

-------------------------------------------------- Dr. Tim Greenfield Postdoctoral Research Associate Department of Earth Sciences University of Cambridge tg286@cam.ac.uk From: Pascal Audet <notifications@github.com> Reply to: paudetseis/PlateFlex <reply@reply.github.com> Date: Wednesday, 29 January 2020 at 05:48 To: paudetseis/PlateFlex <PlateFlex@noreply.github.com> Cc: Tim Greenfield <tg286@cam.ac.uk>, Mention <mention@noreply.github.com> Subject: Re: [paudetseis/PlateFlex] Problems Installing (#2) @tmgreenfield1101<https://github.com/tmgreenfield1101> Thank you for reporting this. I see that the problem comes from linking the librairies with your system-wide fortran compiler. The installer detected a /usr/bin/gfortran compiler but the f2py librairies seem to be incompatible with the compiler. Here is a quick work around. To make a clean install, remove the build directory in the PlateFlex folder, then delete the pflex environment: conda env remove --name pflex. Now you can re-create the environment with the requirements and activate it. Before installing the software, I suggest you install the gfortran compiler provided via anaconda, which would ensure the librairies are compatible. Since you are in a conda environment, this won't affect your system-wide gfortran. If you are working on a linux OS, type conda install -c anaconda gfortran_linux-64, or if you are on a Mac OS, type conda install -c anaconda gfortran_osx-64. Once gfortran is installed in the pflex environment, you can install the software with python -m pip install .. Let me know if this works. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub<#2?email_source=notifications&email_token=ALXCVON7FIIZSXXRMBWJ4I3RACY3BA5CNFSM4KMLEDBKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEKFIMVY#issuecomment-579503703>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ALXCVOICIDDUZFX2BGEZ3UDRACY3BANCNFSM4KMLEDBA>.

[ijaodola]

Hello Prof., Pascal Audet, nice to write you on this plateform. I have read your papers on Te and others such as Kirby, Perez-Gussinye and a lot of others. The multitaper and wavelet software suite for Te estimation looks easier to run and debug on the cygwin terminal but going through this new software you developed is very much complex to me. I can't even get my bearing from the suite to installation to input and plotting. In a more detailed steps, how can I use this method for Te estimation on my Cygwin or Fedora terminal. Am very much curious about this methodology. I need help as a young researcher. I am used to cygwin mainly and you commented that it can work on cgywin but am extremely very confused and worried. Your great help will go a long way for we young researchers. Many thanks.

@tmgreenfield1101 Thank you for reporting this. I see that the problem comes from linking the librairies with your system-wide fortran compiler. The installer detected a /usr/bin/gfortran compiler but the f2py librairies seem to be incompatible with the compiler. Here is a quick work around.

To make a clean install, remove the build directory in the PlateFlex folder, then delete the pflex environment: conda env remove --name pflex. Now you can re-create the environment with the requirements and activate it. Before installing the software, I suggest you install the gfortran compiler provided via anaconda, which would ensure the librairies are compatible. Since you are in a conda environment, this won't affect your system-wide gfortran. If you are working on a linux OS, type conda install -c anaconda gfortran_linux-64, or if you are on a Mac OS, type conda install -c anaconda gfortran_osx-64.

Once gfortran is installed in the pflex environment, you can install the software with python -m pip install ..

Let me know if this works.

Hello Prof., Pascal Audet, nice to write you on this plateform. I have read your papers on Te and others such as Kirby, Perez-Gussinye and a lot of others. The multitaper and wavelet software suite for Te estimation looks easier to run and debug on the cygwin terminal but going through this new software you developed is very much complex to me. I can't even get my bearing from the suite to installation to input and plotting. In a more detailed steps, how can I use this method for Te estimation on my Cygwin or Fedora terminal. Am very much curious about this methodology. I need help as a young researcher. I am used to cygwin mainly and you commented that it can work on cgywin but am extremely very confused and worried. Your great help will go a long way for we young researchers. Many thanks.

[ijaodola]

Hello Prof., Pascal Audet, nice to write you on this plateform. I have read your papers on Te and others such as Kirby, Perez-Gussinye and a lot of others. The multitaper and wavelet software suite for Te estimation looks easier to run and debug on the cygwin terminal but going through this new software you developed is very much complex to me. I can't even get my bearing from the suite to installation to input and plotting. In a more detailed steps, how can I use this method for Te estimation on my Cygwin or Fedora terminal. Am very much curious about this methodology. I need help as a young researcher. I am used to cygwin mainly and you commented that it can work on cgywin but am extremely very confused and worried. Your great help will go a long way for we young researchers. Many thanks.