Hi, I'm trying to install pyroms on ubuntu in a virtual box machine. I followed the installation steps but had the following error when I tried "pip install -e pyroms/pyroms". I need help diagnosing this error:
Installed /home/jkansong/pyroms/pyroms
running develop
running build_scripts
running egg_info
running build_src
build_src
building extension "pyroms._interp" sources
f2py options: []
adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/pyroms/fortranobject.c' to sources.
adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/pyroms' to include_dirs.
building extension "pyroms._obs_interp" sources
f2py options: []
adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/pyroms/fortranobject.c' to sources.
adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/pyroms' to include_dirs.
adding 'build/src.linux-x86_64-3.7/pyroms/_obs_interp-f2pywrappers.f' to sources.
building extension "pyroms._remapping" sources
f2py options: []
adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/pyroms/fortranobject.c' to sources.
adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/pyroms' to include_dirs.
building extension "pyroms._remapping_fast" sources
f2py options: []
adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/pyroms/fortranobject.c' to sources.
adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/pyroms' to include_dirs.
building extension "pyroms._remapping_fast_weighted" sources
f2py options: []
adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/pyroms/fortranobject.c' to sources.
adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/pyroms' to include_dirs.
building extension "pyroms._iso" sources
f2py options: []
adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/pyroms/fortranobject.c' to sources.
adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/pyroms' to include_dirs.
build_src: building npy-pkg config files
writing pyroms.egg-info/PKG-INFO
writing dependency_links to pyroms.egg-info/dependency_links.txt
writing top-level names to pyroms.egg-info/top_level.txt
reading manifest file 'pyroms.egg-info/SOURCES.txt'
writing manifest file 'pyroms.egg-info/SOURCES.txt'
running build_ext
customize UnixCCompiler
C compiler: /home/jkansong/anaconda3/envs/python3/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 -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -fPIC
creating /tmp/tmp9h6jcc5h/tmp
creating /tmp/tmp9h6jcc5h/tmp/tmp9h6jcc5h
compile options: '-MMD -MF /tmp/tmp9h6jcc5h/file.c.d -c'
x86_64-conda_cos6-linux-gnu-cc: /tmp/tmp9h6jcc5h/file.c
customize UnixCCompiler using build_ext
get_default_fcompiler: matching types: '['gnu95', 'intel', 'lahey', 'pg', 'nv', 'absoft', 'nag', 'vast', 'compaq', 'intele', 'intelem', 'gnu', 'g95', 'pathf95', 'nagfor']'
customize Gnu95FCompiler
Found executable /home/jkansong/anaconda3/envs/python3/bin/x86_64-conda_cos6-linux-gnu-gfortran
Found executable /home/jkansong/anaconda3/envs/python3/bin/x86_64-conda_cos6-linux-gnu-ld
Found executable /home/jkansong/anaconda3/envs/python3/bin/x86_64-conda_cos6-linux-gnu-ar
Found executable /home/jkansong/anaconda3/envs/python3/bin/x86_64-conda_cos6-linux-gnu-ranlib
customize Gnu95FCompiler
customize Gnu95FCompiler using build_ext
building 'pyroms._interp' extension
compiling C sources
C compiler: /home/jkansong/anaconda3/envs/python3/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 -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -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/pyroms
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/pyroms
compile options: '-Ibuild/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/pyroms -I/home/jkansong/anaconda3/envs/python3/lib/python3.7/site-packages/numpy/core/include -I/home/jkansong/anaconda3/envs/python3/include/python3.7m -I/home/jkansong/anaconda3/envs/python3/include/python3.7m -c'
x86_64-conda_cos6-linux-gnu-cc: build/src.linux-x86_64-3.7/pyroms/_interpmodule.c
x86_64-conda_cos6-linux-gnu-cc: build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/pyroms/fortranobject.c
In file included from /home/jkansong/anaconda3/envs/python3/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822:0,
from /home/jkansong/anaconda3/envs/python3/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /home/jkansong/anaconda3/envs/python3/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/pyroms/fortranobject.h:13,
from build/src.linux-x86_64-3.7/pyroms/_interpmodule.c:16:
/home/jkansong/anaconda3/envs/python3/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 /home/jkansong/anaconda3/envs/python3/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822:0,
from /home/jkansong/anaconda3/envs/python3/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /home/jkansong/anaconda3/envs/python3/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/pyroms/fortranobject.h:13,
from build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/pyroms/fortranobject.c:2:
/home/jkansong/anaconda3/envs/python3/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/pyroms/_interpmodule.c:109:12: warning: 'f2py_size' defined but not used [-Wunused-function]
static int f2py_size(PyArrayObject* var, ...)
^~~~~~~~~
compiling Fortran sources
Fortran f77 compiler: /home/jkansong/anaconda3/envs/python3/bin/x86_64-conda_cos6-linux-gnu-gfortran -Wall -g -ffixed-form -fno-second-underscore -fPIC -fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -O3 -funroll-loops
Fortran f90 compiler: /home/jkansong/anaconda3/envs/python3/bin/x86_64-conda_cos6-linux-gnu-gfortran -Wall -g -fno-second-underscore -fPIC -fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -O3 -funroll-loops
Fortran fix compiler: /home/jkansong/anaconda3/envs/python3/bin/x86_64-conda_cos6-linux-gnu-gfortran -Wall -g -ffixed-form -fno-second-underscore -Wall -g -fno-second-underscore -fPIC -fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -O3 -funroll-loops
creating build/temp.linux-x86_64-3.7/pyroms
creating build/temp.linux-x86_64-3.7/pyroms/src
compile options: '-Ibuild/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/pyroms -I/home/jkansong/anaconda3/envs/python3/lib/python3.7/site-packages/numpy/core/include -I/home/jkansong/anaconda3/envs/python3/include/python3.7m -I/home/jkansong/anaconda3/envs/python3/include/python3.7m -c'
x86_64-conda_cos6-linux-gnu-gfortran:f77: ./pyroms/src/interp.f
./pyroms/src/interp.f:162:0:
integer i, ii, j, n, ni
Warning: 'ii' may be used uninitialized in this function [-Wmaybe-uninitialized]
/home/jkansong/anaconda3/envs/python3/bin/x86_64-conda_cos6-linux-gnu-gfortran -Wall -g -Wall -g -shared -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/pyroms/_interpmodule.o build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/pyroms/fortranobject.o build/temp.linux-x86_64-3.7/pyroms/src/interp.o -lgfortran -o pyroms/_interp.cpython-37m-x86_64-linux-gnu.so
/home/jkansong/anaconda3/envs/python3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: cannot find -lgfortran
/home/jkansong/anaconda3/envs/python3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: cannot find -lgfortran
collect2: error: ld returned 1 exit status
Warning: distutils distribution has been initialized, it may be too late to add an extension _interp
Warning: distutils distribution has been initialized, it may be too late to add an extension _obs_interp
Warning: distutils distribution has been initialized, it may be too late to add an extension _remapping
Warning: distutils distribution has been initialized, it may be too late to add an extension _remapping_fast
Warning: distutils distribution has been initialized, it may be too late to add an extension _remapping_fast_weighted
Warning: distutils distribution has been initialized, it may be too late to add an extension _iso
error: Command "/home/jkansong/anaconda3/envs/python3/bin/x86_64-conda_cos6-linux-gnu-gfortran -Wall -g -Wall -g -shared -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/pyroms/_interpmodule.o build/temp.linux-x86_64-3.7/build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/pyroms/fortranobject.o build/temp.linux-x86_64-3.7/pyroms/src/interp.o -lgfortran -o pyroms/_interp.cpython-37m-x86_64-linux-gnu.so" failed with exit status 1
----------------------------------------
ERROR: Command errored out with exit status 1: /home/jkansong/anaconda3/envs/python3/bin/python3.7 -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/home/jkansong/pyroms/pyroms/setup.py'"'"'; file='"'"'/home/jkansong/pyroms/pyroms/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' develop --no-deps Check the logs for full command output.
Hi, I'm trying to install pyroms on ubuntu in a virtual box machine. I followed the installation steps but had the following error when I tried "pip install -e pyroms/pyroms". I need help diagnosing this error:
ERROR: Command errored out with exit status 1: command: /home/jkansong/anaconda3/envs/python3/bin/python3.7 -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/home/jkansong/pyroms/pyroms/setup.py'"'"'; file='"'"'/home/jkansong/pyroms/pyroms/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' develop --no-deps cwd: /home/jkansong/pyroms/pyroms/ Complete output (124 lines): running develop running build_scripts running egg_info running build_src build_src writing pyroms.egg-info/PKG-INFO writing dependency_links to pyroms.egg-info/dependency_links.txt writing top-level names to pyroms.egg-info/top_level.txt reading manifest file 'pyroms.egg-info/SOURCES.txt' writing manifest file 'pyroms.egg-info/SOURCES.txt' running build_ext Creating /home/jkansong/anaconda3/envs/python3/lib/python3.7/site-packages/pyroms.egg-link (link to .) Adding pyroms 0.2.0 to easy-install.pth file
ERROR: Command errored out with exit status 1: /home/jkansong/anaconda3/envs/python3/bin/python3.7 -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/home/jkansong/pyroms/pyroms/setup.py'"'"'; file='"'"'/home/jkansong/pyroms/pyroms/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' develop --no-deps Check the logs for full command output.
THANK YOU! Joseph K. Ansong