Error installing via pip latest version 1.1.7 on ubuntu

[stoiver]

Just tried to install using pip and obtained the following errors

netCDF4.c:18206:10: error: ‘NC_FORMAT_UNDEFINED’ undeclared (first use in this function) case NC_FORMAT_UNDEFINED:

Was working fine with version 1.1.6

[jswhit]

Apparently, it's not using the correct path to netcdf.h - which should be provided by nc-config. Can you post the full build output?

[stoiver]

On a fairly clean version of ubuntu14.04 I installed the following packages

sudo apt-get install -q -y git gfortran python-dev python-numpy \ python-scipy \ python-matplotlib netcdf-bin \ libnetcdf-dev libhdf5-serial-dev \ python-gdal python-pip

And then

sudo pip install netCDF4

The output from this:

Downloading/unpacking netCDF4 Running setup.py (path:/tmp/pip_build_root/netCDF4/setup.py) egg_info for package netCDF4 using nc-config ... using netcdf library version 4.1.3

Requirement already satisfied (use --upgrade to upgrade): numpy>=1.3 in /usr/lib/python2.7/dist-packages (from netCDF4) Installing collected packages: netCDF4 Running setup.py install for netCDF4 using nc-config ... using netcdf library version 4.1.3 building 'netCDF4' extension x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/usr/include -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c netCDF4.c -o build/temp.linux-x86_64-2.7/netCDF4.o In file included from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1761:0, from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:17, from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4, from netCDF4.c:239: /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]

warning "Using deprecated NumPy API, disable it by " \

  ^
netCDF4.c: In function ‘**pyx_f_7netCDF4__get_full_format’:
netCDF4.c:18003:9: warning: implicit declaration of function ‘nc_inq_format_extended’ [-Wimplicit-function-declaration]
         __pyx_v_ierr = nc_inq_format_extended(__pyx_v_grpid, (&__pyx_v_formatp), (&__pyx_v_modep));
         ^
netCDF4.c:18074:10: error: ‘NC_FORMAT_NC3’ undeclared (first use in this function)
     case NC_FORMAT_NC3:
          ^
netCDF4.c:18074:10: note: each undeclared identifier is reported only once for each function it appears in
netCDF4.c:18096:10: error: ‘NC_FORMAT_NC_HDF5’ undeclared (first use in this function)
     case NC_FORMAT_NC_HDF5:
          ^
netCDF4.c:18118:10: error: ‘NC_FORMAT_NC_HDF4’ undeclared (first use in this function)
     case NC_FORMAT_NC_HDF4:
          ^
netCDF4.c:18140:10: error: ‘NC_FORMAT_PNETCDF’ undeclared (first use in this function)
     case NC_FORMAT_PNETCDF:
          ^
netCDF4.c:18162:10: error: ‘NC_FORMAT_DAP2’ undeclared (first use in this function)
     case NC_FORMAT_DAP2:
          ^
netCDF4.c:18184:10: error: ‘NC_FORMAT_DAP4’ undeclared (first use in this function)
     case NC_FORMAT_DAP4:
          ^
netCDF4.c:18206:10: error: ‘NC_FORMAT_UNDEFINED’ undeclared (first use in this function)
     case NC_FORMAT_UNDEFINED:
          ^
netCDF4.c: In function ‘__pyx_pf_7netCDF4_7Dataset_58renameGroup’:
netCDF4.c:28783:3: warning: implicit declaration of function ‘nc_rename_grp’ [-Wimplicit-function-declaration]
   __pyx_v_ierr = nc_rename_grp(__pyx_t_6, __pyx_v_newnamec);
   ^
error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
Complete output from command /usr/bin/python -c "import setuptools, tokenize;__file**='/tmp/pip_build_root/netCDF4/setup.py';exec(compile(getattr(tokenize, 'open', open)(**file**).read().replace('\r\n', '\n'), **file**, 'exec'))" install --record /tmp/pip-H7egR_-record/install-record.txt --single-version-externally-managed --compile:
reading from setup.cfg...

using nc-config ...

using netcdf library version 4.1.3

running install

running build

running build_py

creating build

creating build/lib.linux-x86_64-2.7

copying netCDF4_utils.py -> build/lib.linux-x86_64-2.7

creating build/lib.linux-x86_64-2.7/netcdftime

copying netcdftime/netcdftime.py -> build/lib.linux-x86_64-2.7/netcdftime

copying netcdftime/init.py -> build/lib.linux-x86_64-2.7/netcdftime

running build_ext

building 'netCDF4' extension

creating build/temp.linux-x86_64-2.7

x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/usr/include -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c netCDF4.c -o build/temp.linux-x86_64-2.7/netCDF4.o

In file included from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1761:0,

             from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:17,

             from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4,

             from netCDF4.c:239:

/usr/lib/python2.7/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]

warning "Using deprecated NumPy API, disable it by " \

^

netCDF4.c: In function ‘pyx_f_7netCDF4get_full_format’:

netCDF4.c:18003:9: warning: implicit declaration of function ‘nc_inq_format_extended’ [-Wimplicit-function-declaration]

     __pyx_v_ierr = nc_inq_format_extended(__pyx_v_grpid, (&__pyx_v_formatp), (&__pyx_v_modep));

     ^

netCDF4.c:18074:10: error: ‘NC_FORMAT_NC3’ undeclared (first use in this function)

 case NC_FORMAT_NC3:

      ^

netCDF4.c:18074:10: note: each undeclared identifier is reported only once for each function it appears in

netCDF4.c:18096:10: error: ‘NC_FORMAT_NC_HDF5’ undeclared (first use in this function)

 case NC_FORMAT_NC_HDF5:

      ^

netCDF4.c:18118:10: error: ‘NC_FORMAT_NC_HDF4’ undeclared (first use in this function)

 case NC_FORMAT_NC_HDF4:

      ^

netCDF4.c:18140:10: error: ‘NC_FORMAT_PNETCDF’ undeclared (first use in this function)

 case NC_FORMAT_PNETCDF:

      ^

netCDF4.c:18162:10: error: ‘NC_FORMAT_DAP2’ undeclared (first use in this function)

 case NC_FORMAT_DAP2:

      ^

netCDF4.c:18184:10: error: ‘NC_FORMAT_DAP4’ undeclared (first use in this function)

 case NC_FORMAT_DAP4:

      ^

netCDF4.c:18206:10: error: ‘NC_FORMAT_UNDEFINED’ undeclared (first use in this function)

 case NC_FORMAT_UNDEFINED:

      ^

netCDF4.c: In function ‘__pyx_pf_7netCDF4_7Dataset_58renameGroup’:

netCDF4.c:28783:3: warning: implicit declaration of function ‘nc_rename_grp’ [-Wimplicit-function-declaration]

pyx_v_ierr = nc_rename_grp(pyx_t_6, __pyx_v_newnamec);

^

error: command 'x86_64-linux-gnu-gcc' failed with exit status 1

---

Cleaning up... Command /usr/bin/python -c "import setuptools, tokenize;file='/tmp/pip_buildroot/netCDF4/setup.py';exec(compile(getattr(tokenize, 'open', open)(file).read().replace('\r\n', '\n'), file, 'exec'))" install --record /tmp/pip-H7egR-record/install-record.txt --single-version-externally-managed --compile failed with error code 1 in /tmp/pip_build_root/netCDF4

Traceback (most recent call last): File "/usr/bin/pip", line 9, in load_entry_point('pip==1.5.4', 'console_scripts', 'pip')() File "/usr/lib/python2.7/dist-packages/pip/init.py", line 185, in main return command.main(cmd_args) File "/usr/lib/python2.7/dist-packages/pip/basecommand.py", line 161, in main text = '\n'.join(complete_log) UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 27: ordinal not in range(128)

[jswhit]

I inadvertently uploaded netCDF-1.1.7 with support for new API features not found in version 4.1.3 of the library. I've fixed this now by uploading a new tarball.

[jswhit]

Note - if you also had cython installed, your build would have worked since it would have auto-detected those library features and regenerated netCDF4.c from netCDF4.pyx.

[toelke]

Version 1.1.7.1 works for me.

[stoiver]

Hi Jeff, yes the new version 1.1.7.1 is now working for me. Thanks