Can't setup 0.7.4 on Windows XP machine

[dopplershift]

From blt...@gmail.com on June 20, 2008 07:52:09

What steps will reproduce the problem? 1. Install HDF 1.8.1
2. Install NETCDF-4.0 (stable release version)
3. Set HDF5_DIR, SZIP_DIR and NETCDF4_DIR env variables
4. Run setup.py install What is the expected output? What do you see instead? Expected to install, instead, errored:
Traceback (most recent call last):
File "C:\Python24\Lib\site-packages\netCDF4-0.7.4\setup.py", line 46, in ?
raise ValueError('did not find HDF5 headers and libraries in %s' %
HDF5_dir)

ValueError: did not find HDF5 headers and libraries in C:\hdf5\hdf5lib\release What version of the product are you using? On what operating system? NETCDF4-0.7.4, Windows XP SP2 Please provide any additional information below. I checked the setup.py file and it seems to fail on the finding the version
number in the header file (include/H5pubconf.h). I checked the header file
located in the dir as specified above and did not find this line of code:

define H5_VERSION as needed by setup.

Original issue: http://code.google.com/p/netcdf4-python/issues/detail?id=2

[dopplershift]

From whitaker.jeffrey@gmail.com on June 23, 2008 04:08:45

Did you actually build and install hdf5 1.8.1 and the netcdf-4.0 C libraries? (By
this I mean, did you run ./configure;make;make install?). If so, where did you
install them?

If you set HDF5_DIR to C:\hdf5\hdf5lib\release, the libs must be in
C:\hdf5\hdf5lib\release\lib and the headers in C:\hdf5\hdf5lib\release\include. Is
that correct?

Are you using a posix-like environment for windows like Cygwin or mingw32?

[dopplershift]

From blt...@gmail.com on June 23, 2008 07:57:27

HDF5 installed and built using the directions specified for windows and built using
Microsoft Visual Studio 2005. Tested using the included routines with no failed
marks. So I think that HDF5 installed properly. Installed to c:\HDF5.

The libs and headers are in the folders as you specified above, including the file
H5pubconf.h as I mentioned that the setup file seems to be looking for. There is one
other version of this file in the HDF5 under C:\hdf5\vms\src which does have the
version number that setup.py is looking for, but is a very different file.

As to NetCDF 4.0, I installed this using the prebuilt binaries for windows following
the directions given. I think this might be another weak link here for me. I'm
realizing that the binaries are for 3.6.1? and not 4.0. Although I haven't yet even
gotten to failing on the NetCDF routines yet. I tried building NetCDF 4.0 for windows
and was not successful using VS 2005 and so I went with using the prebuilt binaries,
which I see now probably won't work anyway with your package.

I'm not that sophisticated of a programmer, I just wanted to be able to use the
NetCDF libraries with Python so I can do some ArcGIS programming and be able to read
from NetCDF files. If you have a simpler solution to getting there, I would
appreciate it. I've spent days (literally) trying to get NetCDF and HDF to be
useable on my machine. I think HDF is there, although not where it needs to be for
your program.

I am not using a posix-like environment, although I think that mingw32 is included
with Python? These are for compiling?

[dopplershift]

From whitaker.jeffrey@gmail.com on June 23, 2008 10:16:08

If you don't need the netCDF 4 features, you can use setup-nc3.py to install the
netCDF3 module, which should work with just the version of netcdf (3.6.1) that you
installed. Just set the NETCDF3_DIR env var to point to where you installed the
headers and lib, then run "python setup-nc3.py install".

Don't know why setup.py is failing to recognize your HDF5 installation. It's looking
at H5_VERSION in H5pubconf.h, see for example http://www.sfr-fresh.com/linux/misc/hdf5-1.8.1-linux-16API.tar.gz:a/5-1.8.1-linux-16API/include/H5pubconf.h I must admit that I haven't tested this with visual studio, only with gcc/mingw32
( http://www.mingw.org ).

[dopplershift]

From blt...@gmail.com on June 27, 2008 09:10:18

After several days of playing around with this install, I installed MingW32, Msys to
installed HDF5 and NetCDF4. Set the environment variables properly and the install
now fails using MingW32 a:

File "setup.py", line 67, in ?
raise ValueError('did not find netCDF version 4 headers and libs in %s' %
netCDF4_dir)
ValueError: did not find netCDF version 4 headers and libs in c:/NetCDF/netcdf-4.0

This is not an error about finding the headers, you have it error if it does not find
the directory and if it does not find 'nc_inq_compound'. The error occurs for the
latter issue. There is no such code in the netcdf.h file after install of NetCDF4.
If I trick the setup file and tell it that it is a NetCDF4 directory, it will begin
to install, but fail with erorrs (see below). I also tried the nc3 version, but got
a different sent of errors (not included). Any suggestions about getting through
this would be appreciated.

running install
running build
running scons
customize Mingw32CCompiler
Found executable c:\MinGW\bin\gcc.exe
Ignoring "Python was built with Visual Studio 2003;
extensions must be built with a compiler than can generate compatible binaries.
Visual Studio 2003 was not found on this system. If you have Cygwin installed,
you can try compiling with MingW32, by passing "-c mingw32" to setup.py." (one should
fix me in fcompiler/compaq.py)
customize GnuFCompiler
Found executable c:\MinGW\bin\g77.exe
gnu: no Fortran 90 compiler found
gnu: no Fortran 90 compiler found
Found executable c:\MinGW\bin\g77.exe
customize GnuFCompiler
gnu: no Fortran 90 compiler found
gnu: no Fortran 90 compiler found
customize Mingw32CCompiler
customize Mingw32CCompiler using scons
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
building py_modules sources
building extension "netCDF4" sources
running build_py
running build_ext
customize Mingw32CCompiler
customize Mingw32CCompiler using build_ext
building 'netCDF4' extension
compiling C sources
C compiler: gcc -mno-cygwin -O2 -Wall -Wstrict-prototypes

compile options: '-Ic:/NetCDF/netcdf-4.0\include -Ic:/HDF/hdf5-1.8.1\include
-Ic:\python24\lib\site-packages\numpy\core\include -Ic:\python24\include
-Ic:\python24\PC -c'
gcc -mno-cygwin -O2 -Wall -Wstrict-prototypes -Ic:/NetCDF/netcdf-4.0\include
-Ic:/HDF/hdf5-1.8.1\include -Ic:\python24\lib\site-packages\numpy\core\include
-Ic:\python24\include -Ic:\python24\PC -c netCDF4.c -o
build\temp.win32-2.4\Release\netcdf4.o
netCDF4.c: In function __pyx_f_7netCDF4__get_att': netCDF4.c:567: warning: dereferencing type-punned pointer will break strict-aliasing rules netCDF4.c:628: error:NC_STRING' undeclared (first use in this function)
netCDF4.c:628: error: (Each undeclared identifier is reported only once
netCDF4.c:628: error: for each function it appears in.)
netCDF4.c: In function __pyx_pf_7netCDF4__set_default_format': netCDF4.c:1049: warning: dereferencing type-punned pointer will break strict-aliasing rules netCDF4.c: In functionpyx_f_7netCDF4__set_att':
netCDF4.c:1473: warning: dereferencing type-punned pointer will break strict-aliasing
rules
netCDF4.c:1527: warning: dereferencing type-punned pointer will break strict-aliasing
rules
netCDF4.c:1527: warning: dereferencing type-punned pointer will break strict-aliasing
rules
netCDF4.c:1527: warning: dereferencing type-punned pointer will break strict-aliasing
rules
netCDF4.c:1527: warning: dereferencing type-punned pointer will break strict-aliasing
rules
netCDF4.c: In function __pyx_f_7netCDF4__get_dims': netCDF4.c:1894: warning: implicit declaration of functionnc_inq_dimids'
netCDF4.c: In function __pyx_f_7netCDF4__get_grps': netCDF4.c:2100: warning: implicit declaration of functionnc_inq_grps'
netCDF4.c:2221: warning: implicit declaration of function nc_inq_grpname' netCDF4.c: In function__pyx_f_7netCDF4__get_vars':
netCDF4.c:2473: warning: implicit declaration of function nc_inq_varids' netCDF4.c:2841: warning: dereferencing type-punned pointer will break strict-aliasing rules netCDF4.c:2843: warning: dereferencing type-punned pointer will break strict-aliasing rules netCDF4.c:2942: warning: dereferencing type-punned pointer will break strict-aliasing rules netCDF4.c:2944: warning: dereferencing type-punned pointer will break strict-aliasing rules netCDF4.c: In function__pyx_pf_7netCDF4_7Dataset___init':
netCDF4.c:3086: warning: dereferencing type-punned pointer will break strict-aliasing
rules
netCDF4.c: In function __pyx_pf_7netCDF4_7Dataset_createVariable': netCDF4.c:4042: warning: dereferencing type-punned pointer will break strict-aliasing rules netCDF4.c:4044: warning: dereferencing type-punned pointer will break strict-aliasing rules netCDF4.c:4045: warning: dereferencing type-punned pointer will break strict-aliasing rules netCDF4.c:4046: warning: dereferencing type-punned pointer will break strict-aliasing rules netCDF4.c: In functionpyx_pf_7netCDF4_7Dataset___delattr':
netCDF4.c:4590: warning: dereferencing type-punned pointer will break strict-aliasing
rules
netCDF4.c: In function __pyx_pf_7netCDF4_7Dataset___setattr__': netCDF4.c:4744: warning: dereferencing type-punned pointer will break strict-aliasing rules netCDF4.c: In functionpyx_pf_7netCDF4_7Dataset___getattr':
netCDF4.c:4940: warning: dereferencing type-punned pointer will break strict-aliasing
rules
netCDF4.c: In function __pyx_pf_7netCDF4_5Group___init__': netCDF4.c:5122: warning: implicit declaration of functionnc_def_grp'
netCDF4.c: In function __pyx_pf_7netCDF4_9Dimension_isunlimited': netCDF4.c:5717: warning: implicit declaration of functionnc_inq_unlimdims'
netCDF4.c:5766: warning: dereferencing type-punned pointer will break strict-aliasing
rules
netCDF4.c:5767: warning: dereferencing type-punned pointer will break strict-aliasing
rules
netCDF4.c:5875: warning: dereferencing type-punned pointer will break strict-aliasing
rules
netCDF4.c:5876: warning: dereferencing type-punned pointer will break strict-aliasing
rules
netCDF4.c:5889: warning: dereferencing type-punned pointer will break strict-aliasing
rules
netCDF4.c:5890: warning: dereferencing type-punned pointer will break strict-aliasing
rules
netCDF4.c:5926: warning: dereferencing type-punned pointer will break strict-aliasing
rules
netCDF4.c:5927: warning: dereferencing type-punned pointer will break strict-aliasing
rules
netCDF4.c:5940: warning: dereferencing type-punned pointer will break strict-aliasing
rules
netCDF4.c:5941: warning: dereferencing type-punned pointer will break strict-aliasing
rules
netCDF4.c: In function `pyx_pf_7netCDF4_8Variable___init':
netCDF4.c:6034: warning: dereferencing type-punned pointer will break strict-aliasing
...

[dopplershift]

From blt...@gmail.com on June 27, 2008 09:10:18

...
rules
netCDF4.c:6036: warning: dereferencing type-punned pointer will break strict-aliasing
rules
netCDF4.c:6037: warning: dereferencing type-punned pointer will break strict-aliasing
rules
netCDF4.c:6038: warning: dereferencing type-punned pointer will break strict-aliasing
rules
netCDF4.c:6110: warning: dereferencing type-punned pointer will break strict-aliasing
rules
netCDF4.c:6115: warning: dereferencing type-punned pointer will break strict-aliasing
rules
netCDF4.c:6174: warning: dereferencing type-punned pointer will break strict-aliasing
rules
netCDF4.c:6611: warning: implicit declaration of function nc_def_var_deflate' netCDF4.c:6698: warning: implicit declaration of functionnc_def_var_fletcher32'
netCDF4.c:6946: warning: dereferencing type-punned pointer will break strict-aliasing
rules
netCDF4.c:6946: warning: dereferencing type-punned pointer will break strict-aliasing
rules
netCDF4.c:6946: warning: dereferencing type-punned pointer will break strict-aliasing
rules
netCDF4.c:6946: warning: dereferencing type-punned pointer will break strict-aliasing
rules
netCDF4.c:6964: warning: implicit declaration of function nc_def_var_chunking' netCDF4.c:7051: warning: implicit declaration of functionnc_def_var_endian'
netCDF4.c:7051: error: NC_ENDIAN_LITTLE' undeclared (first use in this function) netCDF4.c:7074: error:NC_ENDIAN_BIG' undeclared (first use in this function)
netCDF4.c:7197: warning: implicit declaration of function nc_def_var_fill' netCDF4.c:7465: warning: dereferencing type-punned pointer will break strict-aliasing rules netCDF4.c:7467: warning: dereferencing type-punned pointer will break strict-aliasing rules netCDF4.c: In functionpyx_pf_7netCDF4_8Variable_filters':
netCDF4.c:8019: warning: dereferencing type-punned pointer will break strict-aliasing
rules
netCDF4.c:8020: warning: dereferencing type-punned pointer will break strict-aliasing
rules
netCDF4.c:8022: warning: dereferencing type-punned pointer will break strict-aliasing
rules
netCDF4.c:8057: warning: implicit declaration of function nc_inq_var_deflate' netCDF4.c:8096: warning: implicit declaration of functionnc_inq_var_fletcher32'
netCDF4.c:8145: warning: dereferencing type-punned pointer will break strict-aliasing
rules
netCDF4.c:8178: warning: dereferencing type-punned pointer will break strict-aliasing
rules
netCDF4.c:8200: warning: dereferencing type-punned pointer will break strict-aliasing
rules
netCDF4.c: In function __pyx_pf_7netCDF4_8Variable_endian': netCDF4.c:8278: warning: implicit declaration of functionnc_inq_var_endian'
netCDF4.c:8317: error: NC_ENDIAN_LITTLE' undeclared (first use in this function) netCDF4.c:8340: error:NC_ENDIAN_BIG' undeclared (first use in this function)
netCDF4.c: In function __pyx_pf_7netCDF4_8Variable_chunking': netCDF4.c:8449: warning: implicit declaration of functionnc_inq_var_chunking'
netCDF4.c: In function __pyx_pf_7netCDF4_8Variable___delattr**': netCDF4.c:8736: warning: dereferencing type-punned pointer will break strict-aliasing rules netCDF4.c: In function pyx_pf_7netCDF4_8Variable___setattr':
netCDF4.c:8933: warning: dereferencing type-punned pointer will break strict-aliasing
rules
netCDF4.c: In function**pyx_pf_7netCDF4_8Variable___getattr**': netCDF4.c:9125: warning: dereferencing type-punned pointer will break strict-aliasing rules netCDF4.c: In function pyx_pf_7netCDF4_8Variable___getitem':
netCDF4.c:9426: warning: dereferencing type-punned pointer will break strict-aliasing
rules
netCDF4.c:9426: warning: dereferencing type-punned pointer will break strict-aliasing
rules
netCDF4.c:9426: warning: dereferencing type-punned pointer will break strict-aliasing
rules
netCDF4.c:9426: warning: dereferencing type-punned pointer will break strict-aliasing
rules
netCDF4.c:9491: warning: dereferencing type-punned pointer will break strict-aliasing
rules
netCDF4.c:9491: warning: dereferencing type-punned pointer will break strict-aliasing
rules
netCDF4.c:9491: warning: dereferencing type-punned pointer will break strict-aliasing
rules
netCDF4.c:9491: warning: dereferencing type-punned pointer will break strict-aliasing
rules
netCDF4.c: In function**pyx_pf_7netCDF4_8Variable___setitem**': netCDF4.c:10051: warning: dereferencing type-punned pointer will break strict-aliasing rules netCDF4.c: In function __pyx_pf_7netCDF4_8Variable_set_auto_maskandscale':
netCDF4.c:10310: warning: dereferencing type-punned pointer will break
strict-aliasing rules
netCDF4.c:10312: warning: dereferencing type-punned pointer will break
strict-aliasing rules
netCDF4.c:10324: warning: dereferencing type-punned pointer will break
strict-aliasing rules
netCDF4.c:10326: warning: dereferencing type-punned pointer will break
strict-aliasing rules
netCDF4.c: In function**pyx_pf_7netCDF4_8Variable__put': netCDF4.c:10610: warning: dereferencing type-punned pointer will break strict-aliasing rules netCDF4.c:10659: warning: dereferencing type-punned pointer will break strict-aliasing rules netCDF4.c:10851: warning: dereferencing type-punned pointer will break strict-aliasing rules netCDF4.c:10851: warning: dereferencing type-punned pointer will break strict-aliasing rules netCDF4.c:10851: warning: dereferencing type-punned pointer will break strict-aliasing rules netCDF4.c:10851: warning: dereferencing type-punned pointer will break strict-aliasing rules netCDF4.c: In function __pyx_pf_7netCDF4_8Variable__get':
netCDF4.c:10979: warning: dereferencing type-punned pointer will break
strict-aliasing rules
netCDF4.c:11005: warning: dereferencing type-punned pointer will break
strict-aliasing rules
netCDF4.c:11007: warning: dereferencing type-punned pointer will break
strict-aliasing rules
netCDF4.c:11065: warning: dereferencing type-punned pointer will break
strict-aliasing rules
netCDF4.c:11067: warning: dereferencing type-punned pointer will break
strict-aliasing rules
netCDF4.c:11256: warning: dereferencing type-punned pointer will break
strict-aliasing rules
netCDF4.c:11305: warning: dereferencing type-punned pointer will break
strict-aliasing rules
netCDF4.c:11356: warning: dereferencing type-punned pointer will break
strict-aliasing rules
netCDF4.c:11356: warning: dereferencing type-punned pointer will break
strict-aliasing rules
netCDF4.c:11356: warning: dereferencing type-punned pointer will break
strict-aliasing rules
netCDF4.c:11356: warning: dereferencing type-punned pointer will break
strict-aliasing rules
netCDF4.c: In function__pyx_pf_7netCDF4_stringtochar': netCDF4.c:11611: warning: dereferencing type-punned pointer will break strict-aliasing rules netCDF4.c: In function __pyx_pf_7netCDF4_getlibversion':
netCDF4.c:12056: warning: assignment discards qualifiers from pointer target type
netCDF4.c: In function`__pyx_pf_7netCDF4_9MFDataset___init':
netCDF4.c:12172: warning: dereferencing typ...

[dopplershift]

From blt...@gmail.com on June 27, 2008 09:10:18

...e-punned pointer will break
strict-aliasing rules
netCDF4.c:12227: warning: dereferencing type-punned pointer will break
strict-aliasing rules
netCDF4.c:12599: warning: dereferencing type-punned pointer will break
strict-aliasing rules
netCDF4.c:12599: warning: dereferencing type-punned pointer will break
strict-aliasing rules
netCDF4.c:12599: warning: dereferencing type-punned pointer will break
strict-aliasing rules
netCDF4.c:12599: warning: dereferencing type-punned pointer will break
strict-aliasing rules
netCDF4.c: In function __pyx_pf_7netCDF4_10_Dimension_isunlimited': netCDF4.c:14193: warning: dereferencing type-punned pointer will break strict-aliasing rules netCDF4.c:14194: warning: dereferencing type-punned pointer will break strict-aliasing rules netCDF4.c: In functionpyx_pf_7netCDF4_9_Variable___getitem':
netCDF4.c:15102: warning: dereferencing type-punned pointer will break
strict-aliasing rules
netCDF4.c:15128: warning: dereferencing type-punned pointer will break
strict-aliasing rules
netCDF4.c:15201: warning: dereferencing type-punned pointer will break
strict-aliasing rules
netCDF4.c:15352: warning: dereferencing type-punned pointer will break
strict-aliasing rules
netCDF4.c:15378: warning: dereferencing type-punned pointer will break
strict-aliasing rules
netCDF4.c: In function initnetCDF4': netCDF4.c:16583: warning: dereferencing type-punned pointer will break strict-aliasing rules netCDF4.c:16587: warning: dereferencing type-punned pointer will break strict-aliasing rules netCDF4.c:16590: warning: dereferencing type-punned pointer will break strict-aliasing rules netCDF4.c:16593: warning: dereferencing type-punned pointer will break strict-aliasing rules netCDF4.c:16809: error:NC_UBYTE' undeclared (first use in this function)
netCDF4.c:16831: error: NC_USHORT' undeclared (first use in this function) netCDF4.c:16853: error:NC_UINT' undeclared (first use in this function)
netCDF4.c:16864: error: NC_INT64' undeclared (first use in this function) netCDF4.c:16875: error:NC_UINT64' undeclared (first use in this function)
netCDF4.c:16939: error: NC_FILL_UBYTE' undeclared (first use in this function) netCDF4.c:16961: error:NC_FILL_USHORT' undeclared (first use in this function)
netCDF4.c:16983: error: NC_FILL_UINT' undeclared (first use in this function) netCDF4.c:16994: error:NC_FILL_INT64' undeclared (first use in this function)
netCDF4.c:17005: error: NC_FILL_UINT64' undeclared (first use in this function) netCDF4.c: In function__Pyx_PyObject_IsTrue':
netCDF4.c:17885: warning: dereferencing type-punned pointer will break
strict-aliasing rules
netCDF4.c:17886: warning: dereferencing type-punned pointer will break
strict-aliasing rules

[dopplershift]

From abw...@gmail.com on June 27, 2008 10:23:25

Did you build netcdf with '--enable-netcdf-4' ? This is the error you would get if only the netcdf version 3
library were built (which is what happens by default if you run configure without --enable-netcdf-4).

-Jeff

[dopplershift]

From blt...@gmail.com on June 30, 2008 10:17:48

I specified --enable-netcdf-4 as above and specified ZLIB and HDF directory locations
and now get the following error:

"Can't find the hdf5 high-level library" when configuring NetCDF4. I have not found
any help on this error online. Have you experienced this error? It gets far through
configure before I get this error. Any suggestions.

Thanks, Andrew

[dopplershift]

From whitaker.jeffrey@gmail.com on June 30, 2008 10:35:21

Andrew: You'll have to specify exactly how you built and installed HDF5 and netCDF.
Note that in the netcdf4-python docs it says that you need to build HDF5 1.8.1 with -
-enable-hl, and when building netcdf4 you have to use --enable-netcdf-4 and --with-
hdf5=.

-Jeff

[dopplershift]

From blt...@gmail.com on July 01, 2008 06:27:30

Jeff,
If I include the statement --enable-netcdf-4 in the ./configure statement for NetCDF4
install, I get the message I mention above, when I do not include this, it manages to
get through this cleanly.

Installed HDF5 NETCDF4 using msys, mingw32

HDF5
$ ./configure --with-zlib=/c/HDF/zlib-1.2.3/include,/c/HDF/zlib-1.2.3/lib
--prefix=/c/HDF/hdf5-1.8.1 --enable-shared --enable-hl

make check
make install

NetCDF5
$ ./configure --enable-docs-install --disable-f77 --with-zlib=/c/HDF/zlib-1.2.3
--with-hdf5=/c/HDF/hdf5-1.8.1 --prefix=/c/NETCDF/netcdf-4.0 --enable-shared

make check
make install

Thanks for your help

Cheers, Andrew

[dopplershift]

From whitaker.jeffrey@gmail.com on July 01, 2008 20:19:45

Andrew; Well, it sure looks right. I don't know why netcdf-4 doesn't detect your HDF5 installation. I think this
is a question for the netcdf folks (netcdfgroup@unidata.ucar.edu). Sorry I can't be of more help.

-Jeff

[dopplershift]

From whitaker.jeffrey@gmail.com on May 25, 2009 06:02:29

Status: Done