pyhdf/hdfext_wrap.c:3543:17: fatal error: hdf.h: No such file or directory #include "hdf.h"

Question

pyhdf/hdfext_wrap.c:3543:17: fatal error: hdf.h: No such file or directory #include "hdf.h"

upuil opened this issue 6 years ago · comments

This problem is same as #7 and when I build the source code is same problem.

[root@bogon python-hdf4-0.9.1]# pip install python-hdf4
Collecting python-hdf4
Using cached https://files.pythonhosted.org/packages/02/07/15a5e258e48a7d252c0efee187ddc4322a8bc8969c65b400aeda1fda2843/python-hdf4-0.9.1.tar.gz
Building wheels for collected packages: python-hdf4
Running setup.py bdist_wheel for python-hdf4 ... error
Complete output from command /opt/anaconda3/bin/python -u -c "import setuptools, tokenize;file='/tmp/pip-install-uvbe00sl/python-hdf4/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-9vsawgde --python-tag cp36:
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 "pyhdf._hdfext" sources
build_src: building npy-pkg config files
running build_py
creating build
creating build/lib.linux-x86_64-3.6
creating build/lib.linux-x86_64-3.6/pyhdf
copying pyhdf/init.py -> build/lib.linux-x86_64-3.6/pyhdf
copying pyhdf/VS.py -> build/lib.linux-x86_64-3.6/pyhdf
copying pyhdf/six.py -> build/lib.linux-x86_64-3.6/pyhdf
copying pyhdf/test_SD.py -> build/lib.linux-x86_64-3.6/pyhdf
copying pyhdf/SD.py -> build/lib.linux-x86_64-3.6/pyhdf
copying pyhdf/HC.py -> build/lib.linux-x86_64-3.6/pyhdf
copying pyhdf/hdfext.py -> build/lib.linux-x86_64-3.6/pyhdf
copying pyhdf/V.py -> build/lib.linux-x86_64-3.6/pyhdf
copying pyhdf/error.py -> build/lib.linux-x86_64-3.6/pyhdf
copying pyhdf/HDF.py -> build/lib.linux-x86_64-3.6/pyhdf
running build_ext
customize UnixCCompiler
customize UnixCCompiler using build_ext
building 'pyhdf._hdfext' extension
compiling C sources
C compiler: gcc -pthread -B /opt/anaconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC

creating build/temp.linux-x86_64-3.6
creating build/temp.linux-x86_64-3.6/pyhdf
compile options: '-I/opt/anaconda3/lib/python3.6/site-packages/numpy/core/include -I/opt/anaconda3/include/python3.6m -c'
extra options: '-DNOSZIP'
gcc: pyhdf/hdfext_wrap.c
pyhdf/hdfext_wrap.c:3543:17: fatal error: hdf.h: No such file or directory
#include "hdf.h"
^
compilation terminated.
pyhdf/hdfext_wrap.c:3543:17: fatal error: hdf.h: No such file or directory
#include "hdf.h"
^
compilation terminated.
error: Command "gcc -pthread -B /opt/anaconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/opt/anaconda3/lib/python3.6/site-packages/numpy/core/include -I/opt/anaconda3/include/python3.6m -c pyhdf/hdfext_wrap.c -o build/temp.linux-x86_64-3.6/pyhdf/hdfext_wrap.o -MMD -MF build/temp.linux-x86_64-3.6/pyhdf/hdfext_wrap.o.d -DNOSZIP" failed with exit status 1

Failed building wheel for python-hdf4
Running setup.py clean for python-hdf4
Failed to build python-hdf4
Installing collected packages: python-hdf4
Running setup.py install for python-hdf4 ... error
Complete output from command /opt/anaconda3/bin/python -u -c "import setuptools, tokenize;file='/tmp/pip-install-uvbe00sl/python-hdf4/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-tjnm5o0i/install-record.txt --single-version-externally-managed --compile:
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 "pyhdf._hdfext" sources
build_src: building npy-pkg config files
running build_py
creating build
creating build/lib.linux-x86_64-3.6
creating build/lib.linux-x86_64-3.6/pyhdf
copying pyhdf/init.py -> build/lib.linux-x86_64-3.6/pyhdf
copying pyhdf/VS.py -> build/lib.linux-x86_64-3.6/pyhdf
copying pyhdf/six.py -> build/lib.linux-x86_64-3.6/pyhdf
copying pyhdf/test_SD.py -> build/lib.linux-x86_64-3.6/pyhdf
copying pyhdf/SD.py -> build/lib.linux-x86_64-3.6/pyhdf
copying pyhdf/HC.py -> build/lib.linux-x86_64-3.6/pyhdf
copying pyhdf/hdfext.py -> build/lib.linux-x86_64-3.6/pyhdf
copying pyhdf/V.py -> build/lib.linux-x86_64-3.6/pyhdf
copying pyhdf/error.py -> build/lib.linux-x86_64-3.6/pyhdf
copying pyhdf/HDF.py -> build/lib.linux-x86_64-3.6/pyhdf
running build_ext
customize UnixCCompiler
customize UnixCCompiler using build_ext
building 'pyhdf._hdfext' extension
compiling C sources
C compiler: gcc -pthread -B /opt/anaconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC

creating build/temp.linux-x86_64-3.6
creating build/temp.linux-x86_64-3.6/pyhdf
compile options: '-I/opt/anaconda3/lib/python3.6/site-packages/numpy/core/include -I/opt/anaconda3/include/python3.6m -c'
extra options: '-DNOSZIP'
gcc: pyhdf/hdfext_wrap.c
pyhdf/hdfext_wrap.c:3543:17: fatal error: hdf.h: No such file or directory
 #include "hdf.h"
                 ^
compilation terminated.
pyhdf/hdfext_wrap.c:3543:17: fatal error: hdf.h: No such file or directory
 #include "hdf.h"
                 ^
compilation terminated.
error: Command "gcc -pthread -B /opt/anaconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/opt/anaconda3/lib/python3.6/site-packages/numpy/core/include -I/opt/anaconda3/include/python3.6m -c pyhdf/hdfext_wrap.c -o build/temp.linux-x86_64-3.6/pyhdf/hdfext_wrap.o -MMD -MF build/temp.linux-x86_64-3.6/pyhdf/hdfext_wrap.o.d -DNOSZIP" failed with exit status 1

----------------------------------------

Command "/opt/anaconda3/bin/python -u -c "import setuptools, tokenize;file='/tmp/pip-install-uvbe00sl/python-hdf4/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-tjnm5o0i/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /tmp/pip-install-uvbe00sl/python-hdf4/

Fazlul Shahriar · Answer 1 · Mon Dec 10 2018 01:30:16 GMT+0800 (China Standard Time)

Where do you have hdf4 installed? Where are the include (.h) files and .so files? What linux distro are you using? Did you manually install hdf4 or using a distro package?

All of these installation problems could be easily solved (at least on Linux) if hdf4 was using pkg-config, but it looks like it doesn't. 😩

Tommy Carstensen · Answer 2 · Fri Apr 17 2020 03:25:15 GMT+0800 (China Standard Time)

I get this error message:

pyhdf/hdfext_wrap.c:3681:10: fatal error: 'hdf.h' file not found