Pip error even when adding --no-use-pep517
gcaria opened this issue · comments
What version of pyhdf, HDF4, and Python are you using?
pyhdf 0.10.2
HDF4 C library version: 4.2
Python version: 3.8.3
What operating system are you using?
CentOS Linux 7
Even adding the --no-use-pep517 to pip (i.e. running pip install pyhdf --no-use-pep517) yields:
Collecting pyhdf
Using cached pyhdf-0.10.2.tar.gz (149 kB)
Building wheels for collected packages: pyhdf
Building wheel for pyhdf (setup.py) ... error
ERROR: Command errored out with exit status 1:
command: /home/gcaria/envs/giacos/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-7624spxi/pyhdf/setup.py'"'"'; __file__='"'"'/tmp/pip-install-7624spxi/pyhdf/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-9ptzseje
cwd: /tmp/pip-install-7624spxi/pyhdf/
Complete output (228 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 "pyhdf._hdfext" sources
build_src: building npy-pkg config files
running build_py
creating build
creating build/lib.linux-x86_64-3.8
creating build/lib.linux-x86_64-3.8/pyhdf
copying pyhdf/HC.py -> build/lib.linux-x86_64-3.8/pyhdf
copying pyhdf/HDF.py -> build/lib.linux-x86_64-3.8/pyhdf
copying pyhdf/SD.py -> build/lib.linux-x86_64-3.8/pyhdf
copying pyhdf/V.py -> build/lib.linux-x86_64-3.8/pyhdf
copying pyhdf/VS.py -> build/lib.linux-x86_64-3.8/pyhdf
copying pyhdf/__init__.py -> build/lib.linux-x86_64-3.8/pyhdf
copying pyhdf/error.py -> build/lib.linux-x86_64-3.8/pyhdf
copying pyhdf/hdfext.py -> build/lib.linux-x86_64-3.8/pyhdf
copying pyhdf/six.py -> build/lib.linux-x86_64-3.8/pyhdf
copying pyhdf/test_SD.py -> build/lib.linux-x86_64-3.8/pyhdf
running build_ext
customize UnixCCompiler
customize UnixCCompiler using build_ext
building 'pyhdf._hdfext' extension
compiling C sources
C compiler: gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -I/home/gcaria/usr/local/include -fPIC
creating build/temp.linux-x86_64-3.8/pyhdf
compile options: '-I/usr/include/hdf/ -I/home/gcaria/usr/local/lib/python3.8/site-packages/numpy/core/include -I/home/gcaria/envs/giacos/include -I/home/gcaria/usr/local/include/python3.8 -c'
extra options: '-DNOSZIP'
gcc: pyhdf/hdfext_wrap.c
In file included from /home/gcaria/usr/local/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822,
from /home/gcaria/usr/local/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /home/gcaria/usr/local/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from /home/gcaria/usr/local/lib/python3.8/site-packages/numpy/core/include/numpy/oldnumeric.h:1,
from pyhdf/hdfext_wrap.c:3859:
/home/gcaria/usr/local/lib/python3.8/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]
17 | #warning "Using deprecated NumPy API, disable it with " \
| ^~~~~~~
pyhdf/hdfext_wrap.c: In function ‘HDFtoNumericType’:
pyhdf/hdfext_wrap.c:3899:9: warning: ‘NPY_CHAR’ is deprecated: Use NPY_STRING [-Wdeprecated-declarations]
3899 | case DFNT_CHAR8 : num = PyArray_CHAR; break;
| ^~~~
In file included from /home/gcaria/usr/local/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /home/gcaria/usr/local/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from /home/gcaria/usr/local/lib/python3.8/site-packages/numpy/core/include/numpy/oldnumeric.h:1,
from pyhdf/hdfext_wrap.c:3859:
/home/gcaria/usr/local/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:84:21: note: declared here
84 | NPY_CHAR NPY_ATTR_DEPRECATE("Use NPY_STRING"),
| ^~~~~~~~
pyhdf/hdfext_wrap.c: In function ‘_SDreaddata_0’:
pyhdf/hdfext_wrap.c:4014:9: warning: ‘NPY_CHAR’ is deprecated: Use NPY_STRING [-Wdeprecated-declarations]
4014 | case PyArray_CHAR:
| ^~~~
In file included from /home/gcaria/usr/local/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /home/gcaria/usr/local/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from /home/gcaria/usr/local/lib/python3.8/site-packages/numpy/core/include/numpy/oldnumeric.h:1,
from pyhdf/hdfext_wrap.c:3859:
/home/gcaria/usr/local/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:84:21: note: declared here
84 | NPY_CHAR NPY_ATTR_DEPRECATE("Use NPY_STRING"),
| ^~~~~~~~
pyhdf/hdfext_wrap.c: In function ‘_SDgetcompress’:
pyhdf/hdfext_wrap.c:4126:36: warning: passing argument 2 of ‘SDgetcompress’ from incompatible pointer type [-Wincompatible-pointer-types]
4126 | status = SDgetcompress(sds_id, comp_type, &c_info);
| ^~~~~~~~~
| |
| int32 * {aka int *}
In file included from pyhdf/hdfext_wrap.c:3682:
/usr/include/hdf/mfhdf.h:186:30: note: expected ‘comp_coder_t *’ but argument is of type ‘int32 *’ {aka ‘int *’}
186 | (int32 id, comp_coder_t* type, comp_info *c_info);
| ~~~~~~~~~~~~~~^~~~
pyhdf/hdfext_wrap.c: In function ‘_wrap_SDcreate’:
pyhdf/hdfext_wrap.c:6028:62: warning: passing argument 5 of ‘SDcreate’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
6028 | result = (int32)SDcreate(arg1,(char const *)arg2,arg3,arg4,(int const *)arg5);
| ^~~~~~~~~~~~~~~~~
In file included from pyhdf/hdfext_wrap.c:3682:
/usr/include/hdf/mfhdf.h:104:64: note: expected ‘int32 *’ {aka ‘int *’} but argument is of type ‘const int *’
104 | (int32 fid, const char *name, int32 nt, int32 rank, int32 *dimsizes);
| ~~~~~~~^~~~~~~~
pyhdf/hdfext_wrap.c: In function ‘_wrap_SDsetdimscale’:
pyhdf/hdfext_wrap.c:6572:48: warning: passing argument 4 of ‘SDsetdimscale’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
6572 | result = (int32)SDsetdimscale(arg1,arg2,arg3,(void const *)arg4);
| ^~~~~~~~~~~~~~~~~~
In file included from pyhdf/hdfext_wrap.c:3682:
/usr/include/hdf/mfhdf.h:159:46: note: expected ‘void *’ but argument is of type ‘const void *’
159 | (int32 id, int32 count, int32 nt, void * data);
| ~~~~~~~^~~~
pyhdf/hdfext_wrap.c: In function ‘_wrap_SDsetfillvalue’:
pyhdf/hdfext_wrap.c:7248:39: warning: passing argument 2 of ‘SDsetfillvalue’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
7248 | result = (int32)SDsetfillvalue(arg1,(void const *)arg2);
| ^~~~~~~~~~~~~~~~~~
In file included from pyhdf/hdfext_wrap.c:3682:
/usr/include/hdf/mfhdf.h:140:26: note: expected ‘void *’ but argument is of type ‘const void *’
140 | (int32 sdsid, void * val);
| ~~~~~~~^~~
pyhdf/hdfext_wrap.c: In function ‘_wrap_SDsetrange’:
pyhdf/hdfext_wrap.c:7284:35: warning: passing argument 2 of ‘SDsetrange’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
7284 | result = (int32)SDsetrange(arg1,(void const *)arg2,(void const *)arg3);
| ^~~~~~~~~~~~~~~~~~
In file included from pyhdf/hdfext_wrap.c:3682:
/usr/include/hdf/mfhdf.h:116:26: note: expected ‘void *’ but argument is of type ‘const void *’
116 | (int32 sdsid, void * pmax, void * pmin);
| ~~~~~~~^~~~
pyhdf/hdfext_wrap.c:7284:54: warning: passing argument 3 of ‘SDsetrange’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
7284 | result = (int32)SDsetrange(arg1,(void const *)arg2,(void const *)arg3);
| ^~~~~~~~~~~~~~~~~~
In file included from pyhdf/hdfext_wrap.c:3682:
/usr/include/hdf/mfhdf.h:116:39: note: expected ‘void *’ but argument is of type ‘const void *’
116 | (int32 sdsid, void * pmax, void * pmin);
| ~~~~~~~^~~~
pyhdf/hdfext_wrap.c: In function ‘_wrap_VSsizeof’:
pyhdf/hdfext_wrap.c:8199:32: warning: passing argument 2 of ‘VSsizeof’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
8199 | result = (intn)VSsizeof(arg1,(char const *)arg2);
| ^~~~~~~~~~~~~~~~~~
In file included from /usr/include/hdf/hdf.h:154,
from pyhdf/hdfext_wrap.c:3681:
/usr/include/hdf/hproto.h:1644:38: note: expected ‘char *’ but argument is of type ‘const char *’
1644 | (int32 vkey, char * fields);
| ~~~~~~~~^~~~~~
pyhdf/hdfext_wrap.c: In function ‘_wrap_VSfexist’:
pyhdf/hdfext_wrap.c:8647:32: warning: passing argument 2 of ‘VSfexist’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
8647 | result = (intn)VSfexist(arg1,(char const *)arg2);
| ^~~~~~~~~~~~~~~~~~
In file included from /usr/include/hdf/hdf.h:154,
from pyhdf/hdfext_wrap.c:3681:
/usr/include/hdf/hproto.h:1641:38: note: expected ‘char *’ but argument is of type ‘const char *’
1641 | (int32 vkey, char * fields);
| ~~~~~~~~^~~~~~
pyhdf/hdfext_wrap.c: In function ‘_SDreaddata_0’:
pyhdf/hdfext_wrap.c:4033:12: warning: ‘o’ may be used uninitialized in this function [-Wmaybe-uninitialized]
4033 | return o;
| ^
pyhdf/hdfext_wrap.c: In function ‘_wrap__SDgetcompress’:
pyhdf/hdfext_wrap.c:748:27: warning: ‘temp4’ may be used uninitialized in this function [-Wmaybe-uninitialized]
748 | #define PyInt_FromLong(x) PyLong_FromLong(x)
| ^~~~~~~~~~~~~~~
pyhdf/hdfext_wrap.c:7307:9: note: ‘temp4’ was declared here
7307 | int32 temp4 ;
| ^~~~~
pyhdf/hdfext_wrap.c:748:27: warning: ‘temp5’ may be used uninitialized in this function [-Wmaybe-uninitialized]
748 | #define PyInt_FromLong(x) PyLong_FromLong(x)
| ^~~~~~~~~~~~~~~
pyhdf/hdfext_wrap.c:7309:9: note: ‘temp5’ was declared here
7309 | int32 temp5 ;
| ^~~~~
pyhdf/hdfext_wrap.c:748:27: warning: ‘temp6’ may be used uninitialized in this function [-Wmaybe-uninitialized]
748 | #define PyInt_FromLong(x) PyLong_FromLong(x)
| ^~~~~~~~~~~~~~~
pyhdf/hdfext_wrap.c:7311:9: note: ‘temp6’ was declared here
7311 | int32 temp6 ;
| ^~~~~
pyhdf/hdfext_wrap.c:748:27: warning: ‘temp7’ may be used uninitialized in this function [-Wmaybe-uninitialized]
748 | #define PyInt_FromLong(x) PyLong_FromLong(x)
| ^~~~~~~~~~~~~~~
pyhdf/hdfext_wrap.c:7313:9: note: ‘temp7’ was declared here
7313 | int32 temp7 ;
| ^~~~~
pyhdf/hdfext_wrap.c:748:27: warning: ‘temp3’ may be used uninitialized in this function [-Wmaybe-uninitialized]
748 | #define PyInt_FromLong(x) PyLong_FromLong(x)
| ^~~~~~~~~~~~~~~
pyhdf/hdfext_wrap.c:7305:9: note: ‘temp3’ was declared here
7305 | int32 temp3 ;
| ^~~~~
gcc -pthread -shared -L/home/gcaria/usr/local/lib/../lib64 -L/home/gcaria/usr/local/lib -L/home/gcaria/usr/local/lib -I/home/gcaria/usr/local/include build/temp.linux-x86_64-3.8/pyhdf/hdfext_wrap.o -L/home/gcaria/usr/local/lib -L/home/gcaria/usr/local/lib64 -L/home/gcaria/usr/local/lib -L/home/gcaria/usr/local/lib64 -L -L/usr/lib -L/usr/local/lib -L/lib -lmfhdf -ldf -ljpeg -lz -o build/lib.linux-x86_64-3.8/pyhdf/_hdfext.cpython-38-x86_64-linux-gnu.so
/usr/bin/ld: /home/gcaria/usr/local/lib/libmfhdf.a(mfsd.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libmfhdf.a(putget.o): relocation R_X86_64_32S against `.rodata' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libmfhdf.a(putgetg.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libmfhdf.a(string.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libmfhdf.a(var.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libmfhdf.a(array.o): relocation R_X86_64_32S against `.rodata' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libmfhdf.a(attr.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libmfhdf.a(cdf.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libmfhdf.a(dim.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libmfhdf.a(file.o): relocation R_X86_64_32 against undefined symbol `rlim' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libmfhdf.a(hdfsds.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libmfhdf.a(iarray.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libmfhdf.a(error.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libmfhdf.a(nssdc.o): relocation R_X86_64_32S against `.rodata' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libmfhdf.a(xdrposix.o): relocation R_X86_64_32S against `.data' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(dfconv.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(dfgroup.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(dfknat.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(dfkswap.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(hblocks.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(hchunks.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(hcomp.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(herr.o): relocation R_X86_64_32S against `.rodata' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(hextelt.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(hfile.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(hfiledd.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(mcache.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(mfan.o): relocation R_X86_64_32 against symbol `ANIanncmp' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(mstdio.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(tbbt.o): relocation R_X86_64_32 against `.rodata.str1.8' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(vattr.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(vg.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(vgp.o): relocation R_X86_64_32 against symbol `vfdestroynode' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(vhi.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(vio.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(vparse.o): relocation R_X86_64_32S against `.bss' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(vrw.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(vsfld.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(atom.o): relocation R_X86_64_32S against `.bss' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(bitvect.o): relocation R_X86_64_32S against `.rodata' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(cdeflate.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(cnbit.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(cnone.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(crle.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(cskphuff.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(cszip.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(dynarray.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(glist.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(hbitio.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(hbuffer.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(hcompri.o): relocation R_X86_64_32 against `.rodata' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(vconv.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(dfcomp.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(dfimcomp.o): relocation R_X86_64_32 against `.bss' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(dfjpeg.o): relocation R_X86_64_32S against symbol `hdf_init_destination' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(dfrle.o): relocation R_X86_64_32S against `.bss' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(dfunjpeg.o): relocation R_X86_64_32S against symbol `hdf_init_source' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: final link failed: Nonrepresentable section on output
collect2: error: ld returned 1 exit status
error: Command "gcc -pthread -shared -L/home/gcaria/usr/local/lib/../lib64 -L/home/gcaria/usr/local/lib -L/home/gcaria/usr/local/lib -I/home/gcaria/usr/local/include build/temp.linux-x86_64-3.8/pyhdf/hdfext_wrap.o -L/home/gcaria/usr/local/lib -L/home/gcaria/usr/local/lib64 -L/home/gcaria/usr/local/lib -L/home/gcaria/usr/local/lib64 -L -L/usr/lib -L/usr/local/lib -L/lib -lmfhdf -ldf -ljpeg -lz -o build/lib.linux-x86_64-3.8/pyhdf/_hdfext.cpython-38-x86_64-linux-gnu.so" failed with exit status 1
----------------------------------------
ERROR: Failed building wheel for pyhdf
Running setup.py clean for pyhdf
Failed to build pyhdf
Installing collected packages: pyhdf
Running setup.py install for pyhdf ... error
ERROR: Command errored out with exit status 1:
command: /home/gcaria/envs/giacos/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-7624spxi/pyhdf/setup.py'"'"'; __file__='"'"'/tmp/pip-install-7624spxi/pyhdf/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-4kzqzl_w/install-record.txt --single-version-externally-managed --compile --install-headers /home/gcaria/envs/giacos/include/site/python3.8/pyhdf
cwd: /tmp/pip-install-7624spxi/pyhdf/
Complete output (228 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 "pyhdf._hdfext" sources
build_src: building npy-pkg config files
running build_py
creating build
creating build/lib.linux-x86_64-3.8
creating build/lib.linux-x86_64-3.8/pyhdf
copying pyhdf/HC.py -> build/lib.linux-x86_64-3.8/pyhdf
copying pyhdf/HDF.py -> build/lib.linux-x86_64-3.8/pyhdf
copying pyhdf/SD.py -> build/lib.linux-x86_64-3.8/pyhdf
copying pyhdf/V.py -> build/lib.linux-x86_64-3.8/pyhdf
copying pyhdf/VS.py -> build/lib.linux-x86_64-3.8/pyhdf
copying pyhdf/__init__.py -> build/lib.linux-x86_64-3.8/pyhdf
copying pyhdf/error.py -> build/lib.linux-x86_64-3.8/pyhdf
copying pyhdf/hdfext.py -> build/lib.linux-x86_64-3.8/pyhdf
copying pyhdf/six.py -> build/lib.linux-x86_64-3.8/pyhdf
copying pyhdf/test_SD.py -> build/lib.linux-x86_64-3.8/pyhdf
running build_ext
customize UnixCCompiler
customize UnixCCompiler using build_ext
building 'pyhdf._hdfext' extension
compiling C sources
C compiler: gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -I/home/gcaria/usr/local/include -fPIC
creating build/temp.linux-x86_64-3.8/pyhdf
compile options: '-I/usr/include/hdf/ -I/home/gcaria/usr/local/lib/python3.8/site-packages/numpy/core/include -I/home/gcaria/envs/giacos/include -I/home/gcaria/usr/local/include/python3.8 -c'
extra options: '-DNOSZIP'
gcc: pyhdf/hdfext_wrap.c
In file included from /home/gcaria/usr/local/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822,
from /home/gcaria/usr/local/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /home/gcaria/usr/local/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from /home/gcaria/usr/local/lib/python3.8/site-packages/numpy/core/include/numpy/oldnumeric.h:1,
from pyhdf/hdfext_wrap.c:3859:
/home/gcaria/usr/local/lib/python3.8/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]
17 | #warning "Using deprecated NumPy API, disable it with " \
| ^~~~~~~
pyhdf/hdfext_wrap.c: In function ‘HDFtoNumericType’:
pyhdf/hdfext_wrap.c:3899:9: warning: ‘NPY_CHAR’ is deprecated: Use NPY_STRING [-Wdeprecated-declarations]
3899 | case DFNT_CHAR8 : num = PyArray_CHAR; break;
| ^~~~
In file included from /home/gcaria/usr/local/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /home/gcaria/usr/local/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from /home/gcaria/usr/local/lib/python3.8/site-packages/numpy/core/include/numpy/oldnumeric.h:1,
from pyhdf/hdfext_wrap.c:3859:
/home/gcaria/usr/local/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:84:21: note: declared here
84 | NPY_CHAR NPY_ATTR_DEPRECATE("Use NPY_STRING"),
| ^~~~~~~~
pyhdf/hdfext_wrap.c: In function ‘_SDreaddata_0’:
pyhdf/hdfext_wrap.c:4014:9: warning: ‘NPY_CHAR’ is deprecated: Use NPY_STRING [-Wdeprecated-declarations]
4014 | case PyArray_CHAR:
| ^~~~
In file included from /home/gcaria/usr/local/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /home/gcaria/usr/local/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from /home/gcaria/usr/local/lib/python3.8/site-packages/numpy/core/include/numpy/oldnumeric.h:1,
from pyhdf/hdfext_wrap.c:3859:
/home/gcaria/usr/local/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:84:21: note: declared here
84 | NPY_CHAR NPY_ATTR_DEPRECATE("Use NPY_STRING"),
| ^~~~~~~~
pyhdf/hdfext_wrap.c: In function ‘_SDgetcompress’:
pyhdf/hdfext_wrap.c:4126:36: warning: passing argument 2 of ‘SDgetcompress’ from incompatible pointer type [-Wincompatible-pointer-types]
4126 | status = SDgetcompress(sds_id, comp_type, &c_info);
| ^~~~~~~~~
| |
| int32 * {aka int *}
In file included from pyhdf/hdfext_wrap.c:3682:
/usr/include/hdf/mfhdf.h:186:30: note: expected ‘comp_coder_t *’ but argument is of type ‘int32 *’ {aka ‘int *’}
186 | (int32 id, comp_coder_t* type, comp_info *c_info);
| ~~~~~~~~~~~~~~^~~~
pyhdf/hdfext_wrap.c: In function ‘_wrap_SDcreate’:
pyhdf/hdfext_wrap.c:6028:62: warning: passing argument 5 of ‘SDcreate’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
6028 | result = (int32)SDcreate(arg1,(char const *)arg2,arg3,arg4,(int const *)arg5);
| ^~~~~~~~~~~~~~~~~
In file included from pyhdf/hdfext_wrap.c:3682:
/usr/include/hdf/mfhdf.h:104:64: note: expected ‘int32 *’ {aka ‘int *’} but argument is of type ‘const int *’
104 | (int32 fid, const char *name, int32 nt, int32 rank, int32 *dimsizes);
| ~~~~~~~^~~~~~~~
pyhdf/hdfext_wrap.c: In function ‘_wrap_SDsetdimscale’:
pyhdf/hdfext_wrap.c:6572:48: warning: passing argument 4 of ‘SDsetdimscale’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
6572 | result = (int32)SDsetdimscale(arg1,arg2,arg3,(void const *)arg4);
| ^~~~~~~~~~~~~~~~~~
In file included from pyhdf/hdfext_wrap.c:3682:
/usr/include/hdf/mfhdf.h:159:46: note: expected ‘void *’ but argument is of type ‘const void *’
159 | (int32 id, int32 count, int32 nt, void * data);
| ~~~~~~~^~~~
pyhdf/hdfext_wrap.c: In function ‘_wrap_SDsetfillvalue’:
pyhdf/hdfext_wrap.c:7248:39: warning: passing argument 2 of ‘SDsetfillvalue’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
7248 | result = (int32)SDsetfillvalue(arg1,(void const *)arg2);
| ^~~~~~~~~~~~~~~~~~
In file included from pyhdf/hdfext_wrap.c:3682:
/usr/include/hdf/mfhdf.h:140:26: note: expected ‘void *’ but argument is of type ‘const void *’
140 | (int32 sdsid, void * val);
| ~~~~~~~^~~
pyhdf/hdfext_wrap.c: In function ‘_wrap_SDsetrange’:
pyhdf/hdfext_wrap.c:7284:35: warning: passing argument 2 of ‘SDsetrange’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
7284 | result = (int32)SDsetrange(arg1,(void const *)arg2,(void const *)arg3);
| ^~~~~~~~~~~~~~~~~~
In file included from pyhdf/hdfext_wrap.c:3682:
/usr/include/hdf/mfhdf.h:116:26: note: expected ‘void *’ but argument is of type ‘const void *’
116 | (int32 sdsid, void * pmax, void * pmin);
| ~~~~~~~^~~~
pyhdf/hdfext_wrap.c:7284:54: warning: passing argument 3 of ‘SDsetrange’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
7284 | result = (int32)SDsetrange(arg1,(void const *)arg2,(void const *)arg3);
| ^~~~~~~~~~~~~~~~~~
In file included from pyhdf/hdfext_wrap.c:3682:
/usr/include/hdf/mfhdf.h:116:39: note: expected ‘void *’ but argument is of type ‘const void *’
116 | (int32 sdsid, void * pmax, void * pmin);
| ~~~~~~~^~~~
pyhdf/hdfext_wrap.c: In function ‘_wrap_VSsizeof’:
pyhdf/hdfext_wrap.c:8199:32: warning: passing argument 2 of ‘VSsizeof’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
8199 | result = (intn)VSsizeof(arg1,(char const *)arg2);
| ^~~~~~~~~~~~~~~~~~
In file included from /usr/include/hdf/hdf.h:154,
from pyhdf/hdfext_wrap.c:3681:
/usr/include/hdf/hproto.h:1644:38: note: expected ‘char *’ but argument is of type ‘const char *’
1644 | (int32 vkey, char * fields);
| ~~~~~~~~^~~~~~
pyhdf/hdfext_wrap.c: In function ‘_wrap_VSfexist’:
pyhdf/hdfext_wrap.c:8647:32: warning: passing argument 2 of ‘VSfexist’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
8647 | result = (intn)VSfexist(arg1,(char const *)arg2);
| ^~~~~~~~~~~~~~~~~~
In file included from /usr/include/hdf/hdf.h:154,
from pyhdf/hdfext_wrap.c:3681:
/usr/include/hdf/hproto.h:1641:38: note: expected ‘char *’ but argument is of type ‘const char *’
1641 | (int32 vkey, char * fields);
| ~~~~~~~~^~~~~~
pyhdf/hdfext_wrap.c: In function ‘_SDreaddata_0’:
pyhdf/hdfext_wrap.c:4033:12: warning: ‘o’ may be used uninitialized in this function [-Wmaybe-uninitialized]
4033 | return o;
| ^
pyhdf/hdfext_wrap.c: In function ‘_wrap__SDgetcompress’:
pyhdf/hdfext_wrap.c:748:27: warning: ‘temp4’ may be used uninitialized in this function [-Wmaybe-uninitialized]
748 | #define PyInt_FromLong(x) PyLong_FromLong(x)
| ^~~~~~~~~~~~~~~
pyhdf/hdfext_wrap.c:7307:9: note: ‘temp4’ was declared here
7307 | int32 temp4 ;
| ^~~~~
pyhdf/hdfext_wrap.c:748:27: warning: ‘temp5’ may be used uninitialized in this function [-Wmaybe-uninitialized]
748 | #define PyInt_FromLong(x) PyLong_FromLong(x)
| ^~~~~~~~~~~~~~~
pyhdf/hdfext_wrap.c:7309:9: note: ‘temp5’ was declared here
7309 | int32 temp5 ;
| ^~~~~
pyhdf/hdfext_wrap.c:748:27: warning: ‘temp6’ may be used uninitialized in this function [-Wmaybe-uninitialized]
748 | #define PyInt_FromLong(x) PyLong_FromLong(x)
| ^~~~~~~~~~~~~~~
pyhdf/hdfext_wrap.c:7311:9: note: ‘temp6’ was declared here
7311 | int32 temp6 ;
| ^~~~~
pyhdf/hdfext_wrap.c:748:27: warning: ‘temp7’ may be used uninitialized in this function [-Wmaybe-uninitialized]
748 | #define PyInt_FromLong(x) PyLong_FromLong(x)
| ^~~~~~~~~~~~~~~
pyhdf/hdfext_wrap.c:7313:9: note: ‘temp7’ was declared here
7313 | int32 temp7 ;
| ^~~~~
pyhdf/hdfext_wrap.c:748:27: warning: ‘temp3’ may be used uninitialized in this function [-Wmaybe-uninitialized]
748 | #define PyInt_FromLong(x) PyLong_FromLong(x)
| ^~~~~~~~~~~~~~~
pyhdf/hdfext_wrap.c:7305:9: note: ‘temp3’ was declared here
7305 | int32 temp3 ;
| ^~~~~
gcc -pthread -shared -L/home/gcaria/usr/local/lib/../lib64 -L/home/gcaria/usr/local/lib -L/home/gcaria/usr/local/lib -I/home/gcaria/usr/local/include build/temp.linux-x86_64-3.8/pyhdf/hdfext_wrap.o -L/home/gcaria/usr/local/lib -L/home/gcaria/usr/local/lib64 -L/home/gcaria/usr/local/lib -L/home/gcaria/usr/local/lib64 -L -L/usr/lib -L/usr/local/lib -L/lib -lmfhdf -ldf -ljpeg -lz -o build/lib.linux-x86_64-3.8/pyhdf/_hdfext.cpython-38-x86_64-linux-gnu.so
/usr/bin/ld: /home/gcaria/usr/local/lib/libmfhdf.a(mfsd.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libmfhdf.a(putget.o): relocation R_X86_64_32S against `.rodata' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libmfhdf.a(putgetg.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libmfhdf.a(string.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libmfhdf.a(var.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libmfhdf.a(array.o): relocation R_X86_64_32S against `.rodata' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libmfhdf.a(attr.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libmfhdf.a(cdf.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libmfhdf.a(dim.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libmfhdf.a(file.o): relocation R_X86_64_32 against undefined symbol `rlim' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libmfhdf.a(hdfsds.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libmfhdf.a(iarray.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libmfhdf.a(error.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libmfhdf.a(nssdc.o): relocation R_X86_64_32S against `.rodata' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libmfhdf.a(xdrposix.o): relocation R_X86_64_32S against `.data' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(dfconv.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(dfgroup.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(dfknat.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(dfkswap.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(hblocks.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(hchunks.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(hcomp.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(herr.o): relocation R_X86_64_32S against `.rodata' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(hextelt.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(hfile.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(hfiledd.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(mcache.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(mfan.o): relocation R_X86_64_32 against symbol `ANIanncmp' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(mstdio.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(tbbt.o): relocation R_X86_64_32 against `.rodata.str1.8' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(vattr.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(vg.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(vgp.o): relocation R_X86_64_32 against symbol `vfdestroynode' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(vhi.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(vio.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(vparse.o): relocation R_X86_64_32S against `.bss' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(vrw.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(vsfld.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(atom.o): relocation R_X86_64_32S against `.bss' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(bitvect.o): relocation R_X86_64_32S against `.rodata' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(cdeflate.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(cnbit.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(cnone.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(crle.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(cskphuff.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(cszip.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(dynarray.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(glist.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(hbitio.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(hbuffer.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(hcompri.o): relocation R_X86_64_32 against `.rodata' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(vconv.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(dfcomp.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(dfimcomp.o): relocation R_X86_64_32 against `.bss' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(dfjpeg.o): relocation R_X86_64_32S against symbol `hdf_init_destination' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(dfrle.o): relocation R_X86_64_32S against `.bss' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: /home/gcaria/usr/local/lib/libdf.a(dfunjpeg.o): relocation R_X86_64_32S against symbol `hdf_init_source' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: final link failed: Nonrepresentable section on output
collect2: error: ld returned 1 exit status
error: Command "gcc -pthread -shared -L/home/gcaria/usr/local/lib/../lib64 -L/home/gcaria/usr/local/lib -L/home/gcaria/usr/local/lib -I/home/gcaria/usr/local/include build/temp.linux-x86_64-3.8/pyhdf/hdfext_wrap.o -L/home/gcaria/usr/local/lib -L/home/gcaria/usr/local/lib64 -L/home/gcaria/usr/local/lib -L/home/gcaria/usr/local/lib64 -L -L/usr/lib -L/usr/local/lib -L/lib -lmfhdf -ldf -ljpeg -lz -o build/lib.linux-x86_64-3.8/pyhdf/_hdfext.cpython-38-x86_64-linux-gnu.so" failed with exit status 1
----------------------------------------
ERROR: Command errored out with exit status 1: /home/gcaria/envs/giacos/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-7624spxi/pyhdf/setup.py'"'"'; __file__='"'"'/tmp/pip-install-7624spxi/pyhdf/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-4kzqzl_w/install-record.txt --single-version-externally-managed --compile --install-headers /home/gcaria/envs/giacos/include/site/python3.8/pyhdf Check the logs for full command output.