gcc (4.9 & 8.3) pip build issues
Closed this issue · 1 comments
ml-evs commented
pip install httptools with gcc-8.3 fails, with an error about unrecognized file formats when linking (see below). This is fair enough, maybe this recent version is unsupported.
Collecting httptools
Downloading https://files.pythonhosted.org/packages/1b/03/215969db11abe8741e9c266a4cbe803a372bd86dd35fa0084c4df6d4bd00/httptools-0.0.13.tar.gz (104kB)
|████████████████████████████████| 112kB 7.4MB/s
Building wheels for collected packages: httptools
Building wheel for httptools (setup.py) ... error
ERROR: Complete output from command /home/matthew/.local/conda/envs/optimade/bin/python -u -c 'import setuptools, tokenize;__file__='"'"'/tmp/pip-install-xrfgwi79/httptools/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-8yjnvozz --python-tag cp36:
ERROR: running bdist_wheel
running build
running build_py
creating build
creating build/lib.linux-x86_64-3.6
creating build/lib.linux-x86_64-3.6/httptools
copying httptools/__init__.py -> build/lib.linux-x86_64-3.6/httptools
creating build/lib.linux-x86_64-3.6/httptools/parser
copying httptools/parser/errors.py -> build/lib.linux-x86_64-3.6/httptools/parser
copying httptools/parser/__init__.py -> build/lib.linux-x86_64-3.6/httptools/parser
running egg_info
writing httptools.egg-info/PKG-INFO
writing dependency_links to httptools.egg-info/dependency_links.txt
writing top-level names to httptools.egg-info/top_level.txt
reading manifest file 'httptools.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
writing manifest file 'httptools.egg-info/SOURCES.txt'
copying httptools/parser/parser.c -> build/lib.linux-x86_64-3.6/httptools/parser
running build_ext
building 'httptools.parser.parser' extension
creating build/temp.linux-x86_64-3.6
creating build/temp.linux-x86_64-3.6/httptools
creating build/temp.linux-x86_64-3.6/httptools/parser
creating build/temp.linux-x86_64-3.6/vendor
creating build/temp.linux-x86_64-3.6/vendor/http-parser
gcc -pthread -B /home/matthew/.local/conda/envs/optimade/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/matthew/.local/conda/envs/optimade/include/python3.6m -c httptools/parser/parser.c -o build/temp.linux-x86_64-3.6/httptools/parser/parser.o -O2
gcc -pthread -B /home/matthew/.local/conda/envs/optimade/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/matthew/.local/conda/envs/optimade/include/python3.6m -c vendor/http-parser/http_parser.c -o build/temp.linux-x86_64-3.6/vendor/http-parser/http_parser.o -O2
gcc -pthread -shared -B /home/matthew/.local/conda/envs/optimade/compiler_compat -L/home/matthew/.local/conda/envs/optimade/lib -Wl,-rpath=/home/matthew/.local/conda/envs/optimade/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-3.6/httptools/parser/parser.o build/temp.linux-x86_64-3.6/vendor/http-parser/http_parser.o -o build/lib.linux-x86_64-3.6/httptools/parser/parser.cpython-36m-x86_64-linux-gnu.so
/home/matthew/.local/conda/envs/optimade/compiler_compat/ld: build/temp.linux-x86_64-3.6/httptools/parser/parser.o: unable to initialize decompress status for section .debug_info
/home/matthew/.local/conda/envs/optimade/compiler_compat/ld: build/temp.linux-x86_64-3.6/httptools/parser/parser.o: unable to initialize decompress status for section .debug_info
/home/matthew/.local/conda/envs/optimade/compiler_compat/ld: build/temp.linux-x86_64-3.6/httptools/parser/parser.o: unable to initialize decompress status for section .debug_info
/home/matthew/.local/conda/envs/optimade/compiler_compat/ld: build/temp.linux-x86_64-3.6/httptools/parser/parser.o: unable to initialize decompress status for section .debug_info
build/temp.linux-x86_64-3.6/httptools/parser/parser.o: file not recognized: file format not recognized
collect2: error: ld returned 1 exit status
error: command 'gcc' failed with exit status 1
----------------------------------------
ERROR: Failed building wheel for httptools
Running setup.py clean for httptools
Failed to build httptools
Installing collected packages: httptools
Running setup.py install for httptools ... error
ERROR: Complete output from command /home/matthew/.local/conda/envs/optimade/bin/python -u -c 'import setuptools, tokenize;__file__='"'"'/tmp/pip-install-xrfgwi79/httptools/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-_hgd3hzc/install-record.txt --single-version-externally-managed --compile:
ERROR: running install
running build
running build_py
creating build
creating build/lib.linux-x86_64-3.6
creating build/lib.linux-x86_64-3.6/httptools
copying httptools/__init__.py -> build/lib.linux-x86_64-3.6/httptools
creating build/lib.linux-x86_64-3.6/httptools/parser
copying httptools/parser/errors.py -> build/lib.linux-x86_64-3.6/httptools/parser
copying httptools/parser/__init__.py -> build/lib.linux-x86_64-3.6/httptools/parser
running egg_info
writing httptools.egg-info/PKG-INFO
writing dependency_links to httptools.egg-info/dependency_links.txt
writing top-level names to httptools.egg-info/top_level.txt
reading manifest file 'httptools.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
writing manifest file 'httptools.egg-info/SOURCES.txt'
copying httptools/parser/parser.c -> build/lib.linux-x86_64-3.6/httptools/parser
running build_ext
building 'httptools.parser.parser' extension
creating build/temp.linux-x86_64-3.6
creating build/temp.linux-x86_64-3.6/httptools
creating build/temp.linux-x86_64-3.6/httptools/parser
creating build/temp.linux-x86_64-3.6/vendor
creating build/temp.linux-x86_64-3.6/vendor/http-parser
gcc -pthread -B /home/matthew/.local/conda/envs/optimade/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/matthew/.local/conda/envs/optimade/include/python3.6m -c httptools/parser/parser.c -o build/temp.linux-x86_64-3.6/httptools/parser/parser.o -O2
gcc -pthread -B /home/matthew/.local/conda/envs/optimade/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/matthew/.local/conda/envs/optimade/include/python3.6m -c vendor/http-parser/http_parser.c -o build/temp.linux-x86_64-3.6/vendor/http-parser/http_parser.o -O2
gcc -pthread -shared -B /home/matthew/.local/conda/envs/optimade/compiler_compat -L/home/matthew/.local/conda/envs/optimade/lib -Wl,-rpath=/home/matthew/.local/conda/envs/optimade/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-3.6/httptools/parser/parser.o build/temp.linux-x86_64-3.6/vendor/http-parser/http_parser.o -o build/lib.linux-x86_64-3.6/httptools/parser/parser.cpython-36m-x86_64-linux-gnu.so
/home/matthew/.local/conda/envs/optimade/compiler_compat/ld: build/temp.linux-x86_64-3.6/httptools/parser/parser.o: unable to initialize decompress status for section .debug_info
/home/matthew/.local/conda/envs/optimade/compiler_compat/ld: build/temp.linux-x86_64-3.6/httptools/parser/parser.o: unable to initialize decompress status for section .debug_info
/home/matthew/.local/conda/envs/optimade/compiler_compat/ld: build/temp.linux-x86_64-3.6/httptools/parser/parser.o: unable to initialize decompress status for section .debug_info
/home/matthew/.local/conda/envs/optimade/compiler_compat/ld: build/temp.linux-x86_64-3.6/httptools/parser/parser.o: unable to initialize decompress status for section .debug_info
build/temp.linux-x86_64-3.6/httptools/parser/parser.o: file not recognized: file format not recognized
collect2: error: ld returned 1 exit status
error: command 'gcc' failed with exit status 1
----------------------------------------
ERROR: Command "/home/matthew/.local/conda/envs/optimade/bin/python -u -c 'import setuptools, tokenize;__file__='"'"'/tmp/pip-install-xrfgwi79/httptools/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-_hgd3hzc/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /tmp/pip-install-xrfgwi79/httptools/
I tried again with gcc-4.9 (CC=gcc-4.9 CXX=gcc-4.9), and I receive a different error about a missing library (libmpfr.so.4; I have libmpfr.so.6). Symlinking libmpfr.so.6 to libmpfr.so.4 gets me back to the same error as gcc-8.3:
$ CC=gcc-4.9 CXX=gcc-4.9 pip --no-cache-dir install httptools
Collecting httptools
Downloading https://files.pythonhosted.org/packages/1b/03/215969db11abe8741e9c266a4cbe803a372bd86dd35fa0084c4df6d4bd00/httptools-0.0.13.tar.gz (104kB)
|████████████████████████████████| 112kB 7.5MB/s
Building wheels for collected packages: httptools
Building wheel for httptools (setup.py) ... error
ERROR: Complete output from command /home/matthew/.local/conda/envs/optimade/bin/python -u -c 'import setuptools, tokenize;__file__='"'"'/tmp/pip-install-bso7iy81/httptools/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-pvaohfeg --python-tag cp36:
ERROR: running bdist_wheel
running build
running build_py
creating build
creating build/lib.linux-x86_64-3.6
creating build/lib.linux-x86_64-3.6/httptools
copying httptools/__init__.py -> build/lib.linux-x86_64-3.6/httptools
creating build/lib.linux-x86_64-3.6/httptools/parser
copying httptools/parser/errors.py -> build/lib.linux-x86_64-3.6/httptools/parser
copying httptools/parser/__init__.py -> build/lib.linux-x86_64-3.6/httptools/parser
running egg_info
writing httptools.egg-info/PKG-INFO
writing dependency_links to httptools.egg-info/dependency_links.txt
writing top-level names to httptools.egg-info/top_level.txt
reading manifest file 'httptools.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
writing manifest file 'httptools.egg-info/SOURCES.txt'
copying httptools/parser/parser.c -> build/lib.linux-x86_64-3.6/httptools/parser
running build_ext
building 'httptools.parser.parser' extension
creating build/temp.linux-x86_64-3.6
creating build/temp.linux-x86_64-3.6/httptools
creating build/temp.linux-x86_64-3.6/httptools/parser
creating build/temp.linux-x86_64-3.6/vendor
creating build/temp.linux-x86_64-3.6/vendor/http-parser
gcc-4.9 -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/matthew/.local/conda/envs/optimade/include/python3.6m -c httptools/parser/parser.c -o build/temp.linux-x86_64-3.6/httptools/parser/parser.o -O2
/usr/lib/gcc/x86_64-unknown-linux-gnu/4.9.3/cc1: error while loading shared libraries: libmpfr.so.4: cannot open shared object file: No such file or directory
error: command 'gcc-4.9' failed with exit status 1
----------------------------------------
ERROR: Failed building wheel for httptools
Running setup.py clean for httptools
Failed to build httptools
Installing collected packages: httptools
Running setup.py install for httptools ... error
ERROR: Complete output from command /home/matthew/.local/conda/envs/optimade/bin/python -u -c 'import setuptools, tokenize;__file__='"'"'/tmp/pip-install-bso7iy81/httptools/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-t5796_ix/install-record.txt --single-version-externally-managed --compile:
ERROR: running install
running build
running build_py
creating build
creating build/lib.linux-x86_64-3.6
creating build/lib.linux-x86_64-3.6/httptools
copying httptools/__init__.py -> build/lib.linux-x86_64-3.6/httptools
creating build/lib.linux-x86_64-3.6/httptools/parser
copying httptools/parser/errors.py -> build/lib.linux-x86_64-3.6/httptools/parser
copying httptools/parser/__init__.py -> build/lib.linux-x86_64-3.6/httptools/parser
running egg_info
writing httptools.egg-info/PKG-INFO
writing dependency_links to httptools.egg-info/dependency_links.txt
writing top-level names to httptools.egg-info/top_level.txt
reading manifest file 'httptools.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
writing manifest file 'httptools.egg-info/SOURCES.txt'
copying httptools/parser/parser.c -> build/lib.linux-x86_64-3.6/httptools/parser
running build_ext
building 'httptools.parser.parser' extension
creating build/temp.linux-x86_64-3.6
creating build/temp.linux-x86_64-3.6/httptools
creating build/temp.linux-x86_64-3.6/httptools/parser
creating build/temp.linux-x86_64-3.6/vendor
creating build/temp.linux-x86_64-3.6/vendor/http-parser
gcc-4.9 -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/matthew/.local/conda/envs/optimade/include/python3.6m -c httptools/parser/parser.c -o build/temp.linux-x86_64-3.6/httptools/parser/parser.o -O2
/usr/lib/gcc/x86_64-unknown-linux-gnu/4.9.3/cc1: error while loading shared libraries: libmpfr.so.4: cannot open shared object file: No such file or directory
error: command 'gcc-4.9' failed with exit status 1
----------------------------------------
ERROR: Command "/home/matthew/.local/conda/envs/optimade/bin/python -u -c 'import setuptools, tokenize;__file__='"'"'/tmp/pip-install-bso7iy81/httptools/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-t5796_ix/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /tmp/pip-install-bso7iy81/httptools/
Notice that the third call to the C compiler is to `gcc`, not `gcc-4.9` as set by my environment variables. Running `CC=clang CXX=clang pip --no-cache-dir install httptools` works fine. As GCC is the only compiler guaranteed to be installed in almost every Linux distro, do you know how this could be rectified? Thanks.
ml-evs commented
After some further investigation, the bug goes all the way down to binutils and ELF in their current state on Arch Linux: https://bbs.archlinux.org/viewtopic.php?id=242682