Cython 0.29.2 & 0.29.4 of "Anaconda 2018.12" does not compatible with gcc 8.2.1 on Arch Linux #183
Comments
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You should use cython and compilers from Anaconda Distribution, not your
system ones.
…On Wed, Feb 6, 2019, 1:50 PM Houchen Li ***@***.*** wrote:
I copied the code of fib.pyx from the tutorial and compiled it with Cython
on my Arch Linux (gcc 8.2.1). Then I got the following error:
***@***.*** /home/houchen_li/Projects/HerringModel python setup.py build_ext --inplace
Compiling fib.pyx because it changed.
[1/1] Cythonizing fib.pyx
/opt/anaconda/lib/python3.7/site-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /home/houchen_li/Projects/HerringModel/fib.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
running build_ext
building 'fib' extension
creating build
creating build/temp.linux-x86_64-3.7
gcc -pthread -B /opt/anaconda/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/opt/anaconda/include/python3.7m -c fib.c -o build/temp.linux-x86_64-3.7/fib.o
gcc -pthread -shared -B /opt/anaconda/compiler_compat -L/opt/anaconda/lib -Wl,-rpath=/opt/anaconda/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-3.7/fib.o -o /home/houchen_li/Projects/HerringModel/fib.cpython-37m-x86_64-linux-gnu.so
/opt/anaconda/compiler_compat/ld: build/temp.linux-x86_64-3.7/fib.o: unable to initialize decompress status for section .debug_info
/opt/anaconda/compiler_compat/ld: build/temp.linux-x86_64-3.7/fib.o: unable to initialize decompress status for section .debug_info
/opt/anaconda/compiler_compat/ld: build/temp.linux-x86_64-3.7/fib.o: unable to initialize decompress status for section .debug_info
/opt/anaconda/compiler_compat/ld: build/temp.linux-x86_64-3.7/fib.o: unable to initialize decompress status for section .debug_info
build/temp.linux-x86_64-3.7/fib.o: file not recognized: file format not recognized
collect2: 错误：ld 返回 1
error: command 'gcc' failed with exit status 1
I guess it might because gcc 8.2.1 change to a new syntax so that Cython
is not able to use gcc any more?
Does anyone have ideas?
cython/cython#2824 (comment)
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I've been struggling with the same issue, and haven't been able to find a nice documentation about it. I guess something like a "prepare your build/development environment under conda" or something would be pretty useful. Right now, my gcc and cython are from conda, but still I encounter the same issue pip installing scikit-learn's master. error message: C compiler: gcc -pthread -B /home/adrin/.conda/envs/aif360/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC
creating build/temp.linux-x86_64-3.6/sklearn/__check_build
compile options: '-I/home/adrin/.conda/envs/aif360/lib/python3.6/site-packages/numpy/core/include -I/home/adrin/.conda/envs/aif360/lib/python3.6/site-packages/numpy/core/include -I/home/adrin/.conda/envs/aif360/include/python3.6m -c'
gcc: sklearn/__check_build/_check_build.c
gcc -pthread -shared -B /home/adrin/.conda/envs/aif360/compiler_compat -L/home/adrin/.conda/envs/aif360/lib -Wl,-rpath=/home/adrin/.conda/envs/aif360/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-3.6/sklearn/__check_build/_check_build.o -Lbuild/temp.linux-x86_64-3.6 -o build/lib.linux-x86_64-3.6/sklearn/__check_build/_check_build.cpython-36m-x86_64-linux-gnu.so
/home/adrin/.conda/envs/aif360/compiler_compat/ld: build/temp.linux-x86_64-3.6/sklearn/__check_build/_check_build.o: unable to initialize decompress status for section .debug_info
/home/adrin/.conda/envs/aif360/compiler_compat/ld: build/temp.linux-x86_64-3.6/sklearn/__check_build/_check_build.o: unable to initialize decompress status for section .debug_info
build/temp.linux-x86_64-3.6/sklearn/__check_build/_check_build.o: file not recognized: file format not recognized
collect2: error: ld returned 1 exit status
/home/adrin/.conda/envs/aif360/compiler_compat/ld: build/temp.linux-x86_64-3.6/sklearn/__check_build/_check_build.o: unable to initialize decompress status for section .debug_info
/home/adrin/.conda/envs/aif360/compiler_compat/ld: build/temp.linux-x86_64-3.6/sklearn/__check_build/_check_build.o: unable to initialize decompress status for section .debug_info
build/temp.linux-x86_64-3.6/sklearn/__check_build/_check_build.o: file not recognized: file format not recognized
collect2: error: ld returned 1 exit status
error: Command "gcc -pthread -shared -B /home/adrin/.conda/envs/aif360/compiler_compat -L/home/adrin/.conda/envs/aif360/lib -Wl,-rpath=/home/adrin/.conda/envs/aif360/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-3.6/sklearn/__check_build/_check_build.o -Lbuild/temp.linux-x86_64-3.6 -o build/lib.linux-x86_64-3.6/sklearn/__check_build/_check_build.cpython-36m-x86_64-linux-gnu.so" failed with exit status 1
----------------------------------------
Rolling back uninstall of scikit-learn
Command "/home/adrin/.conda/envs/aif360/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-req-build-2nygabxe/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-tsh82bp8/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /tmp/pip-req-build-2nygabxe/packages:# Name Version Build Channel
aif360-learn 0.1.dev1 <pip>
alabaster 0.7.12 <pip>
AnyQt 0.0.10 <pip>
asn1crypto 0.24.0 <pip>
asn1crypto 0.24.0 py36_0
atomicwrites 1.2.1 <pip>
attrs 18.2.0 <pip>
autopep8 1.4.3 <pip>
backcall 0.1.0 <pip>
beautifulsoup4 4.6.3 py36_0
BlackBoxAuditing 0.1.40 <pip>
blas 1.0 mkl
bleach 3.0.2 <pip>
Bottleneck 1.2.1 <pip>
bzip2 1.0.6 h14c3975_5
ca-certificates 2019.1.23 0
certifi 2018.11.29 py36_0
cffi 1.11.5 py36he75722e_1
chardet 3.0.4 py36_1
chardet 3.0.4 <pip>
cloog 0.18.0 0
cloudpickle 0.6.1 <pip>
commonmark 0.8.1 <pip>
conda 4.5.12 py36_0
conda-build 3.17.6 py36_0
conda-env 2.6.0 1
cryptography 2.4.1 <pip>
cryptography 2.4.2 py36h1ba5d50_0
cvxcanon 0.1.1 py36_0 cvxgrp
CVXcanon 0.1.1 <pip>
cvxpy 1.0.6 py36_0 cvxgrp
cycler 0.10.0 <pip>
cython 0.29.4 py36he6710b0_0
dask 0.20.1 <pip>
decorator 4.3.0 <pip>
defusedxml 0.5.0 <pip>
dill 0.2.8.2 py36_0
docutils 0.14 <pip>
ecos 2.0.5 py36_0 cvxgrp
ecos 2.0.5 <pip>
entrypoints 0.2.3 <pip>
expat 2.2.5 hf484d3e_1002 conda-forge
fastcache 1.0.2 <pip>
fastcache 1.0.2 py36h14c3975_2
filelock 3.0.10 py36_0
flake8 3.6.0 <pip>
future 0.17.1 <pip>
gcc 4.8.5 7
glob2 0.6 py36_1
gmp 6.1.2 h6c8ec71_1
icu 58.2 h9c2bf20_1
idna 2.8 py36_0
idna 2.7 <pip>
imagesize 1.1.0 <pip>
intel-openmp 2019.1 144
ipykernel 5.1.0 <pip>
ipython 7.1.1 <pip>
ipython-genutils 0.2.0 <pip>
ipywidgets 7.4.2 <pip>
isl 0.12.2 0
jedi 0.13.1 <pip>
jeepney 0.4 <pip>
jinja2 2.10 py36_0
Jinja2 2.10 <pip>
joblib 0.13.0 <pip>
jsonschema 2.6.0 <pip>
jupyter-client 5.2.3 <pip>
jupyter-core 4.4.0 <pip>
keyring 16.0.2 <pip>
keyrings.alt 3.1 <pip>
kiwisolver 1.0.1 <pip>
lapack 3.6.1 ha44fe06_2 conda-forge
libarchive 3.3.3 h5d8350f_5
libedit 3.1.20170329 h6b74fdf_2
libffi 3.2.1 hd88cf55_4
libgcc 7.2.0 h69d50b8_2
libgcc-ng 8.2.0 hdf63c60_1
libgfortran 3.0.0 1 conda-forge
libgfortran-ng 7.3.0 hdf63c60_0
libiconv 1.15 h14c3975_1004 conda-forge
liblief 0.9.0 h7725739_1
libstdcxx-ng 8.2.0 hdf63c60_1
libxml2 2.9.8 h26e45fe_1
lime 0.1.1.32 <pip>
llvmlite 0.25.0 <pip>
lz4-c 1.8.1.2 h14c3975_0
lzo 2.10 h49e0be7_2
markupsafe 1.1.0 py36h7b6447c_0
MarkupSafe 1.1.0 <pip>
matplotlib 3.0.2 <pip>
mccabe 0.6.1 <pip>
mistune 0.8.4 <pip>
mkl 2019.1 144
mkl_fft 1.0.6 py36hd81dba3_0
mkl_random 1.0.2 py36hd81dba3_0
more-itertools 4.3.0 <pip>
mpc 1.0.3 hec55b23_5
mpfr 3.1.5 h11a74b3_2
multiprocess 0.70.6.1 <pip>
multiprocess 0.70.4 py36_0 cvxgrp
nbconvert 5.4.0 <pip>
nbformat 4.4.0 <pip>
ncurses 6.1 hf484d3e_0
networkx 1.11 <pip>
notebook 5.7.0 <pip>
numba 0.40.1 <pip>
numpy 1.15.4 py36h7e9f1db_0
numpy 1.15.4 <pip>
numpy-base 1.15.4 py36hde5b4d6_0
openssl 1.1.1a h7b6447c_0
Orange3 3.7.1 <pip>
osqp 0.5.0 <pip>
packaging 19.0 <pip>
pandas 0.23.3 <pip>
pandocfilters 1.4.2 <pip>
parso 0.3.1 <pip>
patchelf 0.9 he6710b0_3
pexpect 4.6.0 <pip>
pickleshare 0.7.5 <pip>
Pillow 5.3.0 <pip>
pip 18.1 py36_0
pip-upgrade-outdated 1.2 <pip>
pkginfo 1.4.2 py36_1
pluggy 0.8.0 <pip>
prometheus-client 0.4.2 <pip>
prompt-toolkit 2.0.7 <pip>
protobuf 3.6.1 <pip>
psutil 5.4.8 py36h7b6447c_0
ptyprocess 0.6.0 <pip>
py 1.7.0 <pip>
py-lief 0.9.0 py36h7725739_1
pycodestyle 2.4.0 <pip>
pycosat 0.6.3 py36h14c3975_0
pycparser 2.19 py36_0
pycparser 2.19 <pip>
pyflakes 2.0.0 <pip>
Pygments 2.2.0 <pip>
pyopenssl 18.0.0 py36_0
pyparsing 2.3.0 <pip>
pyqtgraph 0.10.0 <pip>
pysocks 1.6.8 py36_0
pytest 4.0.0 <pip>
python 3.6.7 h0371630_0
python-dateutil 2.7.5 <pip>
python-libarchive-c 2.8 py36_6
pytz 2018.7 py36_0
PyWavelets 1.0.1 <pip>
pyyaml 3.13 py36h14c3975_0
pyzmq 17.1.2 <pip>
readline 7.0 h7b6447c_5
readme-renderer 24.0 <pip>
requests 2.20.1 <pip>
requests 2.21.0 py36_0
requests-toolbelt 0.8.0 <pip>
ruamel_yaml 0.15.46 py36h14c3975_0
scikit-image 0.14.1 <pip>
scikit-learn 0.20.0 <pip>
scipy 1.1.0 <pip>
scipy 1.1.0 py36h7c811a0_2
scs 1.2.6 py36_0 cvxgrp
scs 2.0.2 <pip>
SecretStorage 3.1.0 <pip>
Send2Trash 1.5.0 <pip>
serverfiles 0.2.1 <pip>
setuptools 40.5.0 py36_0
six 1.11.0 <pip>
six 1.12.0 py36_0
snowballstemmer 1.2.1 <pip>
Sphinx 1.8.3 <pip>
sphinx-rtd-theme 0.4.2 <pip>
sphinxcontrib-websupport 1.1.0 <pip>
sqlite 3.25.2 h7b6447c_0
tensorflow 1.1.0 <pip>
terminado 0.8.1 <pip>
testpath 0.4.2 <pip>
tk 8.6.8 hbc83047_0
toolz 0.9.0 py36_0
toolz 0.9.0 <pip>
tornado 5.1.1 <pip>
tqdm 4.28.1 py36h28b3542_0
traitlets 4.3.2 <pip>
twine 1.12.1 <pip>
urllib3 1.24.1 py36_0
urllib3 1.24.1 <pip>
wcwidth 0.1.7 <pip>
webencodings 0.5.1 <pip>
Werkzeug 0.14.1 <pip>
wheel 0.32.2 py36_0
widgetsnbextension 3.4.2 <pip>
xlrd 1.1.0 <pip>
xz 5.2.4 h14c3975_4
yaml 0.1.7 had09818_2
zlib 1.2.11 ha838bed_2
zstd 1.3.7 h0b5b093_0 |
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I have no idea about this issue. In the end, I just stop using anaconda and switch to the system-wide cython. Then all goes fine! |
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I'm also coming up against this issue (also an Arch user). I presume there is some interaction going on with the host setup and the conda internals although I'm not quite sure where I should start digging. Any pointers and I can help debug this issue. |
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The problem is that the system The only thing you can do for now is to ensure our compilers are getting used. |
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@mingwandroid Super, thanks for that workaround, that did the trick! |
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It's not really a workaround as such, you are getting a more homogenous setup this way which is better, though these compilers don't look in system folders which is good for some use-cases but bad for others. |
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That's true. I was confused when I couldn't resolve the issue by |
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No one should use the old Recipes should use the jinja2 functions that conda-build provides though when declaring dependencies on our compilers so e.g.: |
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Thanks for the advice @mingwandroid |
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Thanks, very helpful! If I wanted to supply a list of conda packages for people to install, how can I do this in a OS independent way, i.e. is there a OS agnostic package like |
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I'm sorry I just noticed this, but this is actually in the wrong repo. This is the issue tracker for a very specific piece of software, not for the Anaconda Distribution in general. |
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@mcg1969 Where should this issue go? I'm running into this on every new conda environment that I create and it is really annoying. My workaround has been: |
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Perhaps you intend this to be for https://github.com/ContinuumIO/anaconda-issues ? This is an issue tracker for a single, specific piece of software. |
I copied the code of fib.pyx from the tutorial and compiled it with Cython on my Arch Linux (gcc 8.2.1). Then I got the following error:
I guess it might because gcc 8.2.1 change to a new syntax so that Cython is not able to use gcc any more?
Does anyone have ideas?
cython/cython#2824 (comment)
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