Using new compilers on linux fails with "Failed to import the site module"
Zaharid opened this issue · comments
I want to update this recipe:
https://github.com/Zaharid/conda-recipes/tree/master/lhapdf
to use the new compiler infrastructure. I rewrite the meta.yaml
file this way:
package:
name: lhapdf
version: "6.2.1"
source:
url: http://www.hepforge.org/archive/lhapdf/LHAPDF-6.2.1.tar.gz
md5: 9e05567d538fdb4862d4781cd076d7db
fn: LHAPDF-6.2.1.tar.gz
requirements:
build:
- {{compiler('cxx')}}
host:
- python
- cython
run:
- python
build:
number: 0
detect_binary_files_with_prefix: True
test:
commands:
- lhapdf-config
- python -c "import lhapdf"
about:
home: https://lhapdf.hepforge.org/
license: UNKNOWN
I get the following error when trying to build the recipe on a linux (Mint 18.3) laptop:
Failed to import the site module
Traceback (most recent call last):
File "/home/zah/anaconda3/lib/python3.6/site.py", line 544, in <module>
main()
File "/home/zah/anaconda3/lib/python3.6/site.py", line 530, in main
known_paths = addusersitepackages(known_paths)
File "/home/zah/anaconda3/lib/python3.6/site.py", line 282, in addusersitepackages
user_site = getusersitepackages()
File "/home/zah/anaconda3/lib/python3.6/site.py", line 258, in getusersitepackages
user_base = getuserbase() # this will also set USER_BASE
File "/home/zah/anaconda3/lib/python3.6/site.py", line 248, in getuserbase
USER_BASE = get_config_var('userbase')
File "/home/zah/anaconda3/lib/python3.6/sysconfig.py", line 601, in get_config_var
return get_config_vars().get(name)
File "/home/zah/anaconda3/lib/python3.6/sysconfig.py", line 550, in get_config_vars
_init_posix(_CONFIG_VARS)
File "/home/zah/anaconda3/lib/python3.6/sysconfig.py", line 421, in _init_posix
_temp = __import__(name, globals(), locals(), ['build_time_vars'], 0)
ModuleNotFoundError: No module named '_sysconfigdata_x86_64_conda_cos6_linux_gnu'
Traceback (most recent call last):
File "/home/zah/anaconda3/bin/conda-build", line 11, in <module>
sys.exit(main())
File "/home/zah/anaconda3/lib/python3.6/site-packages/conda_build/cli/main_build.py", line 388, in main
execute(sys.argv[1:])
File "/home/zah/anaconda3/lib/python3.6/site-packages/conda_build/cli/main_build.py", line 379, in execute
verify=args.verify)
File "/home/zah/anaconda3/lib/python3.6/site-packages/conda_build/api.py", line 187, in build
need_source_download=need_source_download, config=config, variants=variants)
File "/home/zah/anaconda3/lib/python3.6/site-packages/conda_build/build.py", line 1801, in build_tree
notest=notest,
File "/home/zah/anaconda3/lib/python3.6/site-packages/conda_build/build.py", line 1137, in build
utils.check_call_env(cmd, env=env, cwd=src_dir)
File "/home/zah/anaconda3/lib/python3.6/site-packages/conda_build/utils.py", line 676, in check_call_env
return _func_defaulting_env_to_os_environ(subprocess.check_call, *popenargs, **kwargs)
File "/home/zah/anaconda3/lib/python3.6/site-packages/conda_build/utils.py", line 672, in _func_defaulting_env_to_os_environ
return func(_args, **kwargs)
File "/home/zah/anaconda3/lib/python3.6/subprocess.py", line 291, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['/bin/bash', '-e', '/home/zah/anaconda3/conda-bld/lhapdf_1511638676021/work/conda_build.sh']' returned non-zero exit status 1.
I am not sure where the error comes from. Seems to be some activate script. Note that it seems to be looking at the python
executable in the root environment rather than the one that gets installed.
Full output:
$ conda build lhapdf/
Attempting to finalize metadata for lhapdf
INFO:conda_build.metadata:Attempting to finalize metadata for lhapdf
BUILD START: ['lhapdf-6.2.1-py36ha9410bc_0.tar.bz2']
The following NEW packages will be INSTALLED:
binutils_impl_linux-64: 2.28.1-h04c84fa_2
binutils_linux-64: 7.2.0-hc67e822_14
ca-certificates: 2017.08.26-h1d4fec5_0
certifi: 2017.11.5-py36hf29ccca_0
cython: 0.26.1-py36h21c49d0_0
gcc_impl_linux-64: 7.2.0-hc5ce805_2
gcc_linux-64: 7.2.0-hf1c97a4_14
gxx_impl_linux-64: 7.2.0-hd3faf3d_2
gxx_linux-64: 7.2.0-h4bc98f9_14
libedit: 3.1-heed3624_0
libffi: 3.2.1-hd88cf55_4
libgcc-ng: 7.2.0-h7cc24e2_2
libstdcxx-ng: 7.2.0-h7a57d05_2
ncurses: 6.0-h9df7e31_2
openssl: 1.0.2m-h26d622b_1
pip: 9.0.1-py36h6c6f9ce_4
python: 3.6.3-h6c0c0dc_5
readline: 7.0-ha6073c6_4
setuptools: 36.5.0-py36he42e2e1_0
sqlite: 3.20.1-hb898158_2
tk: 8.6.7-hc745277_3
wheel: 0.30.0-py36hfd4bba0_1
xz: 5.2.3-h55aa19d_2
zlib: 1.2.11-ha838bed_2
Source cache directory is: /home/zah/anaconda3/conda-bld/src_cache
Found source in cache: LHAPDF-6.2.1_9e05567d53.tar.gz
Extracting download
source tree in: /home/zah/anaconda3/conda-bld/lhapdf_1511638676021/work
INFO: activate-binutils_linux-64.sh made the following environmental changes:
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INFO: activate-gcc_linux-64.sh made the following environmental changes:
+CC=/home/zah/anaconda3/conda-bld/lhapdf_1511638676021/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/bin/x86_64-conda_cos6-linux-gnu-cc
+CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/home/zah/anaconda3/conda-bld/lhapdf_1511638676021/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include
+CPPFLAGS=-D_FORTIFY_SOURCE=2 -O2
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INFO: activate-gxx_linux-64.sh made the following environmental changes:
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Failed to import the site module
Traceback (most recent call last):
File "/home/zah/anaconda3/lib/python3.6/site.py", line 544, in <module>
main()
File "/home/zah/anaconda3/lib/python3.6/site.py", line 530, in main
known_paths = addusersitepackages(known_paths)
File "/home/zah/anaconda3/lib/python3.6/site.py", line 282, in addusersitepackages
user_site = getusersitepackages()
File "/home/zah/anaconda3/lib/python3.6/site.py", line 258, in getusersitepackages
user_base = getuserbase() # this will also set USER_BASE
File "/home/zah/anaconda3/lib/python3.6/site.py", line 248, in getuserbase
USER_BASE = get_config_var('userbase')
File "/home/zah/anaconda3/lib/python3.6/sysconfig.py", line 601, in get_config_var
return get_config_vars().get(name)
File "/home/zah/anaconda3/lib/python3.6/sysconfig.py", line 550, in get_config_vars
_init_posix(_CONFIG_VARS)
File "/home/zah/anaconda3/lib/python3.6/sysconfig.py", line 421, in _init_posix
_temp = __import__(name, globals(), locals(), ['build_time_vars'], 0)
ModuleNotFoundError: No module named '_sysconfigdata_x86_64_conda_cos6_linux_gnu'
Traceback (most recent call last):
File "/home/zah/anaconda3/bin/conda-build", line 11, in <module>
sys.exit(main())
File "/home/zah/anaconda3/lib/python3.6/site-packages/conda_build/cli/main_build.py", line 388, in main
execute(sys.argv[1:])
File "/home/zah/anaconda3/lib/python3.6/site-packages/conda_build/cli/main_build.py", line 379, in execute
verify=args.verify)
File "/home/zah/anaconda3/lib/python3.6/site-packages/conda_build/api.py", line 187, in build
need_source_download=need_source_download, config=config, variants=variants)
File "/home/zah/anaconda3/lib/python3.6/site-packages/conda_build/build.py", line 1801, in build_tree
notest=notest,
File "/home/zah/anaconda3/lib/python3.6/site-packages/conda_build/build.py", line 1137, in build
utils.check_call_env(cmd, env=env, cwd=src_dir)
File "/home/zah/anaconda3/lib/python3.6/site-packages/conda_build/utils.py", line 676, in check_call_env
return _func_defaulting_env_to_os_environ(subprocess.check_call, *popenargs, **kwargs)
File "/home/zah/anaconda3/lib/python3.6/site-packages/conda_build/utils.py", line 672, in _func_defaulting_env_to_os_environ
return func(_args, **kwargs)
File "/home/zah/anaconda3/lib/python3.6/subprocess.py", line 291, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['/bin/bash', '-e', '/home/zah/anaconda3/conda-bld/lhapdf_1511638676021/work/conda_build.sh']' returned non-zero exit status 1.
Could you try: conda update conda && conda update python
in the environment from which you are trying to invoke conda build?
Thanks! That seems to fix it. Does it mean that the defaults
channel has to have higher priority than conda-forge
for the compilers to work? Is it possible to use both channels?
Somehow your suggested workaround does not work anymore @msarahan. For reference see https://travis-ci.org/markovmodel/PyEMMA/jobs/438821050 the root env is kept in the state from miniconda3 installer, and then the compiler is being dragged in by conda-build into the build environment. Is there any chance to make this work (again, as it used to work eg. last week or so).
"Mixing" Python from default and cf was not a problem on Linux. What has changed in the meantime?
Thanks a lot for looking into this.
I believe this is a conda-forge issue, as discussed at conda-forge/python-feedstock#203
I'm closing this issue, because I believe it is unrelated to conda-build. Please open a new issue if you would like to explain why you disagree.
sorry for using this issue kind of off-topic.
Hi there, thank you for your contribution!
This issue has been automatically locked because it has not had recent activity after being closed.
Please open a new issue if needed.
Thanks!