Open dgarrimar opened 3 years ago
I think it may be related to the Python version. I made it work by installing limix=1.0.18 (Python 3.5). However, when trying in a test dataset got a new error, which I could reproduce even using the R wrapper (limmbo2):
Error in py_call_impl(callable, dots$args, dots$keywords) :
TypeError: any() takes exactly one argument (2 given)
Detailed traceback:
File "/nfs/users2/rg/dgarrido/.conda/envs/limix/lib/python3.6/site-packages/limmbo/io/input.py", line 270, in addRelatedness
if not any(relatedness, U_relatedness):
Any hint?
I also have a similar error when installing limix<2 on the MacBook recently updated. I have done this on a local conda environment with python 3. Do you have any idea to fix the issue? I want to use LiMMbo for multivariate trait LMM analysis.
Building wheel for limix (setup.py) ... error
ERROR: Command errored out with exit status 1:
command: /opt/miniconda3/envs/scr/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/5f/sltbh41n7yz9b9fx81x4rqcc0000gn/T/pip-install-3ptsu30j/limix_e19578ea694d4452b3777a93561c3960/setup.py'"'"'; __file__='"'"'/private/var/folders/5f/sltbh41n7yz9b9fx81x4rqcc0000gn/T/pip-install-3ptsu30j/limix_e19578ea694d4452b3777a93561c3960/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /private/var/folders/5f/sltbh41n7yz9b9fx81x4rqcc0000gn/T/pip-wheel-bmq1melp
cwd: /private/var/folders/5f/sltbh41n7yz9b9fx81x4rqcc0000gn/T/pip-install-3ptsu30j/limix_e19578ea694d4452b3777a93561c3960/
Complete output (200 lines):
running bdist_wheel
running build
running build_ext
building '_core' extension
creating build
creating build/temp.macosx-10.15.7-x86_64-3.9
creating build/temp.macosx-10.15.7-x86_64-3.9/External
creating build/temp.macosx-10.15.7-x86_64-3.9/External/nlopt
creating build/temp.macosx-10.15.7-x86_64-3.9/External/nlopt/api
creating build/temp.macosx-10.15.7-x86_64-3.9/External/nlopt/auglag
creating build/temp.macosx-10.15.7-x86_64-3.9/External/nlopt/bobyqa
creating build/temp.macosx-10.15.7-x86_64-3.9/External/nlopt/cdirect
creating build/temp.macosx-10.15.7-x86_64-3.9/External/nlopt/cobyla
creating build/temp.macosx-10.15.7-x86_64-3.9/External/nlopt/crs
creating build/temp.macosx-10.15.7-x86_64-3.9/External/nlopt/direct
creating build/temp.macosx-10.15.7-x86_64-3.9/External/nlopt/esch
creating build/temp.macosx-10.15.7-x86_64-3.9/External/nlopt/isres
creating build/temp.macosx-10.15.7-x86_64-3.9/External/nlopt/luksan
creating build/temp.macosx-10.15.7-x86_64-3.9/External/nlopt/mlsl
creating build/temp.macosx-10.15.7-x86_64-3.9/External/nlopt/mma
creating build/temp.macosx-10.15.7-x86_64-3.9/External/nlopt/neldermead
creating build/temp.macosx-10.15.7-x86_64-3.9/External/nlopt/newuoa
creating build/temp.macosx-10.15.7-x86_64-3.9/External/nlopt/praxis
creating build/temp.macosx-10.15.7-x86_64-3.9/External/nlopt/slsqp
creating build/temp.macosx-10.15.7-x86_64-3.9/External/nlopt/stogo
creating build/temp.macosx-10.15.7-x86_64-3.9/External/nlopt/util
creating build/temp.macosx-10.15.7-x86_64-3.9/src
creating build/temp.macosx-10.15.7-x86_64-3.9/src/limix
creating build/temp.macosx-10.15.7-x86_64-3.9/src/limix/LMM
creating build/temp.macosx-10.15.7-x86_64-3.9/src/limix/LMM_forest
creating build/temp.macosx-10.15.7-x86_64-3.9/src/limix/covar
creating build/temp.macosx-10.15.7-x86_64-3.9/src/limix/gp
creating build/temp.macosx-10.15.7-x86_64-3.9/src/limix/io
creating build/temp.macosx-10.15.7-x86_64-3.9/src/limix/likelihood
creating build/temp.macosx-10.15.7-x86_64-3.9/src/limix/mean
creating build/temp.macosx-10.15.7-x86_64-3.9/src/limix/modules
creating build/temp.macosx-10.15.7-x86_64-3.9/src/limix/utils
creating build/temp.macosx-10.15.7-x86_64-3.9/src/interfaces
creating build/temp.macosx-10.15.7-x86_64-3.9/src/interfaces/python
x86_64-apple-darwin13.4.0-clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /opt/miniconda3/envs/scr/include -arch x86_64 -I/opt/miniconda3/envs/scr/include -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /opt/miniconda3/envs/scr/include -arch x86_64 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /opt/miniconda3/envs/scr/include -D_FORTIFY_SOURCE=2 -isystem /opt/miniconda3/envs/scr/include -Isrc -IExternal -IExternal/nlopt -I./External/nlopt/stogo -I./External/nlopt/util -I./External/nlopt/direct -I./External/nlopt/cdirect -I./External/nlopt/praxis -I./External/nlopt/luksan -I./External/nlopt/crs -I./External/nlopt/mlsl -I./External/nlopt/mma -I./External/nlopt/cobyla -I./External/nlopt/newuoa -I./External/nlopt/neldermead -I./External/nlopt/auglag -I./External/nlopt/bobyqa -I./External/nlopt/isres -I./External/nlopt/slsqp -I./External/nlopt/api -I./External/nlopt/esch -I/opt/miniconda3/envs/scr/lib/python3.9/site-packages/numpy/core/include -I/opt/miniconda3/envs/scr/include/python3.9 -c ./External/nlopt/api/deprecated.cpp -o build/temp.macosx-10.15.7-x86_64-3.9/./External/nlopt/api/deprecated.o -std=c++0x
x86_64-apple-darwin13.4.0-clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /opt/miniconda3/envs/scr/include -arch x86_64 -I/opt/miniconda3/envs/scr/include -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /opt/miniconda3/envs/scr/include -arch x86_64 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /opt/miniconda3/envs/scr/include -D_FORTIFY_SOURCE=2 -isystem /opt/miniconda3/envs/scr/include -Isrc -IExternal -IExternal/nlopt -I./External/nlopt/stogo -I./External/nlopt/util -I./External/nlopt/direct -I./External/nlopt/cdirect -I./External/nlopt/praxis -I./External/nlopt/luksan -I./External/nlopt/crs -I./External/nlopt/mlsl -I./External/nlopt/mma -I./External/nlopt/cobyla -I./External/nlopt/newuoa -I./External/nlopt/neldermead -I./External/nlopt/auglag -I./External/nlopt/bobyqa -I./External/nlopt/isres -I./External/nlopt/slsqp -I./External/nlopt/api -I./External/nlopt/esch -I/opt/miniconda3/envs/scr/lib/python3.9/site-packages/numpy/core/include -I/opt/miniconda3/envs/scr/include/python3.9 -c ./External/nlopt/api/f77api.cpp -o build/temp.macosx-10.15.7-x86_64-3.9/./External/nlopt/api/f77api.o -std=c++0x
In file included from ./External/nlopt/api/f77api.cpp:103:
./External/nlopt/api/f77funcs.h:57:14: warning: 'nlopt_minimize_constrained' is deprecated [-Wdeprecated-declarations]
*info = nlopt_minimize_constrained((nlopt_algorithm) *algorithm,
^
./External/nlopt/api/nlopt.h:348:35: note: 'nlopt_minimize_constrained' has been explicitly marked deprecated here
int maxeval, double maxtime) NLOPT_DEPRECATED;
^
./External/nlopt/api/nlopt.h:320:43: note: expanded from macro 'NLOPT_DEPRECATED'
# define NLOPT_DEPRECATED __attribute__((deprecated))
^
In file included from ./External/nlopt/api/f77api.cpp:103:
./External/nlopt/api/f77funcs.h:96:6: warning: 'nlopt_get_local_search_algorithm' is deprecated [-Wdeprecated-declarations]
nlopt_get_local_search_algorithm(&deriv, &nonderiv, maxeval);
^
./External/nlopt/api/nlopt.h:365:25: note: 'nlopt_get_local_search_algorithm' has been explicitly marked deprecated here
int *maxeval) NLOPT_DEPRECATED;
^
./External/nlopt/api/nlopt.h:320:43: note: expanded from macro 'NLOPT_DEPRECATED'
# define NLOPT_DEPRECATED __attribute__((deprecated))
^
In file included from ./External/nlopt/api/f77api.cpp:103:
./External/nlopt/api/f77funcs.h:104:6: warning: 'nlopt_set_local_search_algorithm' is deprecated [-Wdeprecated-declarations]
nlopt_set_local_search_algorithm(deriv, nonderiv, *maxeval);
^
./External/nlopt/api/nlopt.h:368:24: note: 'nlopt_set_local_search_algorithm' has been explicitly marked deprecated here
int maxeval) NLOPT_DEPRECATED;
^
./External/nlopt/api/nlopt.h:320:43: note: expanded from macro 'NLOPT_DEPRECATED'
# define NLOPT_DEPRECATED __attribute__((deprecated))
^
In file included from ./External/nlopt/api/f77api.cpp:103:
./External/nlopt/api/f77funcs.h:109:13: warning: 'nlopt_get_stochastic_population' is deprecated [-Wdeprecated-declarations]
*pop = nlopt_get_stochastic_population();
^
./External/nlopt/api/nlopt.h:370:57: note: 'nlopt_get_stochastic_population' has been explicitly marked deprecated here
NLOPT_EXTERN(int) nlopt_get_stochastic_population(void) NLOPT_DEPRECATED;
^
./External/nlopt/api/nlopt.h:320:43: note: expanded from macro 'NLOPT_DEPRECATED'
# define NLOPT_DEPRECATED __attribute__((deprecated))
^
In file included from ./External/nlopt/api/f77api.cpp:103:
./External/nlopt/api/f77funcs.h:113:6: warning: 'nlopt_set_stochastic_population' is deprecated [-Wdeprecated-declarations]
nlopt_set_stochastic_population(*pop);
^
./External/nlopt/api/nlopt.h:371:61: note: 'nlopt_set_stochastic_population' has been explicitly marked deprecated here
NLOPT_EXTERN(void) nlopt_set_stochastic_population(int pop) NLOPT_DEPRECATED;
^
./External/nlopt/api/nlopt.h:320:43: note: expanded from macro 'NLOPT_DEPRECATED'
# define NLOPT_DEPRECATED __attribute__((deprecated))
^
In file included from ./External/nlopt/api/f77api.cpp:114:
./External/nlopt/api/f77funcs.h:57:14: warning: 'nlopt_minimize_constrained' is deprecated [-Wdeprecated-declarations]
*info = nlopt_minimize_constrained((nlopt_algorithm) *algorithm,
^
./External/nlopt/api/nlopt.h:348:35: note: 'nlopt_minimize_constrained' has been explicitly marked deprecated here
int maxeval, double maxtime) NLOPT_DEPRECATED;
^
./External/nlopt/api/nlopt.h:320:43: note: expanded from macro 'NLOPT_DEPRECATED'
# define NLOPT_DEPRECATED __attribute__((deprecated))
^
In file included from ./External/nlopt/api/f77api.cpp:114:
./External/nlopt/api/f77funcs.h:96:6: warning: 'nlopt_get_local_search_algorithm' is deprecated [-Wdeprecated-declarations]
nlopt_get_local_search_algorithm(&deriv, &nonderiv, maxeval);
^
./External/nlopt/api/nlopt.h:365:25: note: 'nlopt_get_local_search_algorithm' has been explicitly marked deprecated here
int *maxeval) NLOPT_DEPRECATED;
^
./External/nlopt/api/nlopt.h:320:43: note: expanded from macro 'NLOPT_DEPRECATED'
# define NLOPT_DEPRECATED __attribute__((deprecated))
^
In file included from ./External/nlopt/api/f77api.cpp:114:
./External/nlopt/api/f77funcs.h:104:6: warning: 'nlopt_set_local_search_algorithm' is deprecated [-Wdeprecated-declarations]
nlopt_set_local_search_algorithm(deriv, nonderiv, *maxeval);
^
./External/nlopt/api/nlopt.h:368:24: note: 'nlopt_set_local_search_algorithm' has been explicitly marked deprecated here
int maxeval) NLOPT_DEPRECATED;
^
./External/nlopt/api/nlopt.h:320:43: note: expanded from macro 'NLOPT_DEPRECATED'
# define NLOPT_DEPRECATED __attribute__((deprecated))
^
In file included from ./External/nlopt/api/f77api.cpp:114:
./External/nlopt/api/f77funcs.h:109:13: warning: 'nlopt_get_stochastic_population' is deprecated [-Wdeprecated-declarations]
*pop = nlopt_get_stochastic_population();
^
./External/nlopt/api/nlopt.h:370:57: note: 'nlopt_get_stochastic_population' has been explicitly marked deprecated here
NLOPT_EXTERN(int) nlopt_get_stochastic_population(void) NLOPT_DEPRECATED;
^
./External/nlopt/api/nlopt.h:320:43: note: expanded from macro 'NLOPT_DEPRECATED'
# define NLOPT_DEPRECATED __attribute__((deprecated))
^
In file included from ./External/nlopt/api/f77api.cpp:114:
./External/nlopt/api/f77funcs.h:113:6: warning: 'nlopt_set_stochastic_population' is deprecated [-Wdeprecated-declarations]
nlopt_set_stochastic_population(*pop);
^
./External/nlopt/api/nlopt.h:371:61: note: 'nlopt_set_stochastic_population' has been explicitly marked deprecated here
NLOPT_EXTERN(void) nlopt_set_stochastic_population(int pop) NLOPT_DEPRECATED;
^
./External/nlopt/api/nlopt.h:320:43: note: expanded from macro 'NLOPT_DEPRECATED'
# define NLOPT_DEPRECATED __attribute__((deprecated))
^
In file included from ./External/nlopt/api/f77api.cpp:129:
./External/nlopt/api/f77funcs.h:57:14: warning: 'nlopt_minimize_constrained' is deprecated [-Wdeprecated-declarations]
*info = nlopt_minimize_constrained((nlopt_algorithm) *algorithm,
^
./External/nlopt/api/nlopt.h:348:35: note: 'nlopt_minimize_constrained' has been explicitly marked deprecated here
int maxeval, double maxtime) NLOPT_DEPRECATED;
^
./External/nlopt/api/nlopt.h:320:43: note: expanded from macro 'NLOPT_DEPRECATED'
# define NLOPT_DEPRECATED __attribute__((deprecated))
^
In file included from ./External/nlopt/api/f77api.cpp:129:
./External/nlopt/api/f77funcs.h:96:6: warning: 'nlopt_get_local_search_algorithm' is deprecated [-Wdeprecated-declarations]
nlopt_get_local_search_algorithm(&deriv, &nonderiv, maxeval);
^
./External/nlopt/api/nlopt.h:365:25: note: 'nlopt_get_local_search_algorithm' has been explicitly marked deprecated here
int *maxeval) NLOPT_DEPRECATED;
^
./External/nlopt/api/nlopt.h:320:43: note: expanded from macro 'NLOPT_DEPRECATED'
# define NLOPT_DEPRECATED __attribute__((deprecated))
^
In file included from ./External/nlopt/api/f77api.cpp:129:
./External/nlopt/api/f77funcs.h:104:6: warning: 'nlopt_set_local_search_algorithm' is deprecated [-Wdeprecated-declarations]
nlopt_set_local_search_algorithm(deriv, nonderiv, *maxeval);
^
./External/nlopt/api/nlopt.h:368:24: note: 'nlopt_set_local_search_algorithm' has been explicitly marked deprecated here
int maxeval) NLOPT_DEPRECATED;
^
./External/nlopt/api/nlopt.h:320:43: note: expanded from macro 'NLOPT_DEPRECATED'
# define NLOPT_DEPRECATED __attribute__((deprecated))
^
In file included from ./External/nlopt/api/f77api.cpp:129:
./External/nlopt/api/f77funcs.h:109:13: warning: 'nlopt_get_stochastic_population' is deprecated [-Wdeprecated-declarations]
*pop = nlopt_get_stochastic_population();
^
./External/nlopt/api/nlopt.h:370:57: note: 'nlopt_get_stochastic_population' has been explicitly marked deprecated here
NLOPT_EXTERN(int) nlopt_get_stochastic_population(void) NLOPT_DEPRECATED;
^
./External/nlopt/api/nlopt.h:320:43: note: expanded from macro 'NLOPT_DEPRECATED'
# define NLOPT_DEPRECATED __attribute__((deprecated))
^
In file included from ./External/nlopt/api/f77api.cpp:129:
./External/nlopt/api/f77funcs.h:113:6: warning: 'nlopt_set_stochastic_population' is deprecated [-Wdeprecated-declarations]
nlopt_set_stochastic_population(*pop);
^
./External/nlopt/api/nlopt.h:371:61: note: 'nlopt_set_stochastic_population' has been explicitly marked deprecated here
NLOPT_EXTERN(void) nlopt_set_stochastic_population(int pop) NLOPT_DEPRECATED;
^
./External/nlopt/api/nlopt.h:320:43: note: expanded from macro 'NLOPT_DEPRECATED'
# define NLOPT_DEPRECATED __attribute__((deprecated))
^
15 warnings generated.
x86_64-apple-darwin13.4.0-clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /opt/miniconda3/envs/scr/include -arch x86_64 -I/opt/miniconda3/envs/scr/include -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /opt/miniconda3/envs/scr/include -arch x86_64 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /opt/miniconda3/envs/scr/include -D_FORTIFY_SOURCE=2 -isystem /opt/miniconda3/envs/scr/include -Isrc -IExternal -IExternal/nlopt -I./External/nlopt/stogo -I./External/nlopt/util -I./External/nlopt/direct -I./External/nlopt/cdirect -I./External/nlopt/praxis -I./External/nlopt/luksan -I./External/nlopt/crs -I./External/nlopt/mlsl -I./External/nlopt/mma -I./External/nlopt/cobyla -I./External/nlopt/newuoa -I./External/nlopt/neldermead -I./External/nlopt/auglag -I./External/nlopt/bobyqa -I./External/nlopt/isres -I./External/nlopt/slsqp -I./External/nlopt/api -I./External/nlopt/esch -I/opt/miniconda3/envs/scr/lib/python3.9/site-packages/numpy/core/include -I/opt/miniconda3/envs/scr/include/python3.9 -c ./External/nlopt/api/general.cpp -o build/temp.macosx-10.15.7-x86_64-3.9/./External/nlopt/api/general.o -std=c++0x
In file included from ./External/nlopt/api/general.cpp:26:
In file included from ./External/nlopt/api/nlopt-internal.h:27:
./External/nlopt/util/nlopt-util.h:28:10: fatal error: 'config.h' file not found
#include "config.h"
^~~~~~~~~~
1 error generated.
error: command '/opt/miniconda3/envs/scr/bin/x86_64-apple-darwin13.4.0-clang' failed with exit code 1
----------------------------------------
ERROR: Failed building wheel for limix
Hi,
When running
pip install "limix<2"
, in a brand new conda env it raises errors about missing dependencies (numpy, Cython, gcc) which I can fix by explicitly installing them. However, after that it raises the following error, which I cannot solve:Commands employed and OS/software info:
this errors out because of the dependencies, so:
and try back again
pip install "limix <2"
, which gives the error shown above.Thanks!