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HannahVMeyer / limmbo

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Error when installing limix<2 #8

Open dgarrimar opened 3 years ago

dgarrimar commented 3 years ago

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:

 Building wheels for collected packages: limix-legacy, ncephes
  Building wheel for limix-legacy (setup.py) ... error
  ERROR: Command errored out with exit status 1:
   command: /home/dgarrimar/software/miniconda3/envs/limmbo/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-zk6tlgef/limix-legacy_b7195639ef414a7782116489e50de21f/setup.py'"'"'; __file__='"'"'/tmp/pip-install-zk6tlgef/limix-legacy_b7195639ef414a7782116489e50de21f/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-_tv9k8v9
[...]

Commands employed and OS/software info:

conda create -n limmbo python=3.8
conda activate limmbo
pip install "limix <2"

this errors out because of the dependencies, so:

pip install Cpython
pip install numpy
pip install gcc_linux-64

and try back again pip install "limix <2", which gives the error shown above.

>>> sinfo()
-----
sinfo       0.3.1
-----
Python 3.8.5 (default, Sep  4 2020, 07:30:14) [GCC 7.3.0]
Linux-4.19.128-microsoft-standard-x86_64-with-glibc2.10
4 logical CPU cores, x86_64
-----
Session information updated at 2021-01-20 13:04

Thanks!

dgarrimar commented 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?

hkim89 commented 2 years ago

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