Comments (5)
See here for details:
https://github.com/omerwe/polyfun/blob/master/polyfun.yml
from echolocator.
bgen
is the only other package that's new, but when i try to install it, it can't be installed in my current echoR env. But i can confirm that the echolocatoR implementation of PolyFun ran all the way through without it:
...
...
ERROR: Could not build wheels for bgen, which is required to install pyproject.toml-based projects
https://github.com/RajLabMSSM/echolocatoR/blob/master/inst/conda/echoR.yml
I think this is because the only place i see bgen being used is a step within finemapper.py where it imports genotype files. echolocatoR
doesn't currently use this particular script (just the subscripts used by finemapper.py)
@omerwe let me know if this sounds right to you.
Conda output
⋊> ~/Desktop pip install bgen==1.2.10 (echoR) 17:52:24
Collecting bgen==1.2.10
Downloading bgen-1.2.10.tar.gz (664 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 665.0/665.0 KB 10.1 MB/s eta 0:00:00
Installing build dependencies ... done
Getting requirements to build wheel ... done
Preparing metadata (pyproject.toml) ... done
Requirement already satisfied: numpy in /opt/anaconda3/envs/echoR/lib/python3.9/site-packages (from bgen==1.2.10) (1.21.5)
Building wheels for collected packages: bgen
Building wheel for bgen (pyproject.toml) ... error
error: subprocess-exited-with-error
× Building wheel for bgen (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [80 lines of output]
running bdist_wheel
running build
running build_py
creating build
creating build/lib.macosx-10.9-x86_64-3.9
creating build/lib.macosx-10.9-x86_64-3.9/bgen
copying src/bgen/index.py -> build/lib.macosx-10.9-x86_64-3.9/bgen
copying src/bgen/__init__.py -> build/lib.macosx-10.9-x86_64-3.9/bgen
running build_ext
building 'bgen.reader' extension
creating build/temp.macosx-10.9-x86_64-3.9
creating build/temp.macosx-10.9-x86_64-3.9/src
creating build/temp.macosx-10.9-x86_64-3.9/src/bgen
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/anaconda3/envs/echoR/include -fPIC -O2 -isystem /opt/anaconda3/envs/echoR/include -Isrc/ -Isrc/zstd/lib -I/opt/anaconda3/envs/echoR/include/python3.9 -c src/bgen.cpp -o build/temp.macosx-10.9-x86_64-3.9/src/bgen.o -std=c++11 -I/usr/include -stdlib=libc++ -mmacosx-version-min=10.9 -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -mavx
In file included from src/bgen.cpp:2:
In file included from src/bgen.h:8:
In file included from src/header.h:11:
In file included from src/utils.h:5:
/opt/anaconda3/envs/echoR/bin/../include/c++/v1/cmath:321:9: error: no member named 'signbit' in the global namespace
using ::signbit;
~~^
/opt/anaconda3/envs/echoR/bin/../include/c++/v1/cmath:322:9: error: no member named 'fpclassify' in the global namespace
using ::fpclassify;
~~^
/opt/anaconda3/envs/echoR/bin/../include/c++/v1/cmath:323:9: error: no member named 'isfinite' in the global namespace; did you mean 'finite'?
using ::isfinite;
~~^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/math.h:752:12: note: 'finite' declared here
extern int finite(double)
^
In file included from src/bgen.cpp:2:
In file included from src/bgen.h:8:
In file included from src/header.h:11:
In file included from src/utils.h:5:
/opt/anaconda3/envs/echoR/bin/../include/c++/v1/cmath:324:9: error: no member named 'isinf' in the global namespace
using ::isinf;
~~^
/opt/anaconda3/envs/echoR/bin/../include/c++/v1/cmath:325:9: error: no member named 'isnan' in the global namespace
using ::isnan;
~~^
/opt/anaconda3/envs/echoR/bin/../include/c++/v1/cmath:326:9: error: no member named 'isnormal' in the global namespace
using ::isnormal;
~~^
/opt/anaconda3/envs/echoR/bin/../include/c++/v1/cmath:327:7: error: no member named 'isgreater' in the global namespace; did you mean '::std::greater'?
using ::isgreater;
^~
/opt/anaconda3/envs/echoR/bin/../include/c++/v1/functional:742:29: note: '::std::greater' declared here
struct _LIBCPP_TEMPLATE_VIS greater : binary_function<_Tp, _Tp, bool>
^
In file included from src/bgen.cpp:2:
In file included from src/bgen.h:8:
In file included from src/header.h:11:
In file included from src/utils.h:5:
/opt/anaconda3/envs/echoR/bin/../include/c++/v1/cmath:328:7: error: no member named 'isgreaterequal' in the global namespace; did you mean '::std::greater_equal'?
using ::isgreaterequal;
^~
/opt/anaconda3/envs/echoR/bin/../include/c++/v1/functional:771:29: note: '::std::greater_equal' declared here
struct _LIBCPP_TEMPLATE_VIS greater_equal : binary_function<_Tp, _Tp, bool>
^
In file included from src/bgen.cpp:2:
In file included from src/bgen.h:8:
In file included from src/header.h:11:
In file included from src/utils.h:5:
/opt/anaconda3/envs/echoR/bin/../include/c++/v1/cmath:329:9: error: no member named 'isless' in the global namespace
using ::isless;
~~^
/opt/anaconda3/envs/echoR/bin/../include/c++/v1/cmath:330:9: error: no member named 'islessequal' in the global namespace
using ::islessequal;
~~^
/opt/anaconda3/envs/echoR/bin/../include/c++/v1/cmath:331:9: error: no member named 'islessgreater' in the global namespace
using ::islessgreater;
~~^
/opt/anaconda3/envs/echoR/bin/../include/c++/v1/cmath:332:9: error: no member named 'isunordered' in the global namespace
using ::isunordered;
~~^
/opt/anaconda3/envs/echoR/bin/../include/c++/v1/cmath:333:9: error: no member named 'isunordered' in the global namespace
using ::isunordered;
~~^
13 errors generated.
error: command '/opt/anaconda3/envs/echoR/bin/clang' failed with exit code 1
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for bgen
Failed to build bgen
ERROR: Could not build wheels for bgen, which is required to install pyproject.toml-based projects
from echolocator.
bgen
is also available on anaconda.org. Do none of these versions work for your purposes @omerwe?
https://anaconda.org/conda-forge/bgen/files?page=2
from echolocator.
Hi, we just had a discussion about this in the PolyFun GitHub issues: omerwe/polyfun#86
As you can see there, there are two different python packages called bgen
, and the one on conda-forge is not the one that PolyFun uses. Just yesterday I updated the yml file to demand a specific version of the bgen
package rather than the newest version, following reports that the newest version isn't supported on MacOS (omerwe/polyfun#89). So if you tried before yesterday, please git pull
the latest PolyFun code and try again. If you still run into any issues, please let me know and I'll try to look into it.
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Thanks so much for clarifying, @omerwe! That all makes sense. I'll let you know implementing finemapper.py goes.
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