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schneebergerlab / syri

Synteny and Rearrangement Identifier
https://schneebergerlab.github.io/syri/
MIT License
303 stars 36 forks source link

i was trying to install syri but it ended up with too many warnings and error #206

Closed Hemaprasanth24 closed 11 months ago

Hemaprasanth24 commented 11 months ago

Compiling syri/pyxFiles/synsearchFunctions.pyx because it changed. Compiling syri/pyxFiles/inversions.pyx because it changed. Compiling syri/pyxFiles/tdfunc.pyx because it changed. Compiling syri/pyxFiles/findshv.pyx because it changed. Compiling syri/pyxFiles/findsv.pyx because it changed. Compiling syri/pyxFiles/writeout.pyx because it changed. [1/6] Cythonizing syri/pyxFiles/findshv.pyx [2/6] Cythonizing syri/pyxFiles/findsv.pyx [3/6] Cythonizing syri/pyxFiles/inversions.pyx warning: syri/pyxFiles/function.pxd:17:37: Buffer unpacking not optimized away. warning: syri/pyxFiles/function.pxd:17:37: Buffer unpacking not optimized away. warning: syri/pyxFiles/function.pxd:17:73: Buffer unpacking not optimized away. warning: syri/pyxFiles/function.pxd:17:73: Buffer unpacking not optimized away. warning: syri/pyxFiles/function.pxd:17:125: Buffer unpacking not optimized away. warning: syri/pyxFiles/function.pxd:17:125: Buffer unpacking not optimized away. warning: syri/pyxFiles/function.pxd:17:164: Buffer unpacking not optimized away. warning: syri/pyxFiles/function.pxd:17:164: Buffer unpacking not optimized away. warning: syri/pyxFiles/inversions.pyx:162:46: Index should be typed for more efficient access [4/6] Cythonizing syri/pyxFiles/synsearchFunctions.pyx warning: syri/pyxFiles/function.pxd:17:37: Buffer unpacking not optimized away. warning: syri/pyxFiles/function.pxd:17:37: Buffer unpacking not optimized away. warning: syri/pyxFiles/function.pxd:17:73: Buffer unpacking not optimized away. warning: syri/pyxFiles/function.pxd:17:73: Buffer unpacking not optimized away. warning: syri/pyxFiles/function.pxd:17:125: Buffer unpacking not optimized away. warning: syri/pyxFiles/function.pxd:17:125: Buffer unpacking not optimized away. warning: syri/pyxFiles/function.pxd:17:164: Buffer unpacking not optimized away. warning: syri/pyxFiles/function.pxd:17:164: Buffer unpacking not optimized away. [5/6] Cythonizing syri/pyxFiles/tdfunc.pyx warning: syri/pyxFiles/function.pxd:17:37: Buffer unpacking not optimized away. warning: syri/pyxFiles/function.pxd:17:37: Buffer unpacking not optimized away. warning: syri/pyxFiles/function.pxd:17:73: Buffer unpacking not optimized away. warning: syri/pyxFiles/function.pxd:17:73: Buffer unpacking not optimized away. warning: syri/pyxFiles/function.pxd:17:125: Buffer unpacking not optimized away. warning: syri/pyxFiles/function.pxd:17:125: Buffer unpacking not optimized away. warning: syri/pyxFiles/function.pxd:17:164: Buffer unpacking not optimized away. warning: syri/pyxFiles/function.pxd:17:164: Buffer unpacking not optimized away. [6/6] Cythonizing syri/pyxFiles/writeout.pyx running install /home/hemaprasanth/anaconda/envs/syri/lib/python3.11/site-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !!

    ********************************************************************************
    Please avoid running ``setup.py`` directly.
    Instead, use pypa/build, pypa/installer or other
    standards-based tools.

    See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
    ********************************************************************************

!! self.initialize_options() /home/hemaprasanth/anaconda/envs/syri/lib/python3.11/site-packages/setuptools/_distutils/cmd.py:66: EasyInstallDeprecationWarning: easy_install command is deprecated. !!

    ********************************************************************************
    Please avoid running ``setup.py`` and ``easy_install``.
    Instead, use pypa/build, pypa/installer or other
    standards-based tools.

    See https://github.com/pypa/setuptools/issues/917 for details.
    ********************************************************************************

!! self.initialize_options() running bdist_egg running egg_info creating syri.egg-info writing syri.egg-info/PKG-INFO writing dependency_links to syri.egg-info/dependency_links.txt writing top-level names to syri.egg-info/top_level.txt writing manifest file 'syri.egg-info/SOURCES.txt' reading manifest file 'syri.egg-info/SOURCES.txt' adding license file 'LICENSE' writing manifest file 'syri.egg-info/SOURCES.txt' installing library code to build/bdist.linux-x86_64/egg running install_lib running build_py creating build creating build/lib.linux-x86_64-cpython-311 creating build/lib.linux-x86_64-cpython-311/syri copying syri/init.py -> build/lib.linux-x86_64-cpython-311/syri creating build/lib.linux-x86_64-cpython-311/syri/scripts copying syri/scripts/syri.py -> build/lib.linux-x86_64-cpython-311/syri/scripts copying syri/scripts/init.py -> build/lib.linux-x86_64-cpython-311/syri/scripts copying syri/scripts/chrrev.py -> build/lib.linux-x86_64-cpython-311/syri/scripts copying syri/scripts/chroder.py -> build/lib.linux-x86_64-cpython-311/syri/scripts copying syri/scripts/func.py -> build/lib.linux-x86_64-cpython-311/syri/scripts copying syri/scripts/test_validatation.py -> build/lib.linux-x86_64-cpython-311/syri/scripts copying syri/scripts/aligner.py -> build/lib.linux-x86_64-cpython-311/syri/scripts running build_ext building 'syri.synsearchFunctions' extension creating build/temp.linux-x86_64-cpython-311 creating build/temp.linux-x86_64-cpython-311/syri creating build/temp.linux-x86_64-cpython-311/syri/pyxFiles gcc -pthread -B /home/hemaprasanth/anaconda/envs/syri/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/hemaprasanth/anaconda/envs/syri/include -fPIC -O2 -isystem /home/hemaprasanth/anaconda/envs/syri/include -fPIC -I/home/hemaprasanth/anaconda/envs/syri/lib/python3.11/site-packages/numpy/core/include -I/home/hemaprasanth/anaconda/envs/syri/include/python3.11 -c syri/pyxFiles/synsearchFunctions.cpp -o build/temp.linux-x86_64-cpython-311/syri/pyxFiles/synsearchFunctions.o In file included from /home/hemaprasanth/anaconda/envs/syri/lib/python3.11/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929, from /home/hemaprasanth/anaconda/envs/syri/lib/python3.11/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /home/hemaprasanth/anaconda/envs/syri/lib/python3.11/site-packages/numpy/core/include/numpy/arrayobject.h:5, from syri/pyxFiles/synsearchFunctions.cpp:1130: /home/hemaprasanth/anaconda/envs/syri/lib/python3.11/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~ g++ -pthread -B /home/hemaprasanth/anaconda/envs/syri/compiler_compat -shared -Wl,--allow-shlib-undefined -Wl,-rpath,/home/hemaprasanth/anaconda/envs/syri/lib -Wl,-rpath-link,/home/hemaprasanth/anaconda/envs/syri/lib -L/home/hemaprasanth/anaconda/envs/syri/lib -Wl,--allow-shlib-undefined -Wl,-rpath,/home/hemaprasanth/anaconda/envs/syri/lib -Wl,-rpath-link,/home/hemaprasanth/anaconda/envs/syri/lib -L/home/hemaprasanth/anaconda/envs/syri/lib build/temp.linux-x86_64-cpython-311/syri/pyxFiles/synsearchFunctions.o -o build/lib.linux-x86_64-cpython-311/syri/synsearchFunctions.cpython-311-x86_64-linux-gnu.so building 'syri.inversions' extension gcc -pthread -B /home/hemaprasanth/anaconda/envs/syri/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/hemaprasanth/anaconda/envs/syri/include -fPIC -O2 -isystem /home/hemaprasanth/anaconda/envs/syri/include -fPIC -I/home/hemaprasanth/anaconda/envs/syri/lib/python3.11/site-packages/numpy/core/include -I/home/hemaprasanth/anaconda/envs/syri/include/python3.11 -c syri/pyxFiles/inversions.cpp -o build/temp.linux-x86_64-cpython-311/syri/pyxFiles/inversions.o In file included from /home/hemaprasanth/anaconda/envs/syri/lib/python3.11/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929, from /home/hemaprasanth/anaconda/envs/syri/lib/python3.11/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /home/hemaprasanth/anaconda/envs/syri/lib/python3.11/site-packages/numpy/core/include/numpy/arrayobject.h:5, from syri/pyxFiles/inversions.cpp:1130: /home/hemaprasanth/anaconda/envs/syri/lib/python3.11/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~ In file included from /home/hemaprasanth/anaconda/envs/syri/include/python3.11/Python.h:11, from syri/pyxFiles/inversions.cpp:30: syri/pyxFiles/inversions.cpp: In function ‘int pyx_import_star_set(PyObject, PyObject, char*)’: /home/hemaprasanth/anaconda/envs/syri/include/python3.11/patchlevel.h:19:33: error: lvalue required as left operand of assignment 19 | #define PY_MAJOR_VERSION 3 | ^ syri/pyxFiles/inversions.cpp:37949:5: note: in expansion of macro ‘PY_MAJOR_VERSION’ 37949 | PY_MAJOR_VERSION = Pyx_PyInt_As_int(o); if (unlikely((PY_MAJOR_VERSION == (int)-1) && PyErr_Occurred())) PYX_ERR(1, 203, pyx_L2_error) | ^~~~ error: command '/usr/bin/gcc' failed with exit code 1

mnshgl0110 commented 11 months ago

It seems that you are using anaconda. Please try installing directly with conda using the following commands:

# Create a new environment and install syri with all dependencies
conda create -n syri_env -c bioconda syri
# Activate the environment
conda activate syri_env
Hemaprasanth24 commented 11 months ago

thanks for your response

On Mon, Aug 7, 2023 at 2:04 PM Manish Goel @.***> wrote:

It seems that you are using anaconda. Please try installing directly with conda using the following commands:

Create a new environment and install syri with all dependencies

conda create -n syri_env -c bioconda syri

Activate the environment

conda activate syri_env

— Reply to this email directly, view it on GitHub https://github.com/schneebergerlab/syri/issues/206#issuecomment-1667433323, or unsubscribe https://github.com/notifications/unsubscribe-auth/A73BTRU226UOLNUBMLSX2MDXUCSAPANCNFSM6AAAAAA3FKVEUA . You are receiving this because you authored the thread.Message ID: @.***>