Closed priyambial123 closed 2 weeks ago
ivargr
commented
5 months ago Hi!
Thanks for reaching out. I think Python 3.8 should work fine. Would you be able to just copy-paste the whole log from the installation process, and then I can look into the conflicts. Maybe there has been some recent updates that cause conflicting packages.
priyambial123
commented
5 months ago Sorry, I checked it is Python 3.12.1. Does kage work with this Python version or should I change it Please find the log below:
pip install kage-genotyper
Collecting kage-genotyper
Using cached kage-genotyper-2.0.5.tar.gz (13.0 MB)
Preparing metadata (setup.py) ... done
Collecting numpy (from kage-genotyper)
Using cached numpy-1.26.3-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (61 kB)
Collecting tqdm (from kage-genotyper)
Using cached tqdm-4.66.1-py3-none-any.whl.metadata (57 kB)
Collecting pyfaidx (from kage-genotyper)
Using cached pyfaidx-0.8.1.1-py3-none-any.whl.metadata (25 kB)
Collecting pathos (from kage-genotyper)
Using cached pathos-0.3.2-py3-none-any.whl.metadata (11 kB)
Collecting cython (from kage-genotyper)
Using cached Cython-3.0.8-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.2 kB)
Collecting scipy (from kage-genotyper)
Using cached scipy-1.12.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (60 kB)
Collecting obgraph>=0.0.35 (from kage-genotyper)
Using cached obgraph-0.0.37.tar.gz (165 kB)
Installing build dependencies ... done
Getting requirements to build wheel ... done
Preparing metadata (pyproject.toml) ... done
Collecting graph_kmer_index>=0.0.29 (from kage-genotyper)
Using cached graph_kmer_index-0.0.29-py3-none-any.whl
Collecting kmer_mapper>=0.0.37 (from kage-genotyper)
Using cached kmer_mapper-0.0.37.tar.gz (130 kB)
Installing build dependencies ... done
Getting requirements to build wheel ... done
Preparing metadata (pyproject.toml) ... done
Collecting npstructures>=0.2.16 (from kage-genotyper)
Using cached npstructures-0.2.16-py2.py3-none-any.whl.metadata (5.1 kB)
Collecting graph_read_simulator>=0.0.7 (from kage-genotyper)
Using cached graph_read_simulator-0.0.20-py3-none-any.whl
Collecting shared_memory_wrapper>=0.0.28 (from kage-genotyper)
Using cached shared_memory_wrapper-0.0.30-py3-none-any.whl
Collecting bionumpy>=1.0.2 (from kage-genotyper)
Using cached bionumpy-1.0.2-py2.py3-none-any.whl.metadata (2.5 kB)
Collecting awkward (from kage-genotyper)
Using cached awkward-2.5.2-py3-none-any.whl.metadata (6.9 kB)
Collecting numba (from kage-genotyper)
Using cached numba-0.59.0-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (2.7 kB)
INFO: pip is looking at multiple versions of kage-genotyper to determine which version is compatible with other requirements. This could take a while.
Collecting kage-genotyper
Using cached kage-genotyper-2.0.4.tar.gz (13.0 MB)
Preparing metadata (setup.py) ... done
Using cached kage-genotyper-2.0.3.tar.gz (12.8 MB)
Preparing metadata (setup.py) ... done
Using cached kage-genotyper-2.0.2.tar.gz (12.8 MB)
Preparing metadata (setup.py) ... done
Using cached kage-genotyper-2.0.1.tar.gz (12.8 MB)
Preparing metadata (setup.py) ... done
Using cached kage-genotyper-2.0.0.tar.gz (12.8 MB)
Preparing metadata (setup.py) ... done
Using cached kage-genotyper-0.2.8.tar.gz (12.8 MB)
Preparing metadata (setup.py) ... done
Using cached kage-genotyper-0.2.7.tar.gz (12.8 MB)
Preparing metadata (setup.py) ... done
INFO: pip is still looking at multiple versions of kage-genotyper to determine which version is compatible with other requirements. This could take a while.
Using cached kage-genotyper-0.2.6.tar.gz (12.8 MB)
Preparing metadata (setup.py) ... done
Using cached kage-genotyper-0.2.5.tar.gz (12.8 MB)
Preparing metadata (setup.py) ... done
Using cached kage-genotyper-0.2.4.tar.gz (12.8 MB)
Preparing metadata (setup.py) ... done
Using cached kage-genotyper-0.2.3.tar.gz (12.8 MB)
Preparing metadata (setup.py) ... done
Using cached kage-genotyper-0.2.2.tar.gz (12.8 MB)
Preparing metadata (setup.py) ... done
INFO: This is taking longer than usual. You might need to provide the dependency resolver with stricter constraints to reduce runtime. See https://pip.pypa.io/warnings/backtracking for guidance. If you want to abort this run, press Ctrl + C.
Using cached kage-genotyper-0.2.1.tar.gz (12.8 MB)
Preparing metadata (setup.py) ... done
Using cached kage-genotyper-0.2.0.tar.gz (12.8 MB)
Preparing metadata (setup.py) ... done
Using cached kage_genotyper-0.1.14-py3-none-any.whl
Collecting sortedcontainers (from graph_kmer_index>=0.0.29->kage-genotyper)
Using cached sortedcontainers-2.4.0-py2.py3-none-any.whl (29 kB)
Collecting biopython (from graph_kmer_index>=0.0.29->kage-genotyper)
Using cached biopython-1.83-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (13 kB)
Collecting SharedArray (from graph_kmer_index>=0.0.29->kage-genotyper)
Using cached SharedArray-3.2.3.tar.gz (19 kB)
Installing build dependencies ... done
Getting requirements to build wheel ... done
Preparing metadata (pyproject.toml) ... done
Collecting simple-read-mutator (from graph_read_simulator>=0.0.7->kage-genotyper)
Using cached simple_read_mutator-0.0.2-py3-none-any.whl
Collecting isal (from kmer_mapper>=0.0.37->kage-genotyper)
Using cached isal-1.5.3-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (9.9 kB)
Collecting dill (from shared_memory_wrapper>=0.0.28->kage-genotyper)
Using cached dill-0.3.8-py3-none-any.whl.metadata (10 kB)
Collecting ppft>=1.7.6.8 (from pathos->kage-genotyper)
Using cached ppft-1.7.6.8-py3-none-any.whl.metadata (12 kB)
Collecting pox>=0.3.4 (from pathos->kage-genotyper)
Using cached pox-0.3.4-py3-none-any.whl.metadata (8.0 kB)
Collecting multiprocess>=0.70.16 (from pathos->kage-genotyper)
Using cached multiprocess-0.70.16-py312-none-any.whl.metadata (7.2 kB)
Requirement already satisfied: setuptools in ./mambaforge/envs/kage/lib/python3.12/site-packages (from pyfaidx->kage-genotyper) (68.2.2)
Collecting importlib-metadata (from pyfaidx->kage-genotyper)
Using cached importlib_metadata-7.0.1-py3-none-any.whl.metadata (4.9 kB)
Collecting zipp>=0.5 (from importlib-metadata->pyfaidx->kage-genotyper)
Using cached zipp-3.17.0-py3-none-any.whl.metadata (3.7 kB)
Using cached bionumpy-1.0.2-py2.py3-none-any.whl (152 kB)
Using cached npstructures-0.2.16-py2.py3-none-any.whl (36 kB)
Using cached numpy-1.26.3-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (18.0 MB)
Using cached Cython-3.0.8-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.5 MB)
Using cached pathos-0.3.2-py3-none-any.whl (82 kB)
Using cached pyfaidx-0.8.1.1-py3-none-any.whl (28 kB)
Using cached scipy-1.12.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (37.8 MB)
Using cached tqdm-4.66.1-py3-none-any.whl (78 kB)
Using cached dill-0.3.8-py3-none-any.whl (116 kB)
Using cached multiprocess-0.70.16-py312-none-any.whl (146 kB)
Using cached pox-0.3.4-py3-none-any.whl (29 kB)
Using cached ppft-1.7.6.8-py3-none-any.whl (56 kB)
Using cached biopython-1.83-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.1 MB)
Using cached importlib_metadata-7.0.1-py3-none-any.whl (23 kB)
Using cached isal-1.5.3-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (260 kB)
Using cached zipp-3.17.0-py3-none-any.whl (7.4 kB)
Building wheels for collected packages: kmer_mapper, obgraph, SharedArray
Building wheel for kmer_mapper (pyproject.toml) ... error
error: subprocess-exited-with-error
× Building wheel for kmer_mapper (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [16 lines of output]
Compiling kmer_mapper/mapper.pyx because it changed.
[1/1] Cythonizing kmer_mapper/mapper.pyx
In file included from /scratch/pip-build-env-km4u_0wy/overlay/lib/python3.12/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929:0,
from /scratch/pip-build-env-km4u_0wy/overlay/lib/python3.12/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /scratch/pip-build-env-km4u_0wy/overlay/lib/python3.12/site-packages/numpy/core/include/numpy/arrayobject.h:5,
from kmer_mapper/mapper.c:1212:
/scratch/pip-build-env-km4u_0wy/overlay/lib/python3.12/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]
#warning "Using deprecated NumPy API, disable it with " \
^
In file included from kmer_mapper/mapper.c:29567:0:
/mambaforge/envs/kage/include/python3.12/internal/pycore_frame.h: In function ‘_PyFrame_Initialize’:
/mambaforge/envs/kage/include/python3.12/internal/pycore_frame.h:134:5: error: ‘for’ loop initial declarations are only allowed in C99 mode
for (int i = null_locals_from; i < code->co_nlocalsplus; i++) {
^
/mambaforge/envs/kage/include/python3.12/internal/pycore_frame.h:134:5: note: use option -std=c99 or -std=gnu99 to compile your code
error: command '/usr/bin/gcc' 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 kmer_mapper
Building wheel for obgraph (pyproject.toml) ... error
error: subprocess-exited-with-error
× Building wheel for obgraph (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [14 lines of output]
In file included from /scratch/pip-build-env-btz62dmo/overlay/lib/python3.12/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929:0,
from /scratch/pip-build-env-btz62dmo/overlay/lib/python3.12/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /scratch/pip-build-env-btz62dmo/overlay/lib/python3.12/site-packages/numpy/core/include/numpy/arrayobject.h:5,
from obgraph/cython_traversing.c:1205:
/scratch/pip-build-env-btz62dmo/overlay/lib/python3.12/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]
#warning "Using deprecated NumPy API, disable it with " \
^
In file included from obgraph/cython_traversing.c:28334:0:
/mambaforge/envs/kage/include/python3.12/internal/pycore_frame.h: In function ‘_PyFrame_Initialize’:
/mambaforge/envs/kage/include/python3.12/internal/pycore_frame.h:134:5: error: ‘for’ loop initial declarations are only allowed in C99 mode
for (int i = null_locals_from; i < code->co_nlocalsplus; i++) {
^
/mambaforge/envs/kage/include/python3.12/internal/pycore_frame.h:134:5: note: use option -std=c99 or -std=gnu99 to compile your code
error: command '/usr/bin/gcc' 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 obgraph
Building wheel for SharedArray (pyproject.toml) ... error
error: subprocess-exited-with-error
× Building wheel for SharedArray (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [19 lines of output]
running bdist_wheel
running build
running build_ext
building 'SharedArray' extension
creating build
creating build/temp.linux-x86_64-cpython-312
creating build/temp.linux-x86_64-cpython-312/src
gcc -pthread -B /mambaforge/envs/kage/compiler_compat -fno-strict-overflow -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /mambaforge/envs/kage/include -fPIC -O2 -isystem /mambaforge/envs/kage/include -fPIC -I/scratch/pip-build-env-rcgqotty/overlay/lib/python3.12/site-packages/numpy/core/include -I/mambaforge/envs/kage/include/python3.12 -c ./src/map_owner.c -o build/temp.linux-x86_64-cpython-312/./src/map_owner.o
gcc -pthread -B /mambaforge/envs/kage/compiler_compat -fno-strict-overflow -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /mambaforge/envs/kage/include -fPIC -O2 -isystem /mambaforge/envs/kage/include -fPIC -I/scratch/pip-build-env-rcgqotty/overlay/lib/python3.12/site-packages/numpy/core/include -I/mambaforge/envs/kage/include/python3.12 -c ./src/map_owner_mlock.c -o build/temp.linux-x86_64-cpython-312/./src/map_owner_mlock.o
gcc -pthread -B/mambaforge/envs/kage/compiler_compat -fno-strict-overflow -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /mambaforge/envs/kage/include -fPIC -O2 -isystem /mambaforge/envs/kage/include -fPIC -I/scratch/pip-build-env-rcgqotty/overlay/lib/python3.12/site-packages/numpy/core/include -I/mambaforge/envs/kage/include/python3.12 -c ./src/map_owner_msync.c -o build/temp.linux-x86_64-cpython-312/./src/map_owner_msync.o
gcc -pthread -B /mambaforge/envs/kage/compiler_compat -fno-strict-overflow -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /mambaforge/envs/kage/include -fPIC -O2 -isystem /mambaforge/envs/kage/include -fPIC -I/scratch/pip-build-env-rcgqotty/overlay/lib/python3.12/site-packages/numpy/core/include -I/mambaforge/envs/kage/include/python3.12 -c ./src/map_owner_munlock.c -o build/temp.linux-x86_64-cpython-312/./src/map_owner_munlock.o
gcc -pthread -B/mambaforge/envs/kage/compiler_compat -fno-strict-overflow -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /mambaforge/envs/kage/include -fPIC -O2 -isystem /mambaforge/envs/kage/include -fPIC -I/scratch/pip-build-env-rcgqotty/overlay/lib/python3.12/site-packages/numpy/core/include -I/mambaforge/envs/kage/include/python3.12 -c ./src/shared_array.c -o build/temp.linux-x86_64-cpython-312/./src/shared_array.o
gcc -pthread -B /mambaforge/envs/kage/compiler_compat -fno-strict-overflow -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /mambaforge/envs/kage/include -fPIC -O2 -isystem /mambaforge/envs/kage/include -fPIC -I/scratch/pip-build-env-rcgqotty/overlay/lib/python3.12/site-packages/numpy/core/include -I/mambaforge/envs/kage/include/python3.12 -c ./src/shared_array_attach.c -o build/temp.linux-x86_64-cpython-312/./src/shared_array_attach.o
./src/shared_array_attach.c: In function ‘do_attach’:
./src/shared_array_attach.c:99:2: error: ‘for’ loop initial declarations are only allowed in C99 mode
for (int i = 0; i < meta->ndims; i++)
^
./src/shared_array_attach.c:99:2: note: use option -std=c99 or -std=gnu99 to compile your code
error: command '/usr/bin/gcc' 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 SharedArray
Failed to build kmer_mapper obgraph SharedArray
ERROR: Could not build wheels for kmer_mapper, obgraph, SharedArray, which is required to install pyproject.toml-based projectsHi!
I looked into this and I think the problem is the Python version, as some of the packages KAGE depends on does not support Python 3.12. Could you try to use either Python 3.8, 3.9 or 3.10? That should work.
priyambial123
commented
5 months ago I tried with Python 3.8 still couldn't install. Please find the below log:
pip install kage-genotyper
Collecting kage-genotyper
Using cached kage-genotyper-2.0.5.tar.gz (13.0 MB)
Preparing metadata (setup.py) ... done
Collecting numpy (from kage-genotyper)
Using cached numpy-1.24.4-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.6 kB)
Collecting tqdm (from kage-genotyper)
Using cached tqdm-4.66.1-py3-none-any.whl.metadata (57 kB)
Collecting pyfaidx (from kage-genotyper)
Using cached pyfaidx-0.8.1.1-py3-none-any.whl.metadata (25 kB)
Collecting pathos (from kage-genotyper)
Using cached pathos-0.3.2-py3-none-any.whl.metadata (11 kB)
Collecting cython (from kage-genotyper)
Using cached Cython-3.0.8-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.2 kB)
Collecting scipy (from kage-genotyper)
Using cached scipy-1.10.1-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (34.5 MB)
Collecting obgraph>=0.0.35 (from kage-genotyper)
Using cached obgraph-0.0.37-cp38-cp38-linux_x86_64.whl
Collecting graph_kmer_index>=0.0.29 (from kage-genotyper)
Using cached graph_kmer_index-0.0.29-py3-none-any.whl
Collecting kmer_mapper>=0.0.37 (from kage-genotyper)
Using cached kmer_mapper-0.0.37-cp38-cp38-linux_x86_64.whl
Collecting npstructures>=0.2.16 (from kage-genotyper)
Using cached npstructures-0.2.16-py2.py3-none-any.whl.metadata (5.1 kB)
Collecting graph_read_simulator>=0.0.7 (from kage-genotyper)
Using cached graph_read_simulator-0.0.20-py3-none-any.whl
Collecting shared_memory_wrapper>=0.0.28 (from kage-genotyper)
Using cached shared_memory_wrapper-0.0.30-py3-none-any.whl
Collecting bionumpy>=1.0.2 (from kage-genotyper)
Using cached bionumpy-1.0.2-py2.py3-none-any.whl.metadata (2.5 kB)
Collecting awkward (from kage-genotyper)
Downloading awkward-2.6.0-py3-none-any.whl.metadata (7.0 kB)
Collecting numba (from kage-genotyper)
Using cached numba-0.58.1-cp38-cp38-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (2.7 kB)
Collecting ray (from kage-genotyper)
Using cached ray-2.9.1-cp38-cp38-manylinux2014_x86_64.whl.metadata (13 kB)
Collecting isal (from kage-genotyper)
Using cached isal-1.5.3-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (9.9 kB)
Collecting sortedcontainers (from graph_kmer_index>=0.0.29->kage-genotyper)
Using cached sortedcontainers-2.4.0-py2.py3-none-any.whl (29 kB)
Collecting biopython (from graph_kmer_index>=0.0.29->kage-genotyper)
Using cached biopython-1.83-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (13 kB)
Collecting SharedArray (from graph_kmer_index>=0.0.29->kage-genotyper)
Using cached SharedArray-3.2.3.tar.gz (19 kB)
Installing build dependencies ... done
Getting requirements to build wheel ... done
Preparing metadata (pyproject.toml) ... done
Collecting simple-read-mutator (from graph_read_simulator>=0.0.7->kage-genotyper)
Using cached simple_read_mutator-0.0.2-py3-none-any.whl
Collecting dill (from shared_memory_wrapper>=0.0.28->kage-genotyper)
Using cached dill-0.3.8-py3-none-any.whl.metadata (10 kB)
Collecting awkward-cpp==29 (from awkward->kage-genotyper)
Downloading awkward_cpp-29-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.2 kB)
Collecting fsspec (from awkward->kage-genotyper)
Downloading fsspec-2023.12.2-py3-none-any.whl.metadata (6.8 kB)
Collecting importlib-metadata>=4.13.0 (from awkward->kage-genotyper)
Using cached importlib_metadata-7.0.1-py3-none-any.whl.metadata (4.9 kB)
Collecting packaging (from awkward->kage-genotyper)
Using cached packaging-23.2-py3-none-any.whl.metadata (3.2 kB)
Collecting typing-extensions>=4.1.0 (from awkward->kage-genotyper)
Using cached typing_extensions-4.9.0-py3-none-any.whl.metadata (3.0 kB)
Collecting importlib_resources (from awkward-cpp==29->awkward->kage-genotyper)
Using cached importlib_resources-6.1.1-py3-none-any.whl.metadata (4.1 kB)
Collecting llvmlite<0.42,>=0.41.0dev0 (from numba->kage-genotyper)
Using cached llvmlite-0.41.1-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (4.8 kB)
Collecting ppft>=1.7.6.8 (from pathos->kage-genotyper)
Using cached ppft-1.7.6.8-py3-none-any.whl.metadata (12 kB)
Collecting pox>=0.3.4 (from pathos->kage-genotyper)
Using cached pox-0.3.4-py3-none-any.whl.metadata (8.0 kB)
Collecting multiprocess>=0.70.16 (from pathos->kage-genotyper)
Using cached multiprocess-0.70.16-py38-none-any.whl.metadata (7.1 kB)
Requirement already satisfied: setuptools in /scicore/home/cichon/thirun0000/micromamba/envs/kage/lib/python3.8/site-packages (from pyfaidx->kage-genotyper) (68.2.2)
Collecting click>=7.0 (from ray->kage-genotyper)
Using cached click-8.1.7-py3-none-any.whl.metadata (3.0 kB)
Collecting filelock (from ray->kage-genotyper)
Using cached filelock-3.13.1-py3-none-any.whl.metadata (2.8 kB)
Collecting jsonschema (from ray->kage-genotyper)
Using cached jsonschema-4.21.1-py3-none-any.whl.metadata (7.8 kB)
Collecting msgpack<2.0.0,>=1.0.0 (from ray->kage-genotyper)
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Building wheels for collected packages: kage-genotyper, SharedArray
Building wheel for kage-genotyper (setup.py) ... done
Created wheel for kage-genotyper: filename=kage_genotyper-2.0.5-py3-none-any.whl size=122432 sha256=f79d14a60b458d34d7197935d6964fbbc8cc59106ff0448e2b96e4c3b89d2439
Stored in directory: /.cache/pip/wheels/13/e2/b6/4830faaeb8eee264aca7478931e6b4eef8fe7da0d5eaa99698
Building wheel for SharedArray (pyproject.toml) ... error
error: subprocess-exited-with-error
× Building wheel for SharedArray (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [19 lines of output]
running bdist_wheel
running build
running build_ext
building 'SharedArray' extension
creating build
creating build/temp.linux-x86_64-cpython-38
creating build/temp.linux-x86_64-cpython-38/src
gcc -pthread -B /micromamba/envs/kage/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/scratch/pip-build-env-laud8so6/overlay/lib/python3.8/site-packages/numpy/core/include -I/micromamba/envs/kage/include/python3.8 -c ./src/map_owner.c -o build/temp.linux-x86_64-cpython-38/./src/map_owner.o
gcc -pthread -B /micromamba/envs/kage/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/scratch/pip-build-env-laud8so6/overlay/lib/python3.8/site-packages/numpy/core/include -I/micromamba/envs/kage/include/python3.8 -c ./src/map_owner_mlock.c -o build/temp.linux-x86_64-cpython-38/./src/map_owner_mlock.o
gcc -pthread -B /micromamba/envs/kage/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/scratch/pip-build-env-laud8so6/overlay/lib/python3.8/site-packages/numpy/core/include -I/micromamba/envs/kage/include/python3.8 -c ./src/map_owner_msync.c -o build/temp.linux-x86_64-cpython-38/./src/map_owner_msync.o
gcc -pthread -B /micromamba/envs/kage/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/scratch/pip-build-env-laud8so6/overlay/lib/python3.8/site-packages/numpy/core/include -I/micromamba/envs/kage/include/python3.8 -c ./src/map_owner_munlock.c -o build/temp.linux-x86_64-cpython-38/./src/map_owner_munlock.o
gcc -pthread -B /micromamba/envs/kage/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/scratch/pip-build-env-laud8so6/overlay/lib/python3.8/site-packages/numpy/core/include -I/micromamba/envs/kage/include/python3.8 -c ./src/shared_array.c -o build/temp.linux-x86_64-cpython-38/./src/shared_array.o
gcc -pthread -B /micromamba/envs/kage/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/scratch/pip-build-env-laud8so6/overlay/lib/python3.8/site-packages/numpy/core/include -I/micromamba/envs/kage/include/python3.8 -c ./src/shared_array_attach.c -o build/temp.linux-x86_64-cpython-38/./src/shared_array_attach.o
./src/shared_array_attach.c: In function ‘do_attach’:
./src/shared_array_attach.c:99:2: error: ‘for’ loop initial declarations are only allowed in C99 mode
for (int i = 0; i < meta->ndims; i++)
^
./src/shared_array_attach.c:99:2: note: use option -std=c99 or -std=gnu99 to compile your code
error: command '/usr/bin/gcc' 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 SharedArray
Successfully built kage-genotyper
Failed to build SharedArray
ERROR: Could not build wheels for SharedArray, which is required to install pyproject.toml-based projectsSorry, I was a bit quick to assume 3.12 was the issue.
Seems the problem is compiling the C code in one of KAGE's dependencies, SharedArray.
Could you try doing the following:
Install SharedArray manually first by running CFLAGS="-std=c99" pip install SharedArray (telling the compiler to use c99) and then install kage-genotyper after that?
You could also try just installing kage with CFLAGS="-std=c99" pip install kage-genotyper, that should probably work in the same way.
priyambial123
commented
5 months ago Install SharedArray manually first by running CFLAGS="-std=c99" pip install SharedArray (telling the compiler to use c99) and then install kage-genotyper
Thank you it worked
ivargr
commented
5 months ago Great! Let me know if you run into any other issues :)
jvtdlne
commented
4 months ago I don't understand what I do thank you so much for your valuable time
priyambial123
commented
2 weeks ago Thank you, I could install shared array and install kage-genotyper
Priya
jvtdlne
commented
6 days ago Please I need help installing on this this phone 510 671 4020 thank you so much for contacting me again
On Thu, Jun 20, 2024, 7:32 AM priya_arasu @.***> wrote:
Thank you, I could install shared array and install kage-genotyper
Priya
— Reply to this email directly, view it on GitHub https://github.com/kage-genotyper/kage/issues/11#issuecomment-2180862588, or unsubscribe https://github.com/notifications/unsubscribe-auth/BFUIRN4BURYDDXIUVUC6NTDZILRZBAVCNFSM6AAAAABCWVBAQCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCOBQHA3DENJYHA . You are receiving this because you are subscribed to this thread.Message ID: @.***>
Hello,
I am trying to install kage. Due to conflicts with packages, I am not able to install it. I first created a conda environment and installed python version 3.8
Then used the commamnd: pip install kage-genotyper
But I am not able to install it. Has anyone fixed this issue.Is there any specific version of python has to be installed. Any help would be greatly appreciated
Thank you
Priya