auto-sklearn
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automl
Exit code 1 while pip installing library
Describe the bug
Library not installing, while installing with pip install auto-sklearn
To Reproduce
Steps to reproduce the behavior:
- Execute command
pip install auto-sklearn(python 3.10)
Expected behavior
The library should have got installed
Actual behavior, stacktrace or logfile
Getting requirements to build wheel ... done
Preparing metadata (pyproject.toml) ... error
error: subprocess-exited-with-error
× Preparing metadata (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [825 lines of output]
<string>:17: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
Partial import of sklearn during the build process.
<string>:116: DeprecationWarning:
`numpy.distutils` is deprecated since NumPy 1.23.0, as a result
of the deprecation of `distutils` itself. It will be removed for
Python >= 3.12. For older Python versions it will remain present.
It is recommended to use `setuptools < 60.0` for those Python versions.
For more details, see:
https://numpy.org/devdocs/reference/distutils_status_migration.html
Error compiling Cython file:
------------------------------------------------------------
...
if n_used_bins <= 1:
free(cat_infos)
return
qsort(cat_infos, n_used_bins, sizeof(categorical_info),
compare_cat_infos)
^
------------------------------------------------------------
sklearn/ensemble/_hist_gradient_boosting/splitting.pyx:912:14: Cannot assign type 'int (const void *, const void *) except? -1 nogil' to 'int (*)(const void *, const void *) noexcept nogil'
Traceback (most recent call last):
File "/tmp/pip-build-env-at5n6u8u/overlay/lib/python3.10/site-packages/Cython/Build/Dependencies.py", line 1325, in cythonize_one_helper
return cythonize_one(*m)
File "/tmp/pip-build-env-at5n6u8u/overlay/lib/python3.10/site-packages/Cython/Build/Dependencies.py", line 1301, in cythonize_one
raise CompileError(None, pyx_file)
Cython.Compiler.Errors.CompileError: sklearn/ensemble/_hist_gradient_boosting/splitting.pyx
warning: sklearn/neighbors/_dist_metrics.pxd:77:67: The keyword 'nogil' should appear at the end of the function signature line. Placing it before 'except' or 'noexcept' will be disallowed in a future version of Cython.
Error compiling Cython file:
------------------------------------------------------------
...
# determine number of levels in the tree, and from this
# the number of nodes in the tree. This results in leaf nodes
# with numbers of points between leaf_size and 2 * leaf_size
self.n_levels = int(
np.log2(fmax(1, (n_samples - 1) / self.leaf_size)) + 1)
self.n_nodes = (2 ** self.n_levels) - 1
^
------------------------------------------------------------
sklearn/neighbors/_binary_tree.pxi:1079:44: Cannot assign type 'double' to 'ITYPE_t'
Traceback (most recent call last):
File "/tmp/pip-build-env-at5n6u8u/overlay/lib/python3.10/site-packages/Cython/Build/Dependencies.py", line 1325, in cythonize_one_helper
return cythonize_one(*m)
File "/tmp/pip-build-env-at5n6u8u/overlay/lib/python3.10/site-packages/Cython/Build/Dependencies.py", line 1301, in cythonize_one
raise CompileError(None, pyx_file)
Cython.Compiler.Errors.CompileError: sklearn/neighbors/_ball_tree.pyx
Error compiling Cython file:
------------------------------------------------------------
...
def __cinit__(self, int n_dimensions, int verbose):
"""Constructor."""
# Parameters of the tree
self.n_dimensions = n_dimensions
self.verbose = verbose
self.n_cells_per_cell = 2 ** self.n_dimensions
^
------------------------------------------------------------
sklearn/neighbors/_quad_tree.pyx:60:34: Cannot assign type 'double' to 'SIZE_t'
Traceback (most recent call last):
File "/tmp/pip-build-env-at5n6u8u/overlay/lib/python3.10/site-packages/Cython/Build/Dependencies.py", line 1325, in cythonize_one_helper
return cythonize_one(*m)
File "/tmp/pip-build-env-at5n6u8u/overlay/lib/python3.10/site-packages/Cython/Build/Dependencies.py", line 1301, in cythonize_one
raise CompileError(None, pyx_file)
Cython.Compiler.Errors.CompileError: sklearn/neighbors/_quad_tree.pyx
Error compiling Cython file:
------------------------------------------------------------
...
free_problem(problem)
free_parameter(param)
raise ValueError(error_msg)
cdef BlasFunctions blas_functions
blas_functions.dot = _dot[double]
^
------------------------------------------------------------
sklearn/svm/_liblinear.pyx:55:29: Cannot assign type 'double (int, double *, int, double *, int) except * nogil' to 'dot_func'
Error compiling Cython file:
------------------------------------------------------------
...
free_parameter(param)
raise ValueError(error_msg)
cdef BlasFunctions blas_functions
blas_functions.dot = _dot[double]
blas_functions.axpy = _axpy[double]
^
------------------------------------------------------------
sklearn/svm/_liblinear.pyx:56:31: Cannot assign type 'void (int, double, double *, int, double *, int) except * nogil' to 'axpy_func'
Error compiling Cython file:
------------------------------------------------------------
...
raise ValueError(error_msg)
cdef BlasFunctions blas_functions
blas_functions.dot = _dot[double]
blas_functions.axpy = _axpy[double]
blas_functions.scal = _scal[double]
^
------------------------------------------------------------
sklearn/svm/_liblinear.pyx:57:31: Cannot assign type 'void (int, double, double *, int) except * nogil' to 'scal_func'
Error compiling Cython file:
------------------------------------------------------------
...
cdef BlasFunctions blas_functions
blas_functions.dot = _dot[double]
blas_functions.axpy = _axpy[double]
blas_functions.scal = _scal[double]
blas_functions.nrm2 = _nrm2[double]
^
------------------------------------------------------------
sklearn/svm/_liblinear.pyx:58:31: Cannot assign type 'double (int, double *, int) except * nogil' to 'nrm2_func'
Traceback (most recent call last):
File "/tmp/pip-build-env-at5n6u8u/overlay/lib/python3.10/site-packages/Cython/Build/Dependencies.py", line 1325, in cythonize_one_helper
return cythonize_one(*m)
File "/tmp/pip-build-env-at5n6u8u/overlay/lib/python3.10/site-packages/Cython/Build/Dependencies.py", line 1301, in cythonize_one
raise CompileError(None, pyx_file)
Cython.Compiler.Errors.CompileError: sklearn/svm/_liblinear.pyx
Error compiling Cython file:
------------------------------------------------------------
...
if error_msg:
# for SVR: epsilon is called p in libsvm
error_repl = error_msg.decode('utf-8').replace("p < 0", "epsilon < 0")
raise ValueError(error_repl)
cdef BlasFunctions blas_functions
blas_functions.dot = _dot[double]
^
------------------------------------------------------------
sklearn/svm/_libsvm.pyx:194:29: Cannot assign type 'double (int, double *, int, double *, int) except * nogil' to 'dot_func'
Error compiling Cython file:
------------------------------------------------------------
...
class_weight_label.data, class_weight.data)
model = set_model(¶m, <int> nSV.shape[0], SV.data, SV.shape,
support.data, support.shape, sv_coef.strides,
sv_coef.data, intercept.data, nSV.data, probA.data, probB.data)
cdef BlasFunctions blas_functions
blas_functions.dot = _dot[double]
^
------------------------------------------------------------
sklearn/svm/_libsvm.pyx:358:29: Cannot assign type 'double (int, double *, int, double *, int) except * nogil' to 'dot_func'
Error compiling Cython file:
------------------------------------------------------------
...
sv_coef.data, intercept.data, nSV.data,
probA.data, probB.data)
cdef np.npy_intp n_class = get_nr(model)
cdef BlasFunctions blas_functions
blas_functions.dot = _dot[double]
^
------------------------------------------------------------
sklearn/svm/_libsvm.pyx:464:29: Cannot assign type 'double (int, double *, int, double *, int) except * nogil' to 'dot_func'
Error compiling Cython file:
------------------------------------------------------------
...
n_class = 1
else:
n_class = get_nr(model)
n_class = n_class * (n_class - 1) // 2
cdef BlasFunctions blas_functions
blas_functions.dot = _dot[double]
^
------------------------------------------------------------
sklearn/svm/_libsvm.pyx:570:29: Cannot assign type 'double (int, double *, int, double *, int) except * nogil' to 'dot_func'
Error compiling Cython file:
------------------------------------------------------------
...
if error_msg:
raise ValueError(error_msg)
cdef np.ndarray[np.float64_t, ndim=1, mode='c'] target
cdef BlasFunctions blas_functions
blas_functions.dot = _dot[double]
^
------------------------------------------------------------
sklearn/svm/_libsvm.pyx:714:29: Cannot assign type 'double (int, double *, int, double *, int) except * nogil' to 'dot_func'
Traceback (most recent call last):
File "/tmp/pip-build-env-at5n6u8u/overlay/lib/python3.10/site-packages/Cython/Build/Dependencies.py", line 1325, in cythonize_one_helper
return cythonize_one(*m)
File "/tmp/pip-build-env-at5n6u8u/overlay/lib/python3.10/site-packages/Cython/Build/Dependencies.py", line 1301, in cythonize_one
raise CompileError(None, pyx_file)
Cython.Compiler.Errors.CompileError: sklearn/svm/_libsvm.pyx
Error compiling Cython file:
------------------------------------------------------------
...
if error_msg:
free_problem(problem)
free_param(param)
raise ValueError(error_msg)
cdef BlasFunctions blas_functions
blas_functions.dot = _dot[double]
^
------------------------------------------------------------
sklearn/svm/_libsvm_sparse.pyx:153:29: Cannot assign type 'double (int, double *, int, double *, int) except * nogil' to 'dot_func'
Error compiling Cython file:
------------------------------------------------------------
...
sv_coef.data, intercept.data,
nSV.data, probA.data, probB.data)
#TODO: use check_model
dec_values = np.empty(T_indptr.shape[0]-1)
cdef BlasFunctions blas_functions
blas_functions.dot = _dot[double]
^
------------------------------------------------------------
sklearn/svm/_libsvm_sparse.pyx:284:29: Cannot assign type 'double (int, double *, int, double *, int) except * nogil' to 'dot_func'
Error compiling Cython file:
------------------------------------------------------------
...
#TODO: use check_model
cdef np.npy_intp n_class = get_nr(model)
cdef int rv
dec_values = np.empty((T_indptr.shape[0]-1, n_class), dtype=np.float64)
cdef BlasFunctions blas_functions
blas_functions.dot = _dot[double]
^
------------------------------------------------------------
sklearn/svm/_libsvm_sparse.pyx:343:29: Cannot assign type 'double (int, double *, int, double *, int) except * nogil' to 'dot_func'
Error compiling Cython file:
------------------------------------------------------------
...
n_class = get_nr(model)
n_class = n_class * (n_class - 1) // 2
dec_values = np.empty((T_indptr.shape[0] - 1, n_class), dtype=np.float64)
cdef BlasFunctions blas_functions
blas_functions.dot = _dot[double]
^
------------------------------------------------------------
sklearn/svm/_libsvm_sparse.pyx:412:29: Cannot assign type 'double (int, double *, int, double *, int) except * nogil' to 'dot_func'
Traceback (most recent call last):
File "/tmp/pip-build-env-at5n6u8u/overlay/lib/python3.10/site-packages/Cython/Build/Dependencies.py", line 1325, in cythonize_one_helper
return cythonize_one(*m)
File "/tmp/pip-build-env-at5n6u8u/overlay/lib/python3.10/site-packages/Cython/Build/Dependencies.py", line 1301, in cythonize_one
raise CompileError(None, pyx_file)
Cython.Compiler.Errors.CompileError: sklearn/svm/_libsvm_sparse.pyx
Error compiling Cython file:
------------------------------------------------------------
...
if not is_samples_sorted[0]:
n_samples = end - start
memcpy(sorted_samples + start, samples + start,
n_samples * sizeof(SIZE_t))
qsort(sorted_samples + start, n_samples, sizeof(SIZE_t),
compare_SIZE_t)
^
------------------------------------------------------------
sklearn/tree/_splitter.pyx:1037:14: Cannot assign type 'int (const void *, const void *) except? -1 nogil' to 'int (*)(const void *, const void *) noexcept nogil'
Traceback (most recent call last):
File "/tmp/pip-build-env-at5n6u8u/overlay/lib/python3.10/site-packages/Cython/Build/Dependencies.py", line 1325, in cythonize_one_helper
return cythonize_one(*m)
File "/tmp/pip-build-env-at5n6u8u/overlay/lib/python3.10/site-packages/Cython/Build/Dependencies.py", line 1301, in cythonize_one
raise CompileError(None, pyx_file)
Cython.Compiler.Errors.CompileError: sklearn/tree/_splitter.pyx
Error compiling Cython file:
------------------------------------------------------------
...
# Initial capacity
cdef int init_capacity
if tree.max_depth <= 10:
init_capacity = (2 ** (tree.max_depth + 1)) - 1
^
------------------------------------------------------------
sklearn/tree/_tree.pyx:151:56: Cannot assign type 'double' to 'int'
Traceback (most recent call last):
File "/tmp/pip-build-env-at5n6u8u/overlay/lib/python3.10/site-packages/Cython/Build/Dependencies.py", line 1325, in cythonize_one_helper
return cythonize_one(*m)
File "/tmp/pip-build-env-at5n6u8u/overlay/lib/python3.10/site-packages/Cython/Build/Dependencies.py", line 1301, in cythonize_one
raise CompileError(None, pyx_file)
Cython.Compiler.Errors.CompileError: sklearn/tree/_tree.pyx
Error compiling Cython file:
------------------------------------------------------------
...
dec(end)
# Construct our arguments
cdef pair[ITYPE_t, DTYPE_t] args
args.first = key
args.second = value
self.my_map.insert(end, args)
^
------------------------------------------------------------
Cython.Compiler.Errors.CompileError: sklearn/ensemble/_hist_gradient_boosting/splitting.pyx
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed
× Encountered error while generating package metadata.
╰─> See above for output.
note: This is an issue with the package mentioned above, not pip.
Environment and installation:
python 3.10
Please give details about your installation:
- OS: Ubuntu 20.04.6 LTS
- Is your installation in a virtual environment or conda environment? Yes (Virtual Environment)
- Python version 3.10
- Auto-sklearn version (latest)
I have the same problem since yesterday, it goes as far as downloading scikit learn, this is in google colab, but it always worked
It's because of the new Cython release a few days ago, and its incompatibility with older scikit-learn. Workaround for now is to
- Install older Cython
- Make sure that scikit-learn uses that Cython when it's built
This answer does both of those.
Hii can you help me please? Even python 3.9 doesn't work for me
Using Python 3.9 solves the issue as well
Hii iam trying to user python3.9 on google colab, did you try it? Can see in my last comment what I did, can you help me solve the problem?
Hii iam trying to user python3.9 on google colab, did you try it? Can see in my last comment what I did, can you help me solve the problem?
I do not use ipython or jupyter notebooks, only command line on Ubuntu 22.04 in a venv. Must be something else in your configuration that is causing the problem.
Hii iam trying to user python3.9 on google colab, did you try it? Can see in my last comment what I did, can you help me solve the problem?
I do not use ipython or jupyter notebooks, only command line on Ubuntu 22.04 in a venv. Must be something else in your configuration that is causing the problem.
So when usign ubuntu even python3.10 works fine, only on google colab that does not work
Did you try restarting the kernel after installing auto-sklearn?
after using restart runtime the session crash.
this is the error:
can see my notebook here
Don't uninstall Ipython is my best guess based on the fact it's looking for a kernel (powered by IPython)
i have a a way to fix it, thank you all and thanks for @AmirAlavi to point it out in other issue.
https://colab.research.google.com/drive/1BXXdGaJX_HxOL-jaL747s_BLYAjPvmCH?usp=sharing
Thanks to all for the help.
El dom, 27 ago 2023 a la(s) 18:10, eyalElb @.***) escribió:
i have a a way to fix it, thank you all and thanks for @AmirAlavi https://github.com/AmirAlavi to point it out in other issue.
https://colab.research.google.com/drive/1BXXdGaJX_HxOL-jaL747s_BLYAjPvmCH?usp=sharing
— Reply to this email directly, view it on GitHub https://github.com/automl/auto-sklearn/issues/1675#issuecomment-1694762859, or unsubscribe https://github.com/notifications/unsubscribe-auth/AUZK3A6WBYNYND5ZEBOCIVLXXOZU3ANCNFSM6AAAAAA2OHYXPM . You are receiving this because you commented.Message ID: @.***>
-- Mg.Ing. Gabriel Novillo Rangone. Profesor Adjunto. UNVIME.
Thanks to Amir's comment, my install succeeded with:
pip install auto-sklearn --no-build-isolation
No, I understand why, but Google Colab stopped working for me, it sends the same error as before. Someone has an explanation. Thank You.
El sáb, 7 oct 2023 a la(s) 12:25, Shellcat-Zero @.***) escribió:
Thanks to Amir's comment, my install succeeded with:
pip install auto-sklearn --no-build-isolation
— Reply to this email directly, view it on GitHub https://github.com/automl/auto-sklearn/issues/1675#issuecomment-1751738274, or unsubscribe https://github.com/notifications/unsubscribe-auth/AUZK3A2HQBH2ZD4FBI3GQL3X6FX6RAVCNFSM6AAAAAA2OHYXPOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTONJRG4ZTQMRXGQ . You are receiving this because you commented.Message ID: @.***>
-- Mg.Ing. Gabriel Novillo Rangone. Profesor Adjunto. UNVIME.
@Shellcat-Zero hi, do you use this pip install auto-sklearn --no-build-isolation and then pip install auto-sklearn in colab with a default python version as 3.10?
@Shellcat-Zero hi, do you use this
pip install auto-sklearn --no-build-isolationand thenpip install auto-sklearnin colab with a default python version as 3.10?
@stupidoge I'm not using colab (just my own Linux environment), but I am using python 3.10. After running into various bugs in auto-sklearn, and finding out that there is major (unreleased) refactoring work going on to fix issues in it, I've since moved on Python FLAML for the same use cases.
No not yet, thanks for asking Kai. This is the error it gives me. [image: image.png]
El mié, 15 nov 2023 a la(s) 13:40, Kai @.***) escribió:
@gabrielnovillorangone https://github.com/gabrielnovillorangone Hi sir, did you solve that problem?
— Reply to this email directly, view it on GitHub https://github.com/automl/auto-sklearn/issues/1675#issuecomment-1812883535, or unsubscribe https://github.com/notifications/unsubscribe-auth/AUZK3A7NFQWVKVGUOHJXWXDYETV6XAVCNFSM6AAAAAA2OHYXPOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQMJSHA4DGNJTGU . You are receiving this because you were mentioned.Message ID: @.***>
-- Mg.Ing. Gabriel Novillo Rangone. Profesor Adjunto. UNVIME.
facing the same issue:
$ pip install scikit-learn==0.23 --no-build-isolation
Collecting scikit-learn==0.23
Using cached scikit-learn-0.23.0.tar.gz (7.2 MB)
Preparing metadata (pyproject.toml) ... error
error: subprocess-exited-with-error
× Preparing metadata (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [13 lines of output]
Partial import of sklearn during the build process.
running dist_info
creating /tmp/pip-modern-metadata-bg3uuqnx/scikit_learn.egg-info
writing /tmp/pip-modern-metadata-bg3uuqnx/scikit_learn.egg-info/PKG-INFO
writing dependency_links to /tmp/pip-modern-metadata-bg3uuqnx/scikit_learn.egg-info/dependency_links.txt
writing requirements to /tmp/pip-modern-metadata-bg3uuqnx/scikit_learn.egg-info/requires.txt
writing top-level names to /tmp/pip-modern-metadata-bg3uuqnx/scikit_learn.egg-info/top_level.txt
writing manifest file '/tmp/pip-modern-metadata-bg3uuqnx/scikit_learn.egg-info/SOURCES.txt'
reading manifest file '/tmp/pip-modern-metadata-bg3uuqnx/scikit_learn.egg-info/SOURCES.txt'
adding license file 'COPYING'
writing manifest file '/tmp/pip-modern-metadata-bg3uuqnx/scikit_learn.egg-info/SOURCES.txt'
creating '/tmp/pip-modern-metadata-bg3uuqnx/scikit_learn-0.23.0.dist-info'
error: invalid command 'bdist_wheel'
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed
× Encountered error while generating package metadata.
╰─> See above for output.
note: This is an issue with the package mentioned above, not pip.
hint: See above for details.
os:
$ cat /etc/os-release
PRETTY_NAME="Debian GNU/Linux 12 (bookworm)"
NAME="Debian GNU/Linux"
VERSION_ID="12"
VERSION="12 (bookworm)"
VERSION_CODENAME=bookworm
ID=debian
HOME_URL="https://www.debian.org/"
SUPPORT_URL="https://www.debian.org/support"
BUG_REPORT_URL="https://bugs.debian.org/"
kernel:
$ uname -a
Linux unknown 6.1.0-18-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.76-1 (2024-02-01) x86_64 GNU/Linux
python version:
$ python --version
Python 3.10.13
