Comments (3)
david-cortes
commented on August 22, 2024
1
As outlined in the toml file, this package requires cython>=3.0.0, so you if are using something like PIP_CONSTRAINTS or some other system built on top of pip that makes it ignore such build nuances, it's up to you to make it satisfy those requirements.
If you didn't set up those things then maybe contact your provider's support as it suggests in the error message.
from isotree.
Ravikumarnl
commented on August 22, 2024
Complete error message is as below: (not copied completely in previous post)
Library installation attempted on the driver node of cluster 0714-111409-o9fj6ac2 and failed. Please refer to the following error message to fix the library or contact Databricks support. Error Code: DRIVER_LIBRARY_INSTALLATION_FAILURE. Error Message: org.apache.spark.SparkException: Process List(bash, /local_disk0/.ephemeral_nfs/cluster_libraries/python/python_start_clusterwide.sh, /local_disk0/.ephemeral_nfs/cluster_libraries/python/bin/pip, install, isotree==0.5.22, --disable-pip-version-check) exited with code 1. ERROR: Command errored out with exit status 1:
command: /local_disk0/.ephemeral_nfs/cluster_libraries/python/bin/python /local_disk0/.ephemeral_nfs/cluster_libraries/python/lib/python3.9/site-packages/pip/_vendor/pep517/in_process/_in_process.py build_wheel /tmp/tmpz3gi_800
cwd: /tmp/pip-install-vnnaag20/isotree_5156cd302e594e3b88594b6810c157c7
Complete output (574 lines):
/databricks/python/lib/python3.9/site-packages/setuptools/_distutils/extension.py:131: UserWarning: Unknown Extension options: 'install_requires'
warnings.warn(msg)
running bdist_wheel
running build
running build_py
creating build
creating build/lib.linux-x86_64-3.9
creating build/lib.linux-x86_64-3.9/isotree
copying isotree/init.py -> build/lib.linux-x86_64-3.9/isotree
running build_ext
--- Checking compiler support for option '-march=native'
--- Checking compiler support for option '-fopenmp'
--- Checking compiler support for '__restrict' qualifier
--- Checking compiler support for option '-O3'
--- Checking compiler support for option '-fno-math-errno'
--- Checking compiler support for option '-fno-trapping-math'
--- Checking compiler support for option '-std=c++17'
--- Checking compiler support for option '-flto=auto'
cythoning isotree/cpp_interface.pyx to isotree/cpp_interface.cpp
Error compiling Cython file:
------------------------------------------------------------
...
void tmat_to_dense(double tmat, double dmat, size_t n, double fill_diag)
void merge_models(IsoForest model, IsoForest other,
ExtIsoForest* ext_model, ExtIsoForest* ext_other,
Imputer* imputer, Imputer* iother,
TreesIndexer* indexer, TreesIndexer* ind_other) except + nogil
^
------------------------------------------------------------
isotree/cpp_interface.pyx:223:89: undeclared name not builtin: nogil
Error compiling Cython file:
------------------------------------------------------------
...
cdef int ret_val = 0
with nogil, boundscheck(False), nonecheck(False), wraparound(False):
ret_val =
fit_iforest(model_ptr, ext_model_ptr,
^
------------------------------------------------------------
isotree/cpp_interface.pyx:823:23: Calling gil-requiring function not allowed without gil
Error compiling Cython file:
------------------------------------------------------------
...
cdef int ret_val = 0
with nogil, boundscheck(False), nonecheck(False), wraparound(False):
ret_val =
fit_iforest(model_ptr, ext_model_ptr,
^
------------------------------------------------------------
isotree/cpp_interface.pyx:823:23: Calling gil-requiring function not allowed without gil
Error compiling Cython file:
------------------------------------------------------------
...
cdef int ret_val = 0
with nogil, boundscheck(False), nonecheck(False), wraparound(False):
ret_val =
fit_iforest(model_ptr, ext_model_ptr,
^
------------------------------------------------------------
isotree/cpp_interface.pyx:823:23: Calling gil-requiring function not allowed without gil
Error compiling Cython file:
------------------------------------------------------------
...
cdef int ret_val = 0
with nogil, boundscheck(False), nonecheck(False), wraparound(False):
ret_val =
fit_iforest(model_ptr, ext_model_ptr,
^
------------------------------------------------------------
isotree/cpp_interface.pyx:823:23: Calling gil-requiring function not allowed without gil
Error compiling Cython file:
------------------------------------------------------------
...
cdef int ret_val = 0
with nogil, boundscheck(False), nonecheck(False), wraparound(False):
ret_val =
fit_iforest(model_ptr, ext_model_ptr,
^
------------------------------------------------------------
isotree/cpp_interface.pyx:823:23: Calling gil-requiring function not allowed without gil
Error compiling Cython file:
------------------------------------------------------------
...
cdef int ret_val = 0
with nogil, boundscheck(False), nonecheck(False), wraparound(False):
ret_val =
fit_iforest(model_ptr, ext_model_ptr,
^
------------------------------------------------------------
isotree/cpp_interface.pyx:823:23: Calling gil-requiring function not allowed without gil
Error compiling Cython file:
------------------------------------------------------------
...
cdef TreesIndexer indexer_ptr = NULL
if not self.indexer.indices.empty():
indexer_ptr = &self.indexer
with nogil, boundscheck(False), nonecheck(False), wraparound(False):
add_tree(model_ptr, ext_model_ptr,
^
------------------------------------------------------------
isotree/cpp_interface.pyx:1024:20: Calling gil-requiring function not allowed without gil
Error compiling Cython file:
------------------------------------------------------------
...
cdef TreesIndexer indexer_ptr = NULL
if not self.indexer.indices.empty():
indexer_ptr = &self.indexer
with nogil, boundscheck(False), nonecheck(False), wraparound(False):
add_tree(model_ptr, ext_model_ptr,
^
------------------------------------------------------------
isotree/cpp_interface.pyx:1024:20: Calling gil-requiring function not allowed without gil
Error compiling Cython file:
------------------------------------------------------------
...
cdef TreesIndexer indexer_ptr = NULL
if not self.indexer.indices.empty():
indexer_ptr = &self.indexer
with nogil, boundscheck(False), nonecheck(False), wraparound(False):
add_tree(model_ptr, ext_model_ptr,
^
------------------------------------------------------------
isotree/cpp_interface.pyx:1024:20: Calling gil-requiring function not allowed without gil
Error compiling Cython file:
------------------------------------------------------------
...
cdef TreesIndexer indexer_ptr = NULL
if not self.indexer.indices.empty():
indexer_ptr = &self.indexer
with nogil, boundscheck(False), nonecheck(False), wraparound(False):
add_tree(model_ptr, ext_model_ptr,
^
------------------------------------------------------------
isotree/cpp_interface.pyx:1024:20: Calling gil-requiring function not allowed without gil
Error compiling Cython file:
------------------------------------------------------------
...
cdef TreesIndexer indexer_ptr = NULL
if not self.indexer.indices.empty():
indexer_ptr = &self.indexer
with nogil, boundscheck(False), nonecheck(False), wraparound(False):
add_tree(model_ptr, ext_model_ptr,
^
------------------------------------------------------------
isotree/cpp_interface.pyx:1024:20: Calling gil-requiring function not allowed without gil
Error compiling Cython file:
------------------------------------------------------------
...
cdef TreesIndexer indexer_ptr = NULL
if not self.indexer.indices.empty():
indexer_ptr = &self.indexer
with nogil, boundscheck(False), nonecheck(False), wraparound(False):
add_tree(model_ptr, ext_model_ptr,
^
------------------------------------------------------------
isotree/cpp_interface.pyx:1024:20: Calling gil-requiring function not allowed without gil
Error compiling Cython file:
------------------------------------------------------------
...
cdef TreesIndexer indexer_ptr = NULL
if not self.indexer.indices.empty():
indexer_ptr = &self.indexer
with nogil, boundscheck(False), nonecheck(False), wraparound(False):
predict_iforest(numeric_data_ptr, categ_data_ptr,
^
------------------------------------------------------------
isotree/cpp_interface.pyx:1164:27: Calling gil-requiring function not allowed without gil
Error compiling Cython file:
------------------------------------------------------------
...
cdef TreesIndexer indexer_ptr = NULL
if not self.indexer.indices.empty():
indexer_ptr = &self.indexer
with nogil, boundscheck(False), nonecheck(False), wraparound(False):
predict_iforest(numeric_data_ptr, categ_data_ptr,
^
------------------------------------------------------------
isotree/cpp_interface.pyx:1164:27: Calling gil-requiring function not allowed without gil
Error compiling Cython file:
------------------------------------------------------------
...
cdef TreesIndexer indexer_ptr = NULL
if not self.indexer.indices.empty():
indexer_ptr = &self.indexer
with nogil, boundscheck(False), nonecheck(False), wraparound(False):
predict_iforest(numeric_data_ptr, categ_data_ptr,
^
------------------------------------------------------------
isotree/cpp_interface.pyx:1164:27: Calling gil-requiring function not allowed without gil
Error compiling Cython file:
------------------------------------------------------------
...
cdef TreesIndexer indexer_ptr = NULL
if not self.indexer.indices.empty():
indexer_ptr = &self.indexer
with nogil, boundscheck(False), nonecheck(False), wraparound(False):
predict_iforest(numeric_data_ptr, categ_data_ptr,
^
------------------------------------------------------------
isotree/cpp_interface.pyx:1164:27: Calling gil-requiring function not allowed without gil
Error compiling Cython file:
------------------------------------------------------------
...
cdef TreesIndexer indexer_ptr = NULL
if not self.indexer.indices.empty():
indexer_ptr = &self.indexer
with nogil, boundscheck(False), nonecheck(False), wraparound(False):
predict_iforest(numeric_data_ptr, categ_data_ptr,
^
------------------------------------------------------------
isotree/cpp_interface.pyx:1164:27: Calling gil-requiring function not allowed without gil
Error compiling Cython file:
------------------------------------------------------------
...
cdef TreesIndexer indexer_ptr = NULL
if not self.indexer.indices.empty():
indexer_ptr = &self.indexer
with nogil, boundscheck(False), nonecheck(False), wraparound(False):
predict_iforest(numeric_data_ptr, categ_data_ptr,
^
------------------------------------------------------------
isotree/cpp_interface.pyx:1164:27: Calling gil-requiring function not allowed without gil
Error compiling Cython file:
------------------------------------------------------------
...
cdef TreesIndexer* indexer_ptr = NULL
if not self.indexer.indices.empty():
indexer_ptr = &self.indexer
with nogil, boundscheck(False), nonecheck(False), wraparound(False):
calc_similarity(numeric_data_ptr, categ_data_ptr,
^
------------------------------------------------------------
isotree/cpp_interface.pyx:1288:27: Calling gil-requiring function not allowed without gil
Error compiling Cython file:
------------------------------------------------------------
...
cdef TreesIndexer* indexer_ptr = NULL
if not self.indexer.indices.empty():
indexer_ptr = &self.indexer
with nogil, boundscheck(False), nonecheck(False), wraparound(False):
calc_similarity(numeric_data_ptr, categ_data_ptr,
^
------------------------------------------------------------
isotree/cpp_interface.pyx:1288:27: Calling gil-requiring function not allowed without gil
Error compiling Cython file:
------------------------------------------------------------
...
cdef TreesIndexer* indexer_ptr = NULL
if not self.indexer.indices.empty():
indexer_ptr = &self.indexer
with nogil, boundscheck(False), nonecheck(False), wraparound(False):
calc_similarity(numeric_data_ptr, categ_data_ptr,
^
------------------------------------------------------------
isotree/cpp_interface.pyx:1288:27: Calling gil-requiring function not allowed without gil
Error compiling Cython file:
------------------------------------------------------------
...
cdef TreesIndexer* indexer_ptr = NULL
if not self.indexer.indices.empty():
indexer_ptr = &self.indexer
with nogil, boundscheck(False), nonecheck(False), wraparound(False):
calc_similarity(numeric_data_ptr, categ_data_ptr,
^
------------------------------------------------------------
isotree/cpp_interface.pyx:1288:27: Calling gil-requiring function not allowed without gil
Error compiling Cython file:
------------------------------------------------------------
...
cdef TreesIndexer* indexer_ptr = NULL
if not self.indexer.indices.empty():
indexer_ptr = &self.indexer
with nogil, boundscheck(False), nonecheck(False), wraparound(False):
calc_similarity(numeric_data_ptr, categ_data_ptr,
^
------------------------------------------------------------
isotree/cpp_interface.pyx:1288:27: Calling gil-requiring function not allowed without gil
Error compiling Cython file:
------------------------------------------------------------
...
cdef TreesIndexer* indexer_ptr = NULL
if not self.indexer.indices.empty():
indexer_ptr = &self.indexer
with nogil, boundscheck(False), nonecheck(False), wraparound(False):
calc_similarity(numeric_data_ptr, categ_data_ptr,
^
------------------------------------------------------------
isotree/cpp_interface.pyx:1288:27: Calling gil-requiring function not allowed without gil
Error compiling Cython file:
------------------------------------------------------------
...
model_ptr = &self.isoforest
else:
ext_model_ptr = &self.ext_isoforest
with nogil, boundscheck(False), nonecheck(False), wraparound(False):
impute_missing_values(numeric_data_ptr, categ_data_ptr, is_col_major,
^
------------------------------------------------------------
isotree/cpp_interface.pyx:1374:33: Calling gil-requiring function not allowed without gil
Error compiling Cython file:
------------------------------------------------------------
...
model_ptr = &self.isoforest
else:
ext_model_ptr = &self.ext_isoforest
with nogil, boundscheck(False), nonecheck(False), wraparound(False):
impute_missing_values(numeric_data_ptr, categ_data_ptr, is_col_major,
^
------------------------------------------------------------
isotree/cpp_interface.pyx:1374:33: Calling gil-requiring function not allowed without gil
Error compiling Cython file:
------------------------------------------------------------
...
model_ptr = &self.isoforest
else:
ext_model_ptr = &self.ext_isoforest
with nogil, boundscheck(False), nonecheck(False), wraparound(False):
impute_missing_values(numeric_data_ptr, categ_data_ptr, is_col_major,
^
------------------------------------------------------------
isotree/cpp_interface.pyx:1374:33: Calling gil-requiring function not allowed without gil
Error compiling Cython file:
------------------------------------------------------------
...
model_ptr = &self.isoforest
else:
ext_model_ptr = &self.ext_isoforest
with nogil, boundscheck(False), nonecheck(False), wraparound(False):
impute_missing_values(numeric_data_ptr, categ_data_ptr, is_col_major,
^
------------------------------------------------------------
isotree/cpp_interface.pyx:1374:33: Calling gil-requiring function not allowed without gil
Error compiling Cython file:
------------------------------------------------------------
...
model_ptr = &self.isoforest
else:
ext_model_ptr = &self.ext_isoforest
with nogil, boundscheck(False), nonecheck(False), wraparound(False):
impute_missing_values(numeric_data_ptr, categ_data_ptr, is_col_major,
^
------------------------------------------------------------
isotree/cpp_interface.pyx:1374:33: Calling gil-requiring function not allowed without gil
Error compiling Cython file:
------------------------------------------------------------
...
model_ptr = &self.isoforest
else:
ext_model_ptr = &self.ext_isoforest
with nogil, boundscheck(False), nonecheck(False), wraparound(False):
impute_missing_values(numeric_data_ptr, categ_data_ptr, is_col_major,
^
------------------------------------------------------------
isotree/cpp_interface.pyx:1374:33: Calling gil-requiring function not allowed without gil
Error compiling Cython file:
------------------------------------------------------------
...
ptr_indexer = &self.indexer
if not other.indexer.indices.empty():
prt_ind_other = &other.indexer
with nogil, boundscheck(False), nonecheck(False), wraparound(False):
merge_models(ptr_model, ptr_other,
^
------------------------------------------------------------
isotree/cpp_interface.pyx:1424:24: Calling gil-requiring function not allowed without gil
Error compiling Cython file:
------------------------------------------------------------
...
else:
ext_model_ptr = &self.ext_isoforest
cdef vector[cpp_string] res
with nogil, boundscheck(False), nonecheck(False), wraparound(False):
res = generate_sql(model_ptr, ext_model_ptr,
^
------------------------------------------------------------
isotree/cpp_interface.pyx:1546:30: Calling gil-requiring function not allowed without gil
Error compiling Cython file:
------------------------------------------------------------
...
else:
ext_model_ptr = &self.ext_isoforest
cdef TreesIndexer* indexer_ptr = &self.indexer
with nogil, boundscheck(False), nonecheck(False), wraparound(False):
set_reference_points(model_ptr, ext_model_ptr, indexer_ptr,
^
------------------------------------------------------------
isotree/cpp_interface.pyx:1687:32: Calling gil-requiring function not allowed without gil
Error compiling Cython file:
------------------------------------------------------------
...
else:
ext_model_ptr = &self.ext_isoforest
cdef TreesIndexer* indexer_ptr = &self.indexer
with nogil, boundscheck(False), nonecheck(False), wraparound(False):
set_reference_points(model_ptr, ext_model_ptr, indexer_ptr,
^
------------------------------------------------------------
isotree/cpp_interface.pyx:1687:32: Calling gil-requiring function not allowed without gil
Error compiling Cython file:
------------------------------------------------------------
...
else:
ext_model_ptr = &self.ext_isoforest
cdef TreesIndexer* indexer_ptr = &self.indexer
with nogil, boundscheck(False), nonecheck(False), wraparound(False):
set_reference_points(model_ptr, ext_model_ptr, indexer_ptr,
^
------------------------------------------------------------
isotree/cpp_interface.pyx:1687:32: Calling gil-requiring function not allowed without gil
Error compiling Cython file:
------------------------------------------------------------
...
else:
ext_model_ptr = &self.ext_isoforest
cdef TreesIndexer* indexer_ptr = &self.indexer
with nogil, boundscheck(False), nonecheck(False), wraparound(False):
set_reference_points(model_ptr, ext_model_ptr, indexer_ptr,
^
------------------------------------------------------------
isotree/cpp_interface.pyx:1687:32: Calling gil-requiring function not allowed without gil
Error compiling Cython file:
------------------------------------------------------------
...
else:
ext_model_ptr = &self.ext_isoforest
cdef TreesIndexer* indexer_ptr = &self.indexer
with nogil, boundscheck(False), nonecheck(False), wraparound(False):
set_reference_points(model_ptr, ext_model_ptr, indexer_ptr,
^
------------------------------------------------------------
isotree/cpp_interface.pyx:1687:32: Calling gil-requiring function not allowed without gil
Error compiling Cython file:
------------------------------------------------------------
...
else:
ext_model_ptr = &self.ext_isoforest
cdef TreesIndexer* indexer_ptr = &self.indexer
with nogil, boundscheck(False), nonecheck(False), wraparound(False):
set_reference_points(model_ptr, ext_model_ptr, indexer_ptr,
^
------------------------------------------------------------
isotree/cpp_interface.pyx:1687:32: Calling gil-requiring function not allowed without gil
building 'isotree._cpp_interface' extension
creating build/temp.linux-x86_64-3.9
creating build/temp.linux-x86_64-3.9/isotree
creating build/temp.linux-x86_64-3.9/src
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -D_USE_XOSHIRO -DNDEBUG -D_FOR_PYTHON "-DCYTHON_EXTERN_C=extern "C"" -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -D_USE_ROBIN_MAP -I/databricks/python/lib/python3.9/site-packages/numpy/core/include -I. -I./src -I/local_disk0/.ephemeral_nfs/cluster_libraries/python/include -I/usr/include/python3.9 -c isotree/cpp_interface.cpp -o build/temp.linux-x86_64-3.9/isotree/cpp_interface.o -march=native -fopenmp -O3 -fno-math-errno -fno-trapping-math -std=c++17 -flto=auto
isotree/cpp_interface.cpp:1:2: error: #error Do not use this file, it is the result of a failed Cython compilation.
1 | #error Do not use this file, it is the result of a failed Cython compilation.
| ^~~~~
error: command '/usr/bin/x86_64-linux-gnu-gcc' failed with exit code 1
----------------------------------------
ERROR: Failed building wheel for isotree
ERROR: Could not build wheels for isotree which use PEP 517 and cannot be installed directly
Done
from isotree.
Ravikumarnl
commented on August 22, 2024
Thanks David, It worked with cython==3.0.0
from isotree.
Related Issues (20)
- What is equivalent to contamination parameter in sklearn? HOT 1
- Mac arm nthreads problem HOT 1
- Error when using fit() and build_imputer=True is misleading HOT 2
- Same category is always imputed when enough trees are grown HOT 3
- pip install issue: cc1plus no such file or directory HOT 5
- pip install issue not fixed but closed HOT 1
- Reproductibility problems with Extented Isolation Forest HOT 8
- How to re-train when a few values are marked as anomalies when they should not have been? HOT 3
- Isotree Isolation forest generating large model pickle file HOT 3
- Training Isotree with Python on Windows then Deserializing with C++ on Raspberry Pi 3B+ (Linux) HOT 7
- Can't install Isotree anymore HOT 3
- memory issues with build_imputer=True HOT 9
- Unexpected behaviour during imputations with all NA features HOT 7
- Problems installing isotree in Sagemaker Studio HOT 4
- Using with python3.8 and numpy==1.24.4 HOT 1
- R package build from source failing on Conda Forge HOT 9
- Running isotree in databricks environment given requirements HOT 1
- Problems building isottree library on Windows using Visual Studio 2022 and CMake HOT 3
- About missing_action HOT 7
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from isotree.