Open kevinphillips81 opened 7 months ago
Running the following command results in what looks like closed connections from the Neptune database, which may relate to the underlying issue as stated above.
!nodestream run sbom --target my-neptune
graph-notebook 4.2.0 requires pandas<=1.5.3,>=1.3.5, but you have pandas 2.2.2 which is incompatible.
This should be resolved with the upgrade of Pandas to a ceiling of v2.2.2 in graph-notebook v4.5.1: https://github.com/aws/graph-notebook/pull/658
The other packages listed are not directly related to graph-notebook.
I'm observing a different error now on installation of either nodestream-plugin-neptune
or nodestream_plugin_sbom
:
ERROR: Could not build wheels for confluent-kafka, which is required to install pyproject.toml-based projects
Full stack trace:
Collecting nodestream-plugin-neptune
Using cached nodestream_plugin_neptune-0.13.0-py3-none-any.whl.metadata (1.1 kB)
Requirement already satisfied: aiobotocore<3.0.0,>=2.12.0 in /home/ec2-user/anaconda3/envs/JupyterSystemEnv/lib/python3.10/site-packages (from nodestream-plugin-neptune) (2.13.1)
Requirement already satisfied: botocore>=1.34.40 in /home/ec2-user/anaconda3/envs/JupyterSystemEnv/lib/python3.10/site-packages (from nodestream-plugin-neptune) (1.34.142)
Collecting cymple<0.12.0,>=0.11.0 (from nodestream-plugin-neptune)
Using cached cymple-0.11.0-py2.py3-none-any.whl.metadata (7.5 kB)
Collecting nodestream<0.14.0,>=0.13.0 (from nodestream-plugin-neptune)
Using cached nodestream-0.13.1-py3-none-any.whl.metadata (3.5 kB)
Collecting botocore>=1.34.40 (from nodestream-plugin-neptune)
Using cached botocore-1.34.131-py3-none-any.whl.metadata (5.7 kB)
Requirement already satisfied: aiohttp<4.0.0,>=3.9.2 in /home/ec2-user/anaconda3/envs/JupyterSystemEnv/lib/python3.10/site-packages (from aiobotocore<3.0.0,>=2.12.0->nodestream-plugin-neptune) (3.9.5)
Requirement already satisfied: wrapt<2.0.0,>=1.10.10 in /home/ec2-user/anaconda3/envs/JupyterSystemEnv/lib/python3.10/site-packages (from aiobotocore<3.0.0,>=2.12.0->nodestream-plugin-neptune) (1.16.0)
Requirement already satisfied: aioitertools<1.0.0,>=0.5.1 in /home/ec2-user/anaconda3/envs/JupyterSystemEnv/lib/python3.10/site-packages (from aiobotocore<3.0.0,>=2.12.0->nodestream-plugin-neptune) (0.11.0)
Requirement already satisfied: jmespath<2.0.0,>=0.7.1 in /home/ec2-user/anaconda3/envs/JupyterSystemEnv/lib/python3.10/site-packages (from botocore>=1.34.40->nodestream-plugin-neptune) (1.0.1)
Requirement already satisfied: python-dateutil<3.0.0,>=2.1 in /home/ec2-user/anaconda3/envs/JupyterSystemEnv/lib/python3.10/site-packages (from botocore>=1.34.40->nodestream-plugin-neptune) (2.9.0)
Requirement already satisfied: urllib3!=2.2.0,<3,>=1.25.4 in /home/ec2-user/anaconda3/envs/JupyterSystemEnv/lib/python3.10/site-packages (from botocore>=1.34.40->nodestream-plugin-neptune) (2.2.2)
Requirement already satisfied: Jinja2<4,>=3 in /home/ec2-user/anaconda3/envs/JupyterSystemEnv/lib/python3.10/site-packages (from nodestream<0.14.0,>=0.13.0->nodestream-plugin-neptune) (3.1.4)
Requirement already satisfied: boto3<2.0.0,>=1.34.127 in /home/ec2-user/anaconda3/envs/JupyterSystemEnv/lib/python3.10/site-packages (from nodestream<0.14.0,>=0.13.0->nodestream-plugin-neptune) (1.34.142)
Collecting cleo<3.0,>=2.0 (from nodestream<0.14.0,>=0.13.0->nodestream-plugin-neptune)
Using cached cleo-2.1.0-py3-none-any.whl.metadata (12 kB)
Collecting confluent-kafka<3.0,>=2.5 (from nodestream<0.14.0,>=0.13.0->nodestream-plugin-neptune)
Using cached confluent-kafka-2.5.0.tar.gz (136 kB)
Preparing metadata (setup.py) ... done
Collecting cookiecutter<3.0,>=2.0 (from nodestream<0.14.0,>=0.13.0->nodestream-plugin-neptune)
Using cached cookiecutter-2.6.0-py3-none-any.whl.metadata (7.3 kB)
Collecting httpx<0.28,>=0.27 (from nodestream<0.14.0,>=0.13.0->nodestream-plugin-neptune)
Using cached httpx-0.27.0-py3-none-any.whl.metadata (7.2 kB)
Requirement already satisfied: pandas<3,>=2 in /home/ec2-user/anaconda3/envs/JupyterSystemEnv/lib/python3.10/site-packages (from nodestream<0.14.0,>=0.13.0->nodestream-plugin-neptune) (2.2.2)
Requirement already satisfied: psutil<7.0,>=6.0 in /home/ec2-user/anaconda3/envs/JupyterSystemEnv/lib/python3.10/site-packages (from nodestream<0.14.0,>=0.13.0->nodestream-plugin-neptune) (6.0.0)
Requirement already satisfied: pyarrow<18.0.0,>=17.0.0 in /home/ec2-user/anaconda3/envs/JupyterSystemEnv/lib/python3.10/site-packages (from nodestream<0.14.0,>=0.13.0->nodestream-plugin-neptune) (17.0.0)
Requirement already satisfied: python-json-logger<3.0,>=2.0 in /home/ec2-user/anaconda3/envs/JupyterSystemEnv/lib/python3.10/site-packages (from nodestream<0.14.0,>=0.13.0->nodestream-plugin-neptune) (2.0.7)
Requirement already satisfied: pyyaml<7.0,>=6.0 in /home/ec2-user/anaconda3/envs/JupyterSystemEnv/lib/python3.10/site-packages (from nodestream<0.14.0,>=0.13.0->nodestream-plugin-neptune) (6.0.1)
Requirement already satisfied: schema<0.8,>=0.7 in /home/ec2-user/anaconda3/envs/JupyterSystemEnv/lib/python3.10/site-packages (from nodestream<0.14.0,>=0.13.0->nodestream-plugin-neptune) (0.7.7)
Collecting uvloop<=0.19.0,>=0.17.0 (from nodestream<0.14.0,>=0.13.0->nodestream-plugin-neptune)
Using cached uvloop-0.19.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (4.9 kB)
Requirement already satisfied: aiosignal>=1.1.2 in /home/ec2-user/anaconda3/envs/JupyterSystemEnv/lib/python3.10/site-packages (from aiohttp<4.0.0,>=3.9.2->aiobotocore<3.0.0,>=2.12.0->nodestream-plugin-neptune) (1.3.1)
Requirement already satisfied: attrs>=17.3.0 in /home/ec2-user/anaconda3/envs/JupyterSystemEnv/lib/python3.10/site-packages (from aiohttp<4.0.0,>=3.9.2->aiobotocore<3.0.0,>=2.12.0->nodestream-plugin-neptune) (23.2.0)
Requirement already satisfied: frozenlist>=1.1.1 in /home/ec2-user/anaconda3/envs/JupyterSystemEnv/lib/python3.10/site-packages (from aiohttp<4.0.0,>=3.9.2->aiobotocore<3.0.0,>=2.12.0->nodestream-plugin-neptune) (1.4.1)
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Requirement already satisfied: yarl<2.0,>=1.0 in /home/ec2-user/anaconda3/envs/JupyterSystemEnv/lib/python3.10/site-packages (from aiohttp<4.0.0,>=3.9.2->aiobotocore<3.0.0,>=2.12.0->nodestream-plugin-neptune) (1.9.4)
Requirement already satisfied: async-timeout<5.0,>=4.0 in /home/ec2-user/anaconda3/envs/JupyterSystemEnv/lib/python3.10/site-packages (from aiohttp<4.0.0,>=3.9.2->aiobotocore<3.0.0,>=2.12.0->nodestream-plugin-neptune) (4.0.3)
INFO: pip is looking at multiple versions of boto3 to determine which version is compatible with other requirements. This could take a while.
Collecting boto3<2.0.0,>=1.34.127 (from nodestream<0.14.0,>=0.13.0->nodestream-plugin-neptune)
Using cached boto3-1.35.4-py3-none-any.whl.metadata (6.6 kB)
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Using cached boto3-1.34.162-py3-none-any.whl.metadata (6.6 kB)
Using cached boto3-1.34.161-py3-none-any.whl.metadata (6.6 kB)
INFO: pip is still looking at multiple versions of boto3 to determine which version is compatible with other requirements. This could take a while.
Using cached boto3-1.34.160-py3-none-any.whl.metadata (6.6 kB)
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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.
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Collecting crashtest<0.5.0,>=0.4.1 (from cleo<3.0,>=2.0->nodestream<0.14.0,>=0.13.0->nodestream-plugin-neptune)
Using cached crashtest-0.4.1-py3-none-any.whl.metadata (1.1 kB)
Collecting rapidfuzz<4.0.0,>=3.0.0 (from cleo<3.0,>=2.0->nodestream<0.14.0,>=0.13.0->nodestream-plugin-neptune)
Using cached rapidfuzz-3.9.6-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (12 kB)
Collecting binaryornot>=0.4.4 (from cookiecutter<3.0,>=2.0->nodestream<0.14.0,>=0.13.0->nodestream-plugin-neptune)
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Collecting click<9.0.0,>=7.0 (from cookiecutter<3.0,>=2.0->nodestream<0.14.0,>=0.13.0->nodestream-plugin-neptune)
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Collecting httpcore==1.* (from httpx<0.28,>=0.27->nodestream<0.14.0,>=0.13.0->nodestream-plugin-neptune)
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Collecting h11<0.15,>=0.13 (from httpcore==1.*->httpx<0.28,>=0.27->nodestream<0.14.0,>=0.13.0->nodestream-plugin-neptune)
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Requirement already satisfied: numpy>=1.22.4 in /home/ec2-user/anaconda3/envs/JupyterSystemEnv/lib/python3.10/site-packages (from pandas<3,>=2->nodestream<0.14.0,>=0.13.0->nodestream-plugin-neptune) (1.23.5)
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Building wheels for collected packages: confluent-kafka
Building wheel for confluent-kafka (setup.py) ... error
error: subprocess-exited-with-error
Ć python setup.py bdist_wheel did not run successfully.
ā exit code: 1
ā°ā> [66 lines of output]
running bdist_wheel
running build
running build_py
creating build
creating build/lib.linux-x86_64-cpython-310
creating build/lib.linux-x86_64-cpython-310/confluent_kafka
copying src/confluent_kafka/__init__.py -> build/lib.linux-x86_64-cpython-310/confluent_kafka
copying src/confluent_kafka/deserializing_consumer.py -> build/lib.linux-x86_64-cpython-310/confluent_kafka
copying src/confluent_kafka/error.py -> build/lib.linux-x86_64-cpython-310/confluent_kafka
copying src/confluent_kafka/serializing_producer.py -> build/lib.linux-x86_64-cpython-310/confluent_kafka
creating build/lib.linux-x86_64-cpython-310/confluent_kafka/_model
copying src/confluent_kafka/_model/__init__.py -> build/lib.linux-x86_64-cpython-310/confluent_kafka/_model
creating build/lib.linux-x86_64-cpython-310/confluent_kafka/_util
copying src/confluent_kafka/_util/__init__.py -> build/lib.linux-x86_64-cpython-310/confluent_kafka/_util
copying src/confluent_kafka/_util/conversion_util.py -> build/lib.linux-x86_64-cpython-310/confluent_kafka/_util
copying src/confluent_kafka/_util/validation_util.py -> build/lib.linux-x86_64-cpython-310/confluent_kafka/_util
creating build/lib.linux-x86_64-cpython-310/confluent_kafka/admin
copying src/confluent_kafka/admin/__init__.py -> build/lib.linux-x86_64-cpython-310/confluent_kafka/admin
copying src/confluent_kafka/admin/_acl.py -> build/lib.linux-x86_64-cpython-310/confluent_kafka/admin
copying src/confluent_kafka/admin/_cluster.py -> build/lib.linux-x86_64-cpython-310/confluent_kafka/admin
copying src/confluent_kafka/admin/_config.py -> build/lib.linux-x86_64-cpython-310/confluent_kafka/admin
copying src/confluent_kafka/admin/_group.py -> build/lib.linux-x86_64-cpython-310/confluent_kafka/admin
copying src/confluent_kafka/admin/_listoffsets.py -> build/lib.linux-x86_64-cpython-310/confluent_kafka/admin
copying src/confluent_kafka/admin/_metadata.py -> build/lib.linux-x86_64-cpython-310/confluent_kafka/admin
copying src/confluent_kafka/admin/_records.py -> build/lib.linux-x86_64-cpython-310/confluent_kafka/admin
copying src/confluent_kafka/admin/_resource.py -> build/lib.linux-x86_64-cpython-310/confluent_kafka/admin
copying src/confluent_kafka/admin/_scram.py -> build/lib.linux-x86_64-cpython-310/confluent_kafka/admin
copying src/confluent_kafka/admin/_topic.py -> build/lib.linux-x86_64-cpython-310/confluent_kafka/admin
creating build/lib.linux-x86_64-cpython-310/confluent_kafka/avro
copying src/confluent_kafka/avro/__init__.py -> build/lib.linux-x86_64-cpython-310/confluent_kafka/avro
copying src/confluent_kafka/avro/cached_schema_registry_client.py -> build/lib.linux-x86_64-cpython-310/confluent_kafka/avro
copying src/confluent_kafka/avro/error.py -> build/lib.linux-x86_64-cpython-310/confluent_kafka/avro
copying src/confluent_kafka/avro/load.py -> build/lib.linux-x86_64-cpython-310/confluent_kafka/avro
creating build/lib.linux-x86_64-cpython-310/confluent_kafka/kafkatest
copying src/confluent_kafka/kafkatest/__init__.py -> build/lib.linux-x86_64-cpython-310/confluent_kafka/kafkatest
copying src/confluent_kafka/kafkatest/verifiable_client.py -> build/lib.linux-x86_64-cpython-310/confluent_kafka/kafkatest
copying src/confluent_kafka/kafkatest/verifiable_consumer.py -> build/lib.linux-x86_64-cpython-310/confluent_kafka/kafkatest
copying src/confluent_kafka/kafkatest/verifiable_producer.py -> build/lib.linux-x86_64-cpython-310/confluent_kafka/kafkatest
creating build/lib.linux-x86_64-cpython-310/confluent_kafka/schema_registry
copying src/confluent_kafka/schema_registry/__init__.py -> build/lib.linux-x86_64-cpython-310/confluent_kafka/schema_registry
copying src/confluent_kafka/schema_registry/avro.py -> build/lib.linux-x86_64-cpython-310/confluent_kafka/schema_registry
copying src/confluent_kafka/schema_registry/error.py -> build/lib.linux-x86_64-cpython-310/confluent_kafka/schema_registry
copying src/confluent_kafka/schema_registry/json_schema.py -> build/lib.linux-x86_64-cpython-310/confluent_kafka/schema_registry
copying src/confluent_kafka/schema_registry/protobuf.py -> build/lib.linux-x86_64-cpython-310/confluent_kafka/schema_registry
copying src/confluent_kafka/schema_registry/schema_registry_client.py -> build/lib.linux-x86_64-cpython-310/confluent_kafka/schema_registry
creating build/lib.linux-x86_64-cpython-310/confluent_kafka/serialization
copying src/confluent_kafka/serialization/__init__.py -> build/lib.linux-x86_64-cpython-310/confluent_kafka/serialization
creating build/lib.linux-x86_64-cpython-310/confluent_kafka/avro/serializer
copying src/confluent_kafka/avro/serializer/__init__.py -> build/lib.linux-x86_64-cpython-310/confluent_kafka/avro/serializer
copying src/confluent_kafka/avro/serializer/message_serializer.py -> build/lib.linux-x86_64-cpython-310/confluent_kafka/avro/serializer
running build_ext
building 'confluent_kafka.cimpl' extension
creating build/temp.linux-x86_64-cpython-310
creating build/temp.linux-x86_64-cpython-310/tmp
creating build/temp.linux-x86_64-cpython-310/tmp/pip-install-i5w4df69
creating build/temp.linux-x86_64-cpython-310/tmp/pip-install-i5w4df69/confluent-kafka_e2d941c4cc5542c89f9fd1972685cb14
creating build/temp.linux-x86_64-cpython-310/tmp/pip-install-i5w4df69/confluent-kafka_e2d941c4cc5542c89f9fd1972685cb14/src
creating build/temp.linux-x86_64-cpython-310/tmp/pip-install-i5w4df69/confluent-kafka_e2d941c4cc5542c89f9fd1972685cb14/src/confluent_kafka
creating build/temp.linux-x86_64-cpython-310/tmp/pip-install-i5w4df69/confluent-kafka_e2d941c4cc5542c89f9fd1972685cb14/src/confluent_kafka/src
gcc -pthread -B /home/ec2-user/anaconda3/envs/JupyterSystemEnv/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/ec2-user/anaconda3/envs/JupyterSystemEnv/include -fPIC -O2 -isystem /home/ec2-user/anaconda3/envs/JupyterSystemEnv/include -fPIC -I/home/ec2-user/anaconda3/envs/JupyterSystemEnv/include/python3.10 -c /tmp/pip-install-i5w4df69/confluent-kafka_e2d941c4cc5542c89f9fd1972685cb14/src/confluent_kafka/src/Admin.c -o build/temp.linux-x86_64-cpython-310/tmp/pip-install-i5w4df69/confluent-kafka_e2d941c4cc5542c89f9fd1972685cb14/src/confluent_kafka/src/Admin.o
In file included from /tmp/pip-install-i5w4df69/confluent-kafka_e2d941c4cc5542c89f9fd1972685cb14/src/confluent_kafka/src/Admin.c:17:0:
/tmp/pip-install-i5w4df69/confluent-kafka_e2d941c4cc5542c89f9fd1972685cb14/src/confluent_kafka/src/confluent_kafka.h:23:10: fatal error: librdkafka/rdkafka.h: No such file or directory
#include <librdkafka/rdkafka.h>
^~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
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 confluent-kafka
Running setup.py clean for confluent-kafka
Failed to build confluent-kafka
ERROR: Could not build wheels for confluent-kafka, which is required to install pyproject.toml-based projects
Community Note
Describe the bug Running the new SBOM notebooks on a Notebook (using Python 3 kernel) created on April 15th, I received the following errors on
01-SBOM-Dependency-Analysis
:To Reproduce Steps to reproduce the behavior:
!pip install -q pyyaml nodestream-plugin-neptune nodestream_plugin_sbom
commandExpected behavior The command should complete successfully.